So What’s the Big Deal About the Higgs Boson, Anyway? A Physics Double Xplainer

The ATLAS detector at the Large Hadron Collider, one of four
detectors to discover a new particle.
By Matthew Francis, physics editor

After decades of searching and many promising results that didn’t pan out, scientists working at the Large Hadron Collider in Europe announced Wednesday they had found a new particle. People got really excited, and for good reason! This discovery is significant no matter how you look at it: If the new particle is the Higgs boson (which it probably is), it provides the missing piece to complete the highly successful Standard Model of particles and interactions. If the new particle isn’t the Higgs boson, well…that’s interesting too.

So what’s the big deal? What is the Higgs boson? What does Wednesday’s announcement really mean? What’s the meaning of life? Without getting too far over my head, let me try to answer at least some of the common questions people have about the Higgs boson, and what the researchers in Europe found. If you’d rather have everything in video form, here’s a great animation by cartoonist Jorge Cham and an elegant explanation by Ian Sample. Ethan Siegel also wrote a picture-laden joyride through Higgs boson physics; you can find a roundup of even more posts and information at Wired and at Boing-Boing. (Disclaimer: my own article about the Higgs is linked both places, so I may be slightly biased.)

Q: What is the Higgs boson?
A: The Higgs boson is a particle predicted by the Standard Model. It’s a manifestation of the “Higgs field”, which explains why some particles have mass and other particles don’t.

Q: Whoa, too fast! What’s a boson?
A: A boson is a large mammal indigenous to North America. No wait, that’s bison. [Ed note: Ha. Ha. Ha.] On the tiniest level, there are two basic types of particles: fermions and bosons. You’re made of fermions: the protons, neutrons, and electrons that are the constituents of atoms are all fermions. On a deeper level, protons and neutrons are built of quarks, which are also fermions. Bosons carry the forces of nature; the most familiar are photons–particles of light–which are manifestations of the electromagnetic force. There are other differences between fermions and bosons, but we don’t need to worry about them for now; if you want more information, I wrote a far longer and more detailed explanation at my personal blog.

Q: What does it mean to be a “manifestation” of a force?
A: The ocean is a huge body of water (duh), but it’s always in motion. You can think of waves as manifestations of the ocean’s motion. The electromagnetic field (which includes stuff like magnets, electric currents, and light) manifests itself in waves, too, but those waves only come in distinct indivisible chunks, which we call photons. The Higgs boson is also a manifestation of a special kind of interaction.

Q: How many kinds of forces are there?
A: There are four fundamental forces of nature: gravity, electromagnetism, and the two nuclear forces, creatively named the weak and strong forces. Gravity and electromagnetism are the forces of our daily lives: Gravity holds us to Earth, and electromagnetism does nearly everything else. If you drop a pencil, gravity makes it fall, but your holding the pencil is electromagnetic, based on how the atoms in your hand interact with the atoms in the pencil. The nuclear forces, on the other hand, are very short-range forces and are involved in (wow!) holding the nuclei of atoms together.

Q: OK, so what does the Higgs boson have to do with the fundamental forces?
A: All the forces of nature have certain things in common, so physicists from Einstein on have tried to describe them all as aspects of a single force. This is called unification, and to this day, nobody has successfully accomplished it. (Sounds like a metaphor for something or other.) However, unification of electromagnetism with the weak force was accomplished, yielding the electroweak theory. Nevertheless, there was a problem in the first version: It simply didn’t work if electrons, quarks, and the like had mass. Because particles obviously do have mass, something was wrong. That’s where the Higgs field and Higgs boson come in. Scottish physicist Peter Higgs and his colleagues figured out that if there was a new kind of field, it could explain both why the electromagnetic force and weak force behave differently and provide mass to the particles.

Q: Wait, I thought mass is fundamental?
A: One of the insights of modern physics is that particles aren’t just single objects: They are defined by interactions. Properties of particles emerge out of their interactions with fields, and mass is one of those properties. (That makes unifying gravity with the other forces challenging, which is a story for another day!) Some particles are more susceptible to interacting with the Higgs. An analogy I read (and apologies for not remembering where I read it) says it’s like different shoes in the snow. A snowshoe corresponds to a low-mass particle: very little snow mass sticks to it. A high-mass particle interacts strongly with the Higgs field, so that’s like hiking boots with big treads: lots of places for the snow to stick. Electrons are snowshoes, but the heaviest quarks are big ol’ hiking boots.

Q: Are there Higgs bosons running around all over the place, just like there are photons everywhere?
A: No, and it’s for the same reason we don’t see the bosons that carry the weak force. Unlike photons, the Higgs boson and the weak force bosons (known as the W and Z bosons — our particle physics friends run out of creative names sometime) are relatively massive. Many massive particles decay quickly into less massive particles, so the Higgs boson is short lived.

Q: So how do you make a Higgs boson?
A: The Higgs field is everywhere (like The Force in Star Wars), but to make a Higgs boson, you have to provide enough energy to make its mass. Einstein’s famous formula E = mc^2 tells us that mass and energy are interchangeable: If you have enough energy (in the right environment), you can make new particles. The Large Hadron Collider (LHC) at CERN in Europe and the Tevatron at Fermilab in the United States are two such environments: Both accelerate particles to close to the speed of light and smash them together. If the collisions are right, they can make a Higgs boson.

Q: Is this new particle actually the Higgs boson then?
A: That’s somewhat tricky. While the Standard Model predicts the existence of a Higgs boson, it doesn’t tell us exactly what the mass should be, which means the energy to make one isn’t certain. However, we have nice limits on the mass the Higgs could have, based on the way it interacts with other particles like the other bosons and quarks. This new particle falls in that range and has other characteristics that say “Higgs.” This is why a lot of physics writers, including me, will say the new particle is probably the Higgs boson, but we’ll hedge our bets until more data come in. The particle is real, though: four different detectors (ATLAS and CMS at CERN, and DZero and CDF at Fermilab) all saw the same particle with the same mass.

Q: But I’m asking you as a friend: Is this the Higgs boson?
A: I admit: a perverse part of me hopes it’s something different. If it isn’t the Higgs boson, it’s something unexpected and may not correspond to anything predicted in any theory! That’s an exciting and intriguing result. However, my bet is that this is the Higgs boson, and many (if not most) of my colleagues would agree.

Q: What’s all this talk about the “God particle”?
A: Physicists HATE it when the Higgs boson is called “the God particle.” Yes, the particle is important, but it’s not godlike. The term came from the title of a book by physicist Leon Lederman; he originally wanted to call it “The Goddamn Particle”, since the Higgs boson was so frustrating to find, but his editor forced a change.

Q: Why should I, as a non-physicist, care about this stuff?
A: While it’s unlikely that the discovery of the Higgs boson will affect you directly, particle colliders like the LHC and Tevatron have spurred development of new technologies. However, that’s not the primary reason to study this. By learning how particles work, we learn about the Universe, including how we fit into it. The search for new particles meshes with cosmology (my own area): It reveals the nature of the Universe we inhabit. I find a profound romance in exploring our Universe, learning about our origins, and discovering things that are far from everyday. If we limit the scope of exploration only to things that have immediate practical use, then we might as well give up on literature, poetry, movies, religion, and the like right now.

Q: If this is the Higgs boson, is that the final piece of the puzzle? Is particle physics done?
A: No, and in fact bigger mysteries remain. The Higgs boson is predicted by the Standard Model, but we know 80% of the mass of the Universe is in the form of dark matter, stuff that doesn’t emit or absorb light. We don’t know exactly what dark matter is, but it’s probably a particle — which means particle colliders may be able to figure it out. Hunting for an unknown particle is harder than looking for one we are pretty sure exists. Finding the Higgs (if I may quote myself) is like The Hobbit: It’s a necessary tale, but the bigger epic of The Lord of the Rings is still to come.

Biology Explainer: The big 4 building blocks of life–carbohydrates, fats, proteins, and nucleic acids

The short version
  • The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
  • Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
  • Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
  • Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.                                                                                                      
  • The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.


Big Molecules with Small Building Blocks

The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.

We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.

You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.

When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.

Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.

The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.

Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.

On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.

The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!

If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.

The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?

If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.

In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.

Sugar and Fuel

A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.

Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.

Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.

Polysaccharides: Fuel and Form

Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.

Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.

Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.

Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.

The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.

Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.

The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.

That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.

These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.

Lipids: The Fatty Trifecta

Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.

Fats: the Good, the Bad, the Neutral

Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?

Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows.  Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.

Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.

Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.

Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.

The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.

You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.

In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.

A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.

Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.

Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.

Phospholipids: An Abundant Fat

You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.

Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.

There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.

Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.

The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.

Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.

Steroids: Here to Pump You Up?

Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.

But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.

Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.

Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.


As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.

Levels of Structure

Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.

For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.

This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.

Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.

The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.

In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.

A Plethora of Purposes

What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.

As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.

Nucleic Acids

How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.

Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.

DNA vs. RNA: A Matter of Structure

DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.

So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.

RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.

DNA vs. RNA: Function Wars

An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.

These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.

RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.

 By Emily Willingham, DXS managing editor 
This material originally appeared in similar form in Emily Willingham’s Complete Idiot’s Guide to College Biology

Colon Cancer Awareness Month: Get your ass screened. We mean it.

Don’t want this growing in your colon?
Get screened. Via Wikimedia Commons.

It started a few months after I had my second son. A pain. Sharp, unrelenting, abdominal. Occasional blood from a place where blood isn’t supposed to appear: the rectum. There. Got the R-word out of the way.

After I had laparoscopy for presumed endometrial scarring as the cause of the pain, the pain nevertheless persisted. So, I was referred to a gastrointestinal (GI) specialist, or gastroenterologist. The GI doc I saw first was a man who, I later, discovered, was the GI doctor for my uncle and my father. They loved him. There probably was a sort of “hail fellow well met” male camaraderie between doctor and patient there that made them sympatico. Me, not so much. He looked at me, looked at my age (36), and decided that all I needed was to take some ibuprofen. He literally sent me home with instructions to take some ibuprofen a few times a day and call him, not in the morning, but maybe in a couple of weeks.

Two years later, after more episodes of blood in the toilet, continued pain, and, pardon me, but I think this information is important, a whole lot of mucus coming out of there, I went to another GI doctor. For whatever reason–even though my symptoms weren’t necessarily a match for colon cancer, even though I didn’t, to my knowledge, have any risk factors for colon cancer, even though I was still quite young to have colon cancer–he decided to do a colonoscopy.

As I emerged from the anesthesia after the procedure, I saw my GI doctor talking with my husband. “How did it go?” I asked, groggy. He sort of smiled at me and said, “You’re not going to remember any of this, but those symptoms you had saved your life.” Unbeknownst to him, amnesia meds don’t work on me–I’ve had ample subsequent opportunities to test that hypothesis–and I did remember it.

How did it save my life? 
What they found in my colon, near where it meets my lower small intestine, was a large, flat growth, about two inches (5 cm) by one inch (2.5 cm). In GI parlance, it was a large, flat (sessile) polyp, which is not a good kind of polyp. Closer analysis of the thing after my GI doctor deftly removed it during a second procedure revealed it to be a tubulovillous adenoma with cancerous tendencies. In fact, my medical records from that doctor now say the word “cancer” on them. 

Adenomas, the type of tumor this was, are “of greatest concern” in the colon. They come in three types: tubular, tubulovillous, and villous. The larger the size, the greater the cancer risk. Mine was large and on its way to becoming cancer. According to my GI doctor, I’d’ve been dead in another 5 years had I not had that colonoscopy and appropriate intervention. 

In other words, if I’d waited until the recommended age for a first colon cancer screening–age 50–I’d have already been dead for seven years. In fact, I would have died this year from colon cancer.

My mind was saying, “This would have been It. This would have been the thing, in a different time, that would have killed me. My potential death was growing inside of me, and I managed to put a stop to it.” 

It’s true: Colon cancer can be prevented
Finding and removing polyps in the colon can prevent colon cancer from developing. But first, you have to have the screening. Because more than 90% of cases of colorectal cancer happen in people ages 50 or older, the starting age for screening is currently set at age 50. 

If you have symptoms like the following, though, don’t delay. If a GI doctor dismisses you as my first one did–that polyp of mine was probably growing in there for a few years–get a second opinion.

  • Blood in or on the stool (as I had)
  • Stomach pain or aches that do not go away (as I had)
  • Unexplained weight loss
  • A change in bowel habits (diarrhea, constipation, frequency)
  • A feeling of incomplete emptying

Colon cancer is associated with some risk factors. These include

  • Age 
  • Having previously had colon polyps or colorectal cancer yourself
  • A family history of polyps or colorectal cancer
  • A history of having inflammatory bowel disease (Crohn’s or ulcerative colitis; not to be confused with irritable bowel syndrome or IBS)
  • A family history of inherited disorders related to polyps of the colon

Of these factors, I thought going into my GI doctors that I had none. Only later did I learn that my father also had had some polyps found and removed, although of the more typical and less-threatening variety and at a later age (in his 50s). In addition, in the past year, my octogenarian maternal grandmother had a large colorectal cancer removed that had likely begun its evolution from a polyp years ago, but she had never undergone screening. I cannot stress enough how important it is for a family to share health history so that these risks can be known and for anyone to have appropriate screening either at the recommended age or in the presence of symptoms.

Speaking of family, there is my own. My having been diagnosed with a precancerous growth at age 38 means that my first-degree relatives–siblings, parents, children–should have screening at least by that age and preferably years before.

There is some understandable reluctance to have a colonoscopy. Outside of the obvious ignominy of having someone shove a tube up your rectum while you lie anesthetized (I woke up during my second–yep, there’s a tube in there), there is the preparation for it. I’ve done just about every prep known to modern medicine, having now had five colonoscopies–all my follow-ups have been clear, and I don’t need another for four years now (!). Yes, they’re unpleasant, and they take quite a bit of willpower. You have to drink what they tell you, take the pills that they tell you, not eat when they tell you, and consume only what they say is OK. You’ll never want to see Jell-O or Gatorade again, and I can’t stare down a bowl of clear bouillon any more without feeling a tad nauseated. 

But the goal of a prep is a completely clean colon. The cleaner you get it, the more accurate your findings will be and the less likely you’ll have to do it again simply because you conducted–pardon me–a  crappy prep. 

March is Colon Cancer Awareness month. Be aware and embrace the reality that polyps happen and that so far, finding them requires this daylong unpleasantness. But also embrace the fact that the prep won’t kill you. Instead, it will help you prevent a cancer that does, in fact, kill 50,000 people a year in the United States alone. 

This year, five years after that first colonoscopy would have been the year I’d’ve been one of those people. Thanks to that procedure, I am instead alive and well enough to tell you about it, and my three young sons still have their mother. I’d starve for a week and drink Gatorade until I puked to make sure of that outcome.
By Emily Willingham, DXS Managing Editor

Biology Xplainer: Evolution and how it happens

Evolution: a population changes over time
First of all, in the context of science, you should never speak of evolution as a “theory.” There is no theory about whether or not evolution happens. It is a fact.

Scientists have, however, developed tested theories about how evolution happens. Although several proposed and tested processes or mechanisms exist, the most prominent and most studied, talked about, and debated, is Charles Darwin’s idea that the choices of nature guide these changes. The fame and importance of his idea, natural selection, has eclipsed the very real existence of other ways that populations can change over time.

Evolution in the biological sense does not occur in individuals, and the kind of evolution we’re talking about here isn’t about life’s origins. Evolution must happen at least at the populationlevel. In other words, it takes place in a group of existing organisms, members of the same species, often in a defined geographical area.

We never speak of individuals evolving in the biological sense. The population, a group of individuals of the same species, is the smallest unit of life that evolves.

To get to the bottom of what happens when a population changes over time, we must examine what’s happening to the gene combinations of the individuals in that population. The most precise way to talk about evolution in the biological sense is to define it as “a change in the allele frequency of a population over time.” A gene, which contains the code for a protein, can occur in different forms, or alleles. These different versions can mean that the trait associated with that protein can differ among individuals. Thanks to mutations, a gene for a trait can exist in a population in these different forms. It’s like having slightly different recipes for making the same cake, each producing a different version of the cake, except in this case, the “cake” is a protein.
Natural selection: One way evolution happens

Charles Darwin, a smart, thoughtful,
observant man. Via Wikimedia.
Charles Darwin, who didn’t know anything about alleles or even genes (so now you know more than he did on that score), understood from his work and observations that nature makes certain choices, and that often, what nature chooses in specific individuals turns up again in the individuals’ offspring. He realized that these characteristics that nature was choosing must pass to some offspring. This notion of heredity–that a feature encoded in the genes can be transmitted to your children–is inherent now in the theory of natural selection and a natural one for most people to accept. In science, an observable or measurable feature or characteristic is called a phenotype, and the genes that are the code for it are called its genotype. The color of my eyes (brown) is a phenotype, and the alleles of the eye color genes I have are the genotype.

What is nature selecting any individual in a population to do? In the theory of natural selection, nature chooses individuals that fit best into the current environment to pass along their “good-fit” genes, either through reproduction or indirectly through supporting the reproducer. Nature chooses organisms to survive and pass along those good-fit genes, so they have greater fitness.

Fitness is an evolutionary concept related to an organism’s reproductive success, either directly (as a parent) or indirectly (say, as an aunt or cousin). It is measured technically based on the proportion of an individual’s alleles that are represented in the next generation. When we talk about “fitness” and “the fittest,” remember that fittest does not mean strong. It relates more to a literal fit, like a square peg in a square hole, or a red dot against a red background. It doesn’t matter if the peg or dot is strong, just whether or not it fits its environment.

One final consideration before we move onto a synthesis of these ideas about differences, heredity, and reproduction: What would happen if the population were uniformly the same genetically for a trait? Well, when the environment changed, nature would have no choice to make. Without a choice, natural selection cannot happen–there is nothing to select. And the choice has to exist already; it does not typically happen in response to a need that the environment dictates. Usually, the ultimate origin for genetic variation–which underlies this choice–is mutation, or a change in a DNA coding sequence, the instructions for building a protein.

Don’t make the mistake of saying that an organism adapts by mutating in response to the environment. The mutations (the variation) must already be present for nature to make a choice based on the existing environment.

The Modern Synthesis

When Darwin presented his ideas about nature’s choices in an environmental context, he did so in a book with a very long title that begins, On the Origin of Species by Means of Natural Selection. Darwinknew his audience and laid out his argument clearly and well, with one stumbling block: How did all that heredity stuff actually work?

We now know–thanks to a meticulous scientist named Gregor Mendel (who also was a monk), our understanding of reproductive cell division, and modern genetics–exactly how it all works. Our traits–whether winners or losers in the fitness Olympics–have genes that determine them. These genes exist in us in pairs, and these pairs separate during division of our reproductive cells so that our offspring receive one member or the other of the pair. When this gene meets its coding partner from the other parent’s cell at fertilization, a new gene pair arises. This pairing may produce a similar outcome to one of the parents or be a novel combination that yields some new version of a trait. But this separating and pairing is how nature keeps things mixed up, setting up choices for selection.

Ernst Mayr, via PLoS.
With a growing understanding in the twentieth century of genetics and its role in evolution by means of natural selection, a great evolutionary biologist named Ernst Mayr (1904–2005) guided a meshing of genetics and evolution (along with other brilliant scientists including Theodosius Dobzhansky, George Simpson, and R.A. Fisher) into what is called The Modern Synthesis. This work encapsulates (dare I say, “synthesizes?”) concisely and beautifully the tenets of natural selection in the context of basic genetic inheritance. As part of his work, Mayr distilled Darwin’s ideas into a series of facts and inferences.

Facts and Inferences

Mayr’s distillation consists of five facts and three inferences, or conclusions, to draw from those facts.
  1. The first fact is that populations have the potential to increase exponentially. A quick look at any graph of human population growth illustrates that we, as a species, appear to be recognizing that potential. For a less successful example, consider the sea turtle. You may have seen the videos of the little turtle hatchlings valiantly flippering their way across the sand to the sea, cheered on by the conservation-minded humans who tended their nests. What the cameras usually don’t show is that the vast majority of these turtle offspring will not live to reproduce. The potential for exponential growth is there, based on number of offspring produced, but…it doesn’t happen.
  2. The second fact is that not all offspring reproduce, and many populations are stable in size. See “sea turtles,” above.
  3. The third fact is that resources are limited. And that leads us to our first conclusion, or inference: there is a struggle among organisms for nutrition, water, habitat, mates, parental attention…the various necessities of survival, depending on the species. The large number of offspring, most of which ultimately don’t survive to reproduce, must compete, or struggle, for the limited resources.
  4. Fact four is that individuals differ from one another. Look around. Even bacteria of the same strain have their differences, with some more able than others to with stand an antibiotic onslaught. Look at a crowd of people. They’re all different in hundreds of ways.
  5. Fact five is that much about us that is different lies in our genes–it is inheritable. Heredity undeniably exists and underlies a lot of our variation.
So we have five facts. Now for the three inferences:

  1. First, there is that struggle for survival, thanks to so many offspring and limited resources. See “sea turtle,” again.
  2. Second, different traits will be passed on differentially. Put another way: Winner traits are more likely to be passed on.
  3. And that takes us to our final conclusion: if enough of these “winner” traits are passed to enough individuals in a population, they will accumulate in that population and change its makeup. In other words, the population will change over time. It will be adapted to its environment. It will evolve.
Other mechanisms of evolution

A pigeon depicted in Charles Darwin’s
Variation of Animals and Plants
Under Domestication
, 1868. U.S.
public domain image, via Wikimedia.
When Darwin presented his idea of natural selection, he knew he had an audience to win over. He pointed out that people select features of organisms all the time and breed them to have those features. Darwin himself was fond of breeding pigeons with a great deal of pigeony variety. He noted that unless the pigeons already possessed traits for us to choose, we not would have that choice to make. But we do have choices. We make super-woolly sheep, dachshunds, and heirloom tomatoes simply by selecting from the variation nature provides and breeding those organisms to make more with those traits. We change the population over time.

Darwin called this process of human-directed evolution artificial selection. It made great sense for Darwinbecause it helped his reader get on board. If people could make these kinds of choices and wreak these kinds of changes, why not nature? In the process, Darwin also described this second way evolution can happen: human-directed evolution. We’re awash in it today, from our accidental development of antibiotic-resistant bacteria to wheat that resists devastating rust.

Genetic drift: fixed or lost

What about traits that have no effect either way, that are just there? One possible example in us might be attached earlobes. Good? Bad? Ugly? Well…they don’t appear to have much to do with whether or not we reproduce. They’re just there.

When a trait leaves nature so apparently disinterested, the alleles underlying it don’t experience selection. Instead, they drift in one direction or another, to extinction or 100 percent frequency. When an allele drifts to disappearance, we say that it is lost from the population. When it drifts to 100 percent presence, we say that it has become fixed. This process of evolution by genetic drift reduces variation in a population. Eventually, everyone will have it, or no one will.

Gene flow: genes in, genes out

Another way for a population to change over time is for it to experience a new infusion of genes or to lose a lot of them. This process of gene flow into or out of the population occurs because of migration in or out. Either of these events can change the allele frequency in a population, and that means that gene flow is another was that evolution can happen.

If gene flow happens between two different species, as can occur more with plants, then not only has the population changed significantly, but the new hybrid that results could be a whole new species. How do you think we get those tangelos?

Horizontal gene transfer

One interesting mechanism of evolution is horizontal gene transfer. When we think of passing along genes, we usually envision a vertical transfer through generations, from parent to offspring. But what if you could just walk up to a person and hand over some of your genes to them, genes that they incorporate into their own genome in each of their cells?

Of course, we don’t really do that–at least, not much, not yet–but microbes do this kind of thing all the time. Viruses that hijack a cell’s genome to reproduce can accidentally leave behind a bit of gene and voila! It’s a gene change. Bacteria can reach out to other living bacteria and transfer genetic material to them, possibly altering the traits of the population.

Evolutionary events

Sometimes, events happen at a large scale that have huge and rapid effects on the overall makeup of a population. These big changes mark some of the turning points in the evolutionary history of many species.

Cheetahs underwent a bottleneck that
has left them with little genetic variation.
Photo credit: Malene Thyssen, via
Bottlenecks: losing variation

The word bottleneck pretty much says it all. Something happens over time to reduce the population so much that only a relatively few individuals survive. A bottleneck of this sort reduces the variability of a population. These events can be natural–such as those resulting from natural disasters–or they can be human induced, such as species bottlenecks we’ve induced through overhunting or habitat reduction.

Founder effect: starting small

Sometimes, the genes flow out of a population. This flow occurs when individuals leave and migrate elsewhere. They take their genes with them (obviously), and the populations they found will initially carry only those genes. Whatever they had with them genetically when they founded the population can affect that population. If there’s a gene that gives everyone a deadly reaction to barbiturates, that population will have a higher-than-usual frequency of people with that response, thanks to this founder effect.

Gene flow leads to two key points to make about evolution: First, a population carries only the genes it inherits and generally acquires new versions through mutation or gene flow. Second, that gene for lethal susceptibility to a drug would be meaningless in a natural selection context as long as the environment didn’t include exposure to that drug. The take-home message is this: What’s OK for one environment may or may not be fit for another environment. The nature of Nature is change, and Nature offers no guarantees.

Hardy-Weinberg: when evolution is absent

With all of these possible mechanisms for evolution under their belts, scientists needed a way to measure whether or not the frequency of specific alleles was changing over time in a given population or staying in equilibrium. Not an easy job. They found–“they” being G. H. Hardy and Wilhelm Weinberg–that the best way to measure this was to predict what the outcome would be if there were no change in allele frequencies. In other words, to predict that from generation to generation, allele frequencies would simply stay in equilibrium. If measurements over time yielded changing frequencies, then the implication would be that evolution has happened.

Defining “Not Evolving”

So what does it mean to not evolve? There are some basic scenarios that must exist for a population not to be experiencing a change in allele frequency, i.e., no evolution. If there is a change, then one of the items in the list below must be false:

·       Very large population (genetic drift can be a strong evolutionary mechanism in small populations)

·       No migrations (in other words, no gene flow)

·       No net mutations (no new variation introduced)

·       Random mating (directed mating is one way nature selects organisms)

·       No natural selection

In other words, a population that is not evolving is experiencing a complete absence of evolutionary processes. If any one of these is absent from a given population, then evolution is occurring and allele frequencies from generation to generation won’t be in equilibrium.

Convergent Evolution

Arguably the most famous of the
egg-laying monotremes, the improbable-
seeming platypus. License.
One of the best examples of the influences of environmental pressures is what happens in similar environments a world apart. Before the modern-day groupings of mammals arose, the continent of Australiaseparated from the rest of the world’s land masses, taking the proto-mammals that lived there with it. Over the ensuing millennia, these proto-mammals in Australiaevolved into the native species we see today on that continent, all marsupialsor monotremes.

Among mammals, there’s a division among those that lay eggs (monotremes), those that do most gestating in a pouch rather than a uterus (marsupials), and eutherians, which use a uterus for gestation (placental mammals).

Elsewhere in the world, most mammals developed from a common eutherian ancestor and, where marsupials still persisted, probably outcompeted them. In spite of this lengthy separation and different ancestry, however, for many of the examples of placental mammals, Australiahas a similar marsupial match. There’s the marsupial rodent that is like the rat. The marsupial wolf that is like the placental wolf. There’s even a marsupial anteater to match the placental one.

How did that happen an ocean apart with no gene flow? The answer is natural selection. The environment that made an organism with anteater characteristics best fit in South America was similar to the environment that made those characteristics a good fit in Australia. Ditto the rats, ditto the wolf.

When similar environments result in unrelated organisms having similar characteristics, we call that process convergent evolution. It’s natural selection in relatively unrelated species in parallel. In both regions, nature uses the same set of environmental features to mold organisms into the best fit.

By Emily Willingham, DXS managing editor

Note: This explanation of evolution and how it happens is not intended to be comprehensive or detailed or to include all possible mechanisms of evolution. It is simply an overview. In addition, it does not address epigenetics, which will be the subject of a different explainer.

Why blueberries won’t turn you blue and other blueberry facts

Blueberries. Credit.

by Adrienne Roehrich, Chemistry Editor

Blueberries in the Northwestern semisphere are the fruit of several shrubs in the genus Vaccinium L.  They grow in all provinces in Canada and all but two of the United States (Nebraska and North Dakota). In the Northwestern semisphere, one can find 43 species of blueberries, depending on the region. Blueberries are found and produced in all hemispheres of the world. However, the species can vary by region.

Kingdom: Plantae (Plants)
Subkingdom: Tracheobionta (Vascular plants)
Subdivision: Spermatophyta (Seed plants)
Division: Magnoliophyta (Flowering plants)
Class: Magnoliopsida (Dictyledons)
Subclass: Dilleniidae
Order: Ericales
Family: Ericaceae
Genus: Vaccinium

There are 43 species and 46 accepted taxa overall. Some of the species include fruits we do not necessarily recognize as blueberry, including farkleberry, bilberry, ohelo, cranberry, huckleberry, whortleberry, deer berry, and lingonberry.  (Source

Blueberries are a very popular fruit in the U.S., and is consumed in fresh, frozen, and canned forms. While blueberries are a great fruit to eat to meet your suggested fruit intake, it also is one of the foods that are purported to have properties that it just does not have. This undeserved reputation results from the high levels of anti-oxidants, leading those predisposed to looking for “super foods” to classify blueberries into the anti-oxidant super food category. While eating more healthy foods is always a good idea, no food has curative effects all on its own.

Other aspects of blueberry nutrition includes it as a source of sugar. One cup (148 g) of blueberries contains about 15 g of sugar and 4 g of fiber, a single gram of protein, and half a gram of fat. If you are counting carbs, this cup has 21 g of them. That one cup of blueberries averages about 85 calories, which is approximately the same as a medium apple or orange. While almost all the vitamins and minerals nutrition gurus like to report on are present to some amount, for the 2000-calorie diet, that one cup of blueberries will provide the recommended daily value of 24% of Vitamin C, 36% of Vitamin K, and 25% of manganese. The remaining values range from 0-4%. (Values obtained from and verified through multiple sources.)

The Wikipedia entry is quite good and well researched (as of August 18, 2012). 

The photo above shows all of the life stages of a blueberry. Berries go from the little red nub at the end of the branch to round and juicy blueberries through fertilization of the ovary, which swells rapidly for about a month, then its growth ceases. The green berry develops with no change in size. The chemicals responsible for the blue color, anthocyanins, begin to turn the berry from green to blue as it develops over about 6 days. The volume of the berry increases during the change in color phase.

Will blueberries turn you blue? In short, no. You can achieve blue skin through the ill-advised practice of drinking silver or you can achieve orangish-yellow skin by eating a large number of carrots. This is because the chemicals causing the skin color are fat soluble and are present in a large quantity in the fat just under the skin, giving the skin those colors. Anthocyanin, the primary chemical causing the blue color in blueberries, is not fat soluble and will not reside in the fat under your skin.

Anthocyanins is a class of over 30 compounds. The chemical structure is generally as shown below. They are polyphenolic, which indicates the 3 ring structures. The “R” indicates different functional groups that change depending on which anthocyanin the structure represents. 

Interestingly, anthocyanins are also pH indicators because their color ranges from yellow to red to blue depending on the local pH. The blue color indicates a neutral pH. The wikipedia page on anthocyanins is also informative (as of August 18, 2012). 

As mentioned before, blueberries are a popular fruit. Recipes abound, but here is one from my own Recipe Codex for Surprise Muffins with blueberries:

  • 6 Tbsp. butter
  • 3/4 cup sugar
  • 2 eggs
  • 1/2 cup milk
  • 1/2 – 1 pint blueberries, fresh or frozen (defrosted)
  • Food coloring, optional
  • 2 cups all-purpose flour
  • 1/4 tsp. salt
  • 1 Tbsp. baking powder
  • Your favorite mini-treat (Hershey’s Kisses, Hugs, Reese’s Mini Cups, strawberry jam, etc.)
  1. Preheat the oven to 350º. In a large bowl, cream the butter and sugar. You can use a wooden spoon, a potato masher or handheld electric mixer. Mix in the eggs, one at a time, and add the milk.
  2. Rinse the strawberries and cut off the green stem. Mash the berries with a potato masher or puree in a blender. Then stir the berries into the butter and milk mixture. TIP: For muffins with a more blue color, add a few drops of blue food coloring.
  3. In a separate bowl, sift the flour, salt and baking powder. Stir well. Add the flour mixture to the berry mixture. Use a wooden spoon to stir until all the white disappears.
  4. Line the muffin tin with paper liners. Drop the batter from a tablespoon to fill the cups halfway.
  5. Add a surprise: an unwrapped mini treat or 1/2 teaspoon of jam. Then spoon more batter to fill almost to the top.
  6. Bake until the muffins begin to brown and a toothpick inserted near the center (but not in the mini-treat) comes out clean, about 20-25 minutes.
  7. Remove the muffins from the tin and cool.
Or perhaps you are in less of a cooking scientist mood and more in a home lab mood. Try this at-home lab with blueberries about dyes. Adapted from the Journal of Chemical Education.

Items You Need
  • 4 microwavable/stove top staff glasses, pots, or containers at least 1/2 cup in volume
  • tablespoons or 1/4 cup measuring cup
  • water
  • spatula
  • alum (available in the grocery store spice aisle)
  • cream of tartar (available in the grocery store spice aisle)
  • hot pads and tongs
  • at least four small (1-2 in.) squares of white cotton cloth
  • yellow onion skins
  • blueberries
  • spoon
  • paper towels
  • vinegar
  • baking soda
  • a dropper
  • notebook for experimental observations
In each step, you will want to record your observations, paying special attention to colors.
  1. Pour 4 tablespoons (1/4 cup) into container 1. Add a pea-sized scoop of alum and about half that amount of cream of tartar and stir. Bring the solution to a boil on the stove top or by microwaving for about 60 seconds. (Your microwave may vary.) Add two small squares of white cotton cloth and boil for two minutes. Set the container aside. The squares will be used in steps 4 and 6.
  2. Tear the outer, papery skin from a yellow onion into pieces no more than 1 inch square. Place enough pieces in a second container to cover its bottom with  2 or 3 layers of onion skin. Add about 4 tablespoons of water to the container. Bring the solution to a boil on the stove top, continuing to boil for 5  minutes.
  3. Wet a new square of cloth with water. Place it in container 2 so it is completely submerged and boil for 1 minute. Using tongs, remove the cloth and rinse it with water. Place the cloth square in the appropriate area on a labeled paper towel.
  4. Use tongs to remove one of the cloth squares from beaker 1. Repeat step 3 using this square. Compare to the dyed cloth square from step 3.
  5. Pour 4 tablespoons of water in a third container. Add 4-5 blueberries to the container and mash them with a spoon. Bring the solution to a boil on the stove, and continue to boil for 5 minutes.
  6. Repeat steps 3 and 4 substituting the blueberry mixture in container 3 for the onion skin mixture in container 2.
  7. Mix a small scoop of baking soda with a tsp of water in a clean container. With a dropper, place 1-2 drops of the baking soda solution in one corner of each cloth square. What happens? Rinse the dropper thoroughly, then place 1-2 drops of vinegar on the opposite corner of each square. What happens? Rinse the fabric squares under cool running water. Is there a change? Allow the squares to dry overnight. Is there any change of the cloth dries?
Optional: Try variations in the procedure such as changing the amount of dye source, the length of time the cloth spends in the dye solution, and the temperature of the dye solution.

Questions to consider
The solution in step 1 is called a mordant. Based on your observations, what is the purpose of a mordant?
Is the dye produced by blueberries really blue? Why might some people not want to wear clothes dyed with blueberries?

All in all, enjoy your blueberries. As a shrub, it is quite pretty. As a fruit, it is quite yummy. And as the tool in an experiment, it is quite fun.

These views are the opinion of the author and do not necessarily reflect or disagree with those of the DXS editorial team.

Making Light in Electronics

By DXS Physics Editor Matthew Francis 

A while back, I wrote about one of the most common ways of making electric light: fluorescent bulbs. Understanding fluorescent lights requires quantum mechanics! While a lot of quantum physics seems pretty removed from our daily lives, it’s essential to most of our modern technology. In fact, reading what I’m writing requires quantum mechanics, since you are using a computer (maybe a handheld computer like an iPad or smart phone, but it’s still a computer) or a printout from a computer.

Modern electronics, including computers and phones, depend on semiconductors. Conductors (like the copper wire in power cords) let electricity flow easily, but semiconductors conduct electricity more reluctantly—but that very reluctance lets us control the flow. While they can’t sustain large currents like conductors can, we can tinker with the chemistry of semiconductors to make them conduct electricity in very precise ways. One of those ways lets semiconductor devices make light: those are known as light-emitting diodes, or LEDs.

You likely have many LEDs in your home: they’re common as indicator lights on appliances, and you might even have LED light bulbs. While they’re pretty expensive right now, the price of LED lights is getting lower all the time, and they have major advantages over both incandescent (old-style) light bulbs and fluorescents. They won’t burn out even as quickly as fluorescent lights (themselves longer-lived than incandescents), and consume less energy. Since they are based on solids rather than gases, they’re not going to break easily, either! But how do they work?

The Electrons in the Band

When I described fluorescent lights in my earlier post, I described how atoms have distinct energy levels inside them, and light is produced when electrons move between those energy levels. Fluorescent lights use gases (generally mercury vapor), so the atoms are relatively widely separated. In solids, including semiconductors, atoms are tightly packed together, forming bonds that don’t break without high pressures or temperatures. In fact, they may also share electrons with each other; a particularly dramatic example of this is in metals, where the electrons in the highest energy levels of the atoms all form a gas that surrounds the atoms. That’s why metals are such good conductors—a little push from a battery or other power source makes those electrons flow in one direction (on average at least), much as a fan creates currents in the air.

Semiconductors are a bit more complicated: their electrons are loosely bound, but still stuck to their host atoms. The way physicists understand this is something known as the band model: just like atoms have energy levels, solids have energy bands. Low energies correspond to electrons stuck to their atoms, which can’t leave; we call these closed shell electrons (for reasons that aren’t important for this particular post). Moderate energies are known as valence electrons, which stay put ordinarily, but can be persuaded to move if given the right incentive. Finally, high energies are conduction electrons, which aren’t tied to a particular atom at all; as their name suggests, they are the ones that carry electric current.

Whether a solid conducts electricity depends on its band structure, and the size of the energy barrier in between the bands, which is called a gap. Large gaps require large energies for electrons to jump them, while smaller gaps are more easily jumped. Conductors have negligible gaps between their valence and conduction bands, while insulators have huge gaps. Semiconductors lie in between; adding extra atoms to a semiconductor can make the gap smaller (a process known as “doping”, which sometimes makes describing it unintentionally funny).

Cars and Roads and Electrons

At low temperatures, semiconductors may not conduct electricity at all, since no electrons can jump the gap into the conduction band. Either warming them up a bit or applying an external electric current gives the electrons the energy they need to move into the conduction band.

I was pondering analogies about band structures to help us understand them, and thought of this one based on cars and roads. Think of closed shells as like parking spaces along a road: cars (which stand in for electrons) are stationary. Valence bands are the slow lane, which is clogged with traffic, so the cars technically can move, but don’t. The conduction bands are fast lanes: cars can really zip, but there’s a traffic barrier between the slow lane and fast lane. (That barrier is the weakest part of my analogy, so remember that we should be thinking of a barrier as something that can be traversed under some conditions but not others.)

One more complication: there are two types of semiconductors, known as n-type and p-type. In n-type, just a few electrons (cars) have access to the conduction band (fast lane) at a time, but in p-type, enough electrons get in to leave holes in the valence band. Applying a current to the semiconductor shifts another valence electron into the hole, but that leaves another hole, and so forth…so it looks like the hole is moving! In fact, physicists refer to this as “hole conduction”, which also sounds odd if you’re not used to it.

Now we’re finally ready to understand LEDs. If you join an n-type semiconductor to a p-type semiconductor, you make something known as a diode. (The prefix di- refers to the number two. If you join three semiconductors, you get a transistor of either the pnp or npn types, depending on the order you use.) The bands (lanes) don’t line up perfectly at the junction: the conduction band in the n-type is generally only slightly higher than the valence band of the p-type, so just a little nudge is needed to move electrons across. This means when they reach the junction between the materials, electrons from the n-type semiconductor can fill the holes on the p-type, which is a decrease in energy. Just as in individual atoms, moving from a higher energy level to a lower energy level makes a photon—and that’s where the LE in the D comes from!

LEDs tend to produce very pure colors, rather than the mixture of colors our eyes perceive as white light. To create LED light bulbs, generally blue LEDs are coated with a phosphorescent material, much like the kind used in fluorescent bulbs. Unlike fluorescents, though, there’s no gas involved, and less heat is lost (though there is still a little bit). Together these factors make LED light bulbs longer-lasting and more efficient even than fluorescents, though currently they are far more expensive.

Despite how common LEDs and other semiconductors are, they’re considered fairly advanced physics. But guess what: if I did my job right, you should understand LED physics now! What is often thought of as “advanced” is really everyday science, and it’s a part of how quantum mechanics (with all its electrons and fascinating interactions on the microscopic level) has helped create our modern world.

Why Can You Hear Around Corners But Not See?

As I sit and type this in my study, I can hear my cats crashing around the living room, which is around the corner from me. There’s a wall between us, so I can’t see them or shoot them with my water pistol (which I would be tempted to do if they were in the same room, before they knock over something fragile). So, just like in my earlier post on mirrors, we’ll start with a question: why can I hear my cats around the corner, but not see them?

Both sound and light are waves, but the way we perceive those waves are very different. I don’t just mean the organs we use – eyes and ears do have major biological differences – but how the characteristics of those waves differ. We perceive differences in light through color, and differences in sound through pitch, but in the end these characteristics mean the same thing: they’re a measure of how big the wave is. The technical term for this is its wavelength: the distance it takes for a wave to start repeating itself.

For visible light, red has the longest wavelength, while violet has the shortest. In between you get the other colors of the rainbow, and if you mix them all together you get white light. Visible light wavelengths are between 400 and 700 nanometers, which is smaller than bacteria (which themselves are smaller than cells in our bodies)! Wavelengths smaller than 400 nanometers get into ultraviolet, X-ray, and gamma-ray territory; wavelengths greater than 700 nanometers comprise infrared, microwaves, and radio waves.

For sound, the situation is a little messier, since our ears respond to frequency, not wavelength. The specific wavelength of sound depends on the temperature and humidity of the air, but if we assume dry room-temperature air, a low-pitched sound has a wavelength of about 17 meters and high-pitched sounds have wavelengths around 2 centimeters. That’s a big range, and not all those sounds will travel around corners. Shorter wavelengths are ultrasound, which are probably most familiar for tracking the health of fetuses: these sound waves can penetrate or reflect off tissue, and by measuring the waves that bounce back, doctors can track blood flow and other developmental processes inside your body. (X-rays go right through soft tissues, so they’re better for looking at bones.) Longer wavelengths are infrasound; animals like elephants use these very low-pitched sounds for communication across long distances.

When a wave meets an opening like a door, it can experience something known as diffraction: the wave passing through the opening spreads out on the other side. However, the wave doesn’t just come through the center of the door: it makes a bunch of waves along the length of the opening, and those waves actually interfere with each other. The wider the door, the more of these new waves are made.

The image to the right shows the interference pattern from a red laser shining through a very narrow opening (smaller than a millimeter). The central maximum is where most of the light coming through the opening ends up, but you also have dark spots where the light interferes and cancels out. The secondary spots on either side of the maximum are much less bright, and you also get tertiary and smaller spots that are fainter still. You get the same pattern for sound, though for obvious reasons I can’t show you a picture of it! The only difference is you exchange brightness for loudness, and dark spots for places where the sound is silenced.

The width and intensity (brightness or loudness) of the spots depend on the ratio of the wavelength to the size of the opening. If the wavelength is bigger than the opening, there isn’t diffraction; if the wavelength is about the size of the opening, then you get strong diffraction, and the central maximum is a lot wider than the opening. If the wavelength is much smaller than the opening, then the central maximum is quite small, and since the secondaries, tertiaries, and so forth are fainter still, the pattern may be hard to detect.

So there’s our answer! A typical doorway is around a meter wide (a little less, usually), so sound with its relatively large wavelengths will create a big central maximum and sufficiently-loud secondaries. That can be enough to hear even if you aren’t in a straight line with the hooligan cats in the other room. A corner is just a very wide doorway, so everything I’ve said about doorways carries over to them too.

Visible light has very small wavelengths, so while you do get light diffraction through doorways, you’d need a microscope to see the pattern! If you have a strong light shining through the door, you’ll get a nice rectangular blaze of light on the opposite wall, but it’s not much bigger than the door, and doesn’t go around corners. However, if you have a cell phone or a cordless phone, the signal from those definitely can go around corners: those are based on microwaves or radio waves, which have much larger wavelengths than visible light.

Similarly, elephants communicate via infrasound over huge distances because rocks, trees, and other obstacles are smaller than the wavelengths they use, so the sound just diffracts right around them. Very handy! Tigers use roars to establish territories, and since they live in dense forests, again infrasound lets their growls travel around the trees easily. (We humans may not hear the infrasound part of the roar, but we can definitely feel it. The lowest notes from large pipe organs or tubas are below our normal hearing range, but they still can contribute to the overall sensation of a musical piece.)

There is one place where diffraction does play a role in our vision: our eyes themselves. Doorways are too big for diffraction, but the pupil in a human eye is about 2 millimeters across, varying depending on whether we’re in a bright or dark place. The size of the central maximum of light cast on our retina is part of what determines how well we see. Diffraction also is why radio telescopes need to be very large, but why an ordinary visible light telescope you might have doesn’t need to be huge – yet the larger it is, the more clearly you’ll be able to see distant planets and galaxies. The telescope is like a big window, so you want to match the size of the window to the wavelength of the light you’re viewing.

Now if you’ll excuse me, I need to go make sure my cats haven’t wrecked the living room.