Monthly Archives: February 2012

The Science of Cooking

Learning the structure and mechanism behind everyday life is one of the things that drew me to science. And there are few better examples of that than cooking, an activity which is pretty necessary and central to life! The way that cooking is taught actually shares a lot with the way that science is taught. Initially you memorize recipes, formulae, and techniques without necessarily having a clear idea of the motivations. But as you gain skill you learn more about the fundamentals and the why of what is happening! In science the fundamentals can be things like the basic forces, atomic interactions, or the use of math to unify behavior at many different size scales. And in cooking, as you search for motivation you begin delving into chemical reactions, mechanical processes that modify ingredients, and the biology of the things being eaten as well as the person doing the eating.

There are a lot of excellent books on this out there, notably On Food and Cooking by Harold McGee. But there’s also a nice online resource, lectures from a popular Harvard course on science and cooking. Each week they invited a guest chef to give a public talk, and do a course lecture and demonstration. Then they had a lecture from the course organizers to go into a specific scientific concept in the guest chef’s demo. And finally, they went into a lab to recreate the dish shown or another dish that built on the same scientific concept. The full list of lectures, covering things like phase changes, browning, emulsions, viscosity, and heat, is available here, and here is the first lecture:

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Electrons, Bonding, and the Periodic Table

The structure of the periodic table of elements is a bit weird the first time you see it, like a castle or a cake. If we just read the periodic table top to bottom and left to right, we are reading off the elements in order of increasing number of protons. However, if this were the only useful ordering on the periodic table, it could be a simple list. The vertically aligned groups on the periodic table actually represent the chemical properties of the elements. Dmitri Mendeleev developed the table in 1869 as a way to both tabulate existing empirical results, and predict what unexplored chemical reactions or undiscovered elements might be possible. It was revolutionary as a scientific tool, but the mechanism behind the periodicity was not understood until decades later. As it turns out, the periodicity of chemical behavior corresponds to the bonding type of the outer electrons in different atoms.

To understand what that means, we can start by looking at the elements on the left side of the periodic table. Hydrogen has only one proton, so the electrically neutral form of hydrogen has only one electron. This single electron is a point particle, jumping around the nucleus. The electron exists in a probability cloud, whose shape is given by the lowest energy solution to the quantum mechanical equations describing the system. These quantum states can be distinguished by differing quantum numbers for various quantities like spin and angular momentum, and we will talk about these in more depth later on. When we add additional electrons, they all want to be in the lowest energy state as well. Sadly for electrons but happily for us, no two electrons are able to occupy the same quantum state: they must differ in at least one quantum number. This is known as the Pauli exclusion principle, and was devised to explain experimental results in the early years of quantum mechanics. So while the single electron in hydrogen gets to be in the lowest energy state available for an electron in that atom, in an atom like oxygen, its eight electrons occupy the eight lowest energy states, as if they are stones stacked in a bucket.

But what’s really interesting about these higher energy electron states is that they have different shapes, as we can see by the mathematical forms that describe the possible probability distributions for electrons. So while the electron cloud in a hydrogen atom is a sphere, there are electron clouds for other atoms that are shaped like dumbbells, spheres cut in two, alternating spherical shells, and lots of other shapes.

The electron cloud shape becomes important because two atoms near each other may be able to minimize their overall energy via electron interactions: in some configurations the sharing of one, two, more, or even a partial number of electrons is energetically preferred, whereas in other configurations sharing electrons is not favorable. This electron sharing, which changes the shape of the electron cloud and affects the chemical reactivity of the atoms involved, is what’s called chemical bonding. When atoms are connected by a chemical bond, there is an energy cost necessary to separate them. But how atoms interact depends fundamentally on the shape of the electron cloud, determining when atoms can or can’t bond to each other. So the periodic table, which was originally developed to group atoms with similar chemical properties and bonding behaviors, actually also groups atoms by the number and arrangement of electrons.

Now, there is a lot more that can be said about bonding. You can talk about the inherent spin of electrons, which is important in bonding and atomic orbital filling, or you can talk about the idea of filled electron shells which make some atoms stable and others reactive, or you can talk about the many kinds of chemical bonds. It’s a very deep topic, and this is just the beginning!

Since every real world object is a collection of bonded atoms, the properties of the things we interact with, and what materials are even able to exist in our world, depend on the shape of the electron cloud. Imagine if the Pauli exclusion principle were not true, and all the electrons in an atom could sit together in the lowest energy state. This would make every electron cloud the same shape, which would remove the incredible variety of chemical bonds in our world, homogenizing material properties. Chemistry would be a lot easier to learn but a lot less interesting, and atomic physics would be completely solved. Stars, planets, and life as we know it might not exist at all.

The Electron Cloud

There is a popular image of the atom that shows the nucleus as a collection of balls, with ball-like electrons following circular orbits around them. The parallels to our own solar system, to the orbits of the moon around the earth and the earth around the sun, strike a chord with most people, but the depiction is inaccurate. It is based on the ideas of several prominent early twentieth century physicists, developed after the discovery of the electron in 1897 showed that atoms were not the smallest building block of nature. There are two serious mistakes in this image, and the actual structure of the atom is a lot more interesting.

The first problem is that the proton itself is not an indivisible particle: it’s composed of three quarks, subatomic particles which were hypothesized in the early sixties and observed in experiments beginning in the late sixties. The same is true of the neutron: it’s also composed of three quarks, though the flavor composition is different than that of the proton. (“Flavor composition”? Yes, quarks come in different flavors.) So those giant balls in the nucleus are actually comprised of smaller particles. At this point we believe quarks to be themselves indivisible, not composed of another even smaller particle.

But the second reason this picture is incorrect is that the electron doesn’t follow a linear orbit around the proton, the way gravitationally orbiting bodies do. In fact, due to the small mass of the nucleus and the even smaller mass of the electron, gravity is the least important force in an atom. The electromagnetic force, between the oppositely charged proton and electron, is much larger than the gravitational force between these tiny objects. But wait, you might say, if there’s such a large attractive force, shouldn’t the electron just spiral into the proton? This quandary illustrates perfectly why we can’t rely on classical physics, which was built up for objects comprised of billions of atoms, for the particles within a single atom. Because yes, if we had two oppositely charged billiard balls that have a weak gravitational interaction and a strong electromagnetic interaction, they will crash into each other! But, the electron is so small and so light that we cannot treat it as a classical object.

Here is where quantum mechanics come into play. Quantum mechanics as a whole is a set of mathematical constructions used to describe quantum objects, and it’s quite different than what’s used for classical, large-scale physics. There are all sorts of interesting consequences of quantum mechanics, such as the Heisenberg Uncertainty Principle, which states that for some pairs of variables, such as energy and time or position and momentum (mass times velocity), how precisely you can measure one depends on how precisely you are measuring the other. For each variable pair, there is a basic uncertainty in the measurement of both, which is very small but becomes relevant at the quantum scale. This shared minimum uncertainty between related variables is a fundamental property of nature. For momentum and position, this leads to that old joke about Heisenberg being pulled over for speeding: the police officer asks, “Do you know how fast you were going?” and Heisenberg responds, “No, but I know exactly where I am!”

What the uncertainty principle means here is that the electron is actually incapable of staying in the nucleus. Imagine a moment in time where the electron is within the nucleus: now its position is very well known, so there is a large uncertainty in its momentum. Thus the velocity may be quite high, which means that a moment later the electron will have moved far from the nucleus. In fact, because of the uncertainty in position, we cannot ever really say where in space the electron is. It is more accurate to talk about its position as determined by a probability cloud, which is denser in places that the electron is more likely to be (near the nucleus) and less dense where it is less likely to be (far from the nucleus). This also takes into account the wave nature of the electron as a quantum object, which we’ll get into another time.

With this knowledge, we can discard that old image of an electron orbiting a nucleus. A single electron, even though it is measurable as an individual, indivisible particle, exists as a cloud around the nucleus. The shape of the cloud is described by quantum mechanics, and as we add more electrons to the atom, we will find a whole gallery of electron cloud shapes. These shapes are the heart of interatomic bonding, as we will see.

The Polymorphism of Chocolate

Have you ever wondered why a chocolate bar that has melted and resolidified doesn’t have the same shine or snap that it did before? We are going to take a quick detour from talking about how atoms can group together to talk about some of the messy, interesting, and delicious chemistry of chocolate.

Chocolate is actually a fermented food, like sourdough bread or beer. To make chocolate, you start by taking the fruit pods of the cacao tree and letting them sit for several days, so that the wild yeasts which are on the surfaces of most fruit can start digesting the sugar in the fruit. After the fermentation, the pods are dried, and the seeds are removed from the dried and fermented fruit flesh; these seeds are called cocoa beans. The beans are roasted, then removed from their shells, and finally ground into a thick paste from which the dissolved fat, cocoa butter, can be removed (or more can be added!). Vanilla, sugar, and other flavors can also be added at this point, but much of the character of the chocolate comes from the initial fermentation and the roasting. Once the flavors are as desired, the chocolate is ready to be tempered!

Tempering is the process of heating a material to a specific temperature and then letting it cool into a solid, where the temperature is chosen so that the solid will have certain properties. It’s important in chocolate because the fats in chocolate have six different crystal phases, that is, different configurations in which they can solidify. This is called polymorphism, and it’s not unique to chocolate! The orientation of the fat molecules relative to each other, and their bonding, determine how easy it is to break apart the solid. This means that the melting temperature for each crystal phase is different, with some phases being easier to break apart than others. The six phases of chocolate are generally numbered with Roman numerals in ascending order of melting temperature, and it’s phase V that has the glossy sheen and satisfying snap that we are used to in commercial chocolate. And as an added virtue, its melting temperature is very close to human body temperature, so that it can melt in your mouth!

So how can chocolate be preferentially solidified in phase V? It has to be heated above the melting temperature of the unwanted phases I-IV, so that none of those crystal structures can form. But if it’s heated above the melting temperature of phase VI, it may resolidify in that phase, which is exactly what happens when you leave a bar of chocolate in the sun and it melts and resolidifies. Thus, the usual tempering procedure in chocolate manufacture is the following: first, heat the chocolate above all the melting points, to get rid of existing crystal phases. Then cool it to around the phase V crystallization temperature, and keep it there for awhile so that that regions of phase V begin to form. If you stir during this process, you will get many small crystals which can act as seeds for the desired crystal phase. Finally, cool the chocolate, causing the phase V seeds to spread so that the entire chocolate bar has the desirable crystal phase.

Chocolate is a great example of how different material properties result from the arrangement of matter at a small scale. And if you’re interested, you can always learn more about the history, manufacture, and usage of chocolate at its wikipedia page.

The Attraction of Low Energy

One of the tricky things about learning, science or other topics, is that so many things are interconnected. You can take separate courses on literature and history, and maybe separating those two things is a reasonable way to categorize information, but really you might have understood the literature better with the historical context, or you might have learned historical motivations better by reading some relevant literature. Until the day comes when we can learn everything at once, we have to learn topics separately and then later on, look back for connections. I mention this because what I am about to talk about is relevant to huge swathes of physics, chemistry, and biology, and can be discussed in a wide variety of ways, and is difficult to really get to the bottom of. But it’s a really useful thing to have in the back of your mind while looking at a lot of scientific ideas.

I am talking about energy minimization.

When we discussed the forces due to electromagnetic and gravitational fields earlier, forces that draw oppositely charged objects together or two objects with mass together, we were talking about energy minimization. This is because, in each of those fields, there is a potential energy associated with sitting at a high field value. Imagine a rock perched on a high precipice, feeling a large gravitational force pulling it downward. Unless it is being supported in a way to counteract that force, it will fall, because it is seeking to minimize its energetic state. Oppositely charged objects drawing together are minimizing their electromagnetic potential energy with respect to each other, by moving toward each other.

At the atomic scale, energy minimization is also a factor, but in a different way. Within a single atom, electrons can be in many states, the equivalent of the rock choosing different positions on the precipice. If there is only one electron, it will go to the lowest energy state. But in atoms with many electrons, additional electrons are required to take higher energy states because the lowest ones are occupied; you can imagine a pile of rocks growing up the side of the precipice. And if an atom had no electrons at all, free electrons nearby would see that atom as very attractive, because atomic states are lower energy than free states.

If you consider multiple atoms coming together, the electrons are still looking to minimize their energy. In some cases this may mean sharing an electron with a neighbor, lowering the energy of both atoms and forming a chemical bond. But for other configurations of electrons, bonds do not lower overall energy, and so these atoms are unlikely to form bonds. In other words, for some atoms, bonding is energetically favorable, and for some atoms it isn’t. We’ll get more into the nuts and bolts of this later on, but you can imagine a whole energy landscape that determines what things bond or don’t, what chemical reactions happen or never start, and thus what macroscopic phenomena are commonplace.

Processes that are more energetically favorable are the ones we see in nature, also called “naturally occuring”. Energy minimization is at the heart of many of these processes, but in such a wide variety of ways that the more you learn, the more you see it around you.

Good Science Communication – Break It Down Now

Before we delve too deeply into what makes good science communication, it would first behoove us to define what we mean – both by science, and communication. So! The first question of the day is: What makes good science?

There are currently a variety of hotly-contested fields such as homeopathy whose supporters protest that they ought to be recognized as valid and respectable. Why, then, are they not? What do they lack that keeps them from being welcomed into the multifaceted and diverse world of the sciences?

In a word? Evidence. Proof. Confirmation. To expand upon that slightly,  a rigorously tested and proven method of investigation involving peer-reviewed research and further study. A scientific theory does not say ‘this is true because we think it is’. It instead strives to disprove itself at every turn, always open to and indeed expecting refutation. Getting any group of scientists to agree on a definition for ‘good’ science may well be impossible, as under their own defintions they are always questioning, always ready to adapt and update their theories when new information comes along.

So what, then, is good communication? Is it merely being clear-spoken, so that your message is obvious? Is it watching yourself for overuse of jargon, so a wide audience can understand you? Is it injecting every story you tell with a sense of drama, to keep them reading on?

I believe all of these principles are useful in communication, however I would take it one step further and say that good communication is built on passion and dedication – passion for your topic and dedication to making it interesting and relevant to those to whom you are trying to convey it. There are myriad ways of communicating a message, but only people with the correct goals will actually get their message across – goals such as clarity, relevance, and decent support and explanation.

You may have the most fascinating information in the world to share ,and yet without paying attention to how you’re saying it, you may not reach a single soul. Without engaging with a wider audience science becomes insular and myopic, and for that reason alone it is valuable for scientists and science writers to continually strive to find the best ways to communicate their passions and interests to the wider world around them.

For an extremely unique and unorthodox method of communicating scientific information, click through here.

Thinking About Collections of Atoms

On a basic level, science is about asking why the world is the way it is, and engineering is about asking, how can we use that to better our condition? There is certainly a lot of interplay between the two; they inform each other and rely on each other. And in my mind, a good scientist should always be a reasonable engineer, and vice versa. So if we want to understand what the science is that underpins a lot of our current technology, we first have to ask a lot of “why” questions about the world around us. Such as, why do different objects and materials have different properties? Why are there different forms that matter can take? Why do some forms appear on Earth and some don’t? Then, once we know what makes materials different from each other, we can start talking about how to use that to do something useful.

So what is the difference between the atoms in a metal table, the atoms in a cup of coffee, and the atoms in our hands? There are two major differences that are relevant: first, the atoms themselves come in a wide variety of types, and second, they can be arranged with other atoms in many unique ways that affect the property of the resultant material. The image below shows how we can arrange the same silicon and oxygen atoms in a random way or an ordered way, to get either silica or quartz. This change in ordered affects the physical properties of the resultant material.

We touched on the many types of atoms before when we discussed the number of protons in an atom. Proton number affects electron number, because of the attractive force between protons and electrons due to their opposite charge. So, for a given number of protons, an atom will end up with a similar number of electrons. How many electrons an atom has is very important, because the cloud of electrons is much larger than the compact nucleus which contains the neutrons and protons, so electrons are the primary means by which an atom interacts with the world.

What “the world” means here is primarily other atoms. So to assemble a solid, we have lots of atoms whose electron clouds are interacting with each other. Atoms can share electrons, they can be attracted to each other if they have opposite charges, and they can form three-dimensional structures to allow many atoms to interact . These interactions are all based around electronic forces, which stem from charge as we discussed earlier. Different kinds of atoms will experience different forces in different environments, so we end up with a whole slew of ways to assemble atoms. We can pack carbon into sheets and get pencil lead, we can jam it together with no ordering and get charcoal, we can compress it until it has a dense, flawless periodic structure and get diamond, or we can mix it with hydrogen to get the long hydrocarbon chains that crude oil is made of. And that’s just carbon!

Now, the obvious question to ask here is why atomic species and ordering vary, and why those variations lead to different material types. We’ll get into the first question shortly, but the second will take a lot longer to answer.