The World Will Not End Tomorrow

The world will not end tomorrow.

The Sun will rise on the morning of December 22 and find most of humanity still living. I can say that with a great deal of confidence, though my scientist’s brain tells me I should say the world “probably” won’t end tomorrow. After all, there’s a tiny chance, a minuscule probability…but it’s so small we don’t have to worry about it, just like we don’t have to worry about being struck down by a meteorite while walking down the street. It could happen, but it almost certainly won’t.

My confidence comes from science. I know it sounds hokey, but it’s true. There’s no scientific reason—absolutely none—to think the world will end tomorrow. Yes, the world will end one day, and Earth has experienced some serious cataclysms in the past that wiped out a significant amount of life, but none of those things are going to happen tomorrow. (I’ll come back to those points in a bit.) We’re very good at science, after centuries of work, and the kinds of violent events that could seriously threaten us won’t take us by surprise.

Why the World Won’t End

So where does this stuff come from? Whose idea was it that “the end of the world will be on December 21, 2012”? The culprit, according to those who buy into the idea, is that the end of the world was predicted by the Mayas in their mythology, and codified in their calendar. However, it’s pretty safe to say that the Mayas didn’t really predict the end of the world, even though I don’t know much about the great Mayan civilization that existed on the Yucatan peninsula in what is now Mexico from antiquity until the Spanish conquest.

See this calendar? It’s being touted as a Mayan
calendar in articles about the “end of the world”,
but it ain’t Mayan. It’s an Aztec calendar. Please
don’t mix up civilizations.

The Mayas were the only people in the Americas known to have developed a complete written language, which is part of how we know a lot about them despite their destruction by the hand of European invaders. In particular, we know about their calendar, and the divisions they used. We use what’s called a decimal system for numbers, based on the 10 fingers of our hands. That’s why we break things up into decades (ten years) and centuries (ten decades), as well as a millennium (ten centuries). The Mayas liked different divisions of time: their b’ak’tun is approximately 394 years, and they placed a certain significance on a cycle of 13 b’ak’tuns. (I suspect the Klingon language in Star Trek borrowed some of its vocabulary from ancient Mayan.)

In the “Long Count,” one version of the Mayan calendar known to us, the present world came to be on August 11, 3114 BC. That world will end at the close of the 13th b’ak’tun from that creation day, which happens to be December 21, 2012. However, there’s good reason to think that the Mayas didn’t believe this would be the end of all things: other calendars exist that refer to an even longer span of years, stretching thousands of years into the future!

Even more importantly, though: the Mayan cosmology (their view of the universe) was cyclic, as in many other religions. This world was not the first in this cosmology, and it won’t be the last. In such a view, the true universe is eternal, and the cycles of time are a kind of divine rebooting, which don’t really end anything. The end of the 13th b’ak’tun might be a transformative event in the Maya cosmology, but it’s not the end of the world.

Frankly, I’m not sure why we should care even if the Mayas did believe this was the end of the world. As I said previously, there’s no scientific reason to think the world will end tomorrow. But maybe you might think there’s a non-scientific reason—divine intervention to wipe out the Earth, perhaps. However, I’d venture to guess that most of us don’t adhere to the Mayan religion. Their gods are not the gods most people worship. The prophesied arrival on Earth of Bolon Yookte’ K’Uh, the Nine-Footed God is not something central to my belief system, and probably not yours either.

In fact, millennial thinking is far more a Christian thing than it is a Mayan thing—or frankly most other religions. When people talk about the supposed end of the world tomorrow, they use the Christian terminology: Armageddon (referring to Megiddo, a place in northern Israel, named in the Book of Revelation as the site of the last battle) or the apocalypse (literally the “uncovering”, when all that was hidden becomes revealed). These weren’t concepts in the Mayan religion, and nothing in the Christian religion says the world will end on December 21, 2012.

The World Will End…Eventually

Some say the world will end in fire,
Some say in ice.
From what I’ve tasted of desire
I hold with those who favor fire.
–Robert Frost

Science tells us the world won’t end tomorrow. It also tells us the Mayan cosmology is wrong: time doesn’t go in cycles forever. Earth began 4.5 billion years ago, and will end in about 5 billion years more—at least as a livable world, which is what counts for us. In between its beginning and end, it is defined by cycles: the length of rotation (days) and the time to travel around the Sun (years), with its associated seasons. Other cycles are pretty arbitrary: centuries and b’ak’tuns don’t have any particular significance in terms of astronomical events.

The end of the world as we know it will happen in about 5 billion years, when the Sun ceases fusing hydrogen into helium in its core. When that happens, the Sun will grow into a red giant star, swallowing up Mercury and Venus. Earth probably won’t be devoured, but with the Sun’s surface so much closer, things will become distinctly unpleasant. It’s unlikely the atmosphere or oceans could survive, meaning the end of most life. (Some microbes could probably continue to live underground. That kind of thing is a story for another day.) However, 5 billion years is a long time from now.
Could another cataclysm overtake us before that time? Yes. As you may know, about 65 million years ago, a large asteroid smashed into Earth, an event that at least helped end the reign of dinosaurs, and ushering the extinction of many other species.

Unfortunately, we can’t rule out the possibility that could happen again. There are enough asteroids and comets in our Solar System that could eventually cross orbital paths with Earth; if a large specimen collided with us, it would be devastating.

However, we’re talking about tomorrow. No asteroid will strike Earth on December 21: astronomers keep careful track of everything near our planet, and nothing we know of is on a collision course with Earth for the near future. Asteroids and comets are really the only things we have to worry about doing serious damage for life on Earth, but you can sleep easy tonight and tomorrow night: we’re safe.

If you could somehow see the planets during
daylight hours, here’s how they would
appear tomorrow at noon. There’s no
alignment. (You can see this for yourself
using the free planetarium program

Some people have talked about fairly far-fetched ideas: alignments of planets, or lining up Earth, the Sun, and the center of the galaxy. The planets of the Solar System aren’t aligned tomorrow—the image shows where several of them are in relation to the Sun at noon. Jupiter isn’t anywhere close to the planets you see. You’d need a pretty strong imagination to say they’re lined up in any way: while they do lie along a line, that’s the way they always are, since they all orbit the Sun more or less in the same plane. Alignment with the galactic center is even more simple to dismiss: about once a year, the Sun appears aligned with the galactic center in the sky. And nothing happens.

Another explanation I’ve seen involves a mysterious planet called “Nibiru” or “Planet X,” which either will collide with Earth or otherwise generate a baleful influence. Phil Plait, the Bad Astronomer, has a lot about the Nibiru nonsense, so I won’t repeat what he says. Suffice to say Nibiru doesn’t exist: there’s no evidence for it, and (surprise!) it’s not anything that came from Mayan mythology to begin with, so there’s no reason to associate it with a December 21 apocalypse.

A Positive Conclusion

Science, I think, is reassuring in the midst of panic. Why people like to scare themselves and others with misguided ideas of the world’s end, I am not qualified to say. I don’t know how many people are convinced the world will end tomorrow, compared with the number of people who are either wholly skeptical or those who might be a little worried. However, let me reassure you again: the world will not end tomorrow. We can take comfort in the knowledge that December 22 will come, 2012 will end, and a new year—a new cycle—will begin. Any remaking of the world is up to us, so rather than worrying about imaginary apocalypses, let’s commit to improving the lives of those who live on our magnificent planet.

A Once-in-a-Lifetime Truly Double X Event: Venus in Transit

By DXS Physics Editor Matthew Francis, who usually brings you Everyday Science. As you will see, this is science of the Not-So-Everyday sort.

Perhaps the most important question to ask in science is “how do we know?” While it’s appropriate to ask this every day, today it feels even more so, as we prepare to witness a very rare astronomical event. This time, it’s happening on June 5, 2012; when this event occurred during the 18th century, it allowed astronomers to make the first precision measurements of the size of our Solar System. Captain James Cook, best known for his exploration of the Pacific (for Europe, that is—the natives already knew what was there), took a set of scientific instruments aboard his ship to Tahiti; other teams of researchers took measurements at those locations.

The rare event they observed was the transit of Venus: when Venus travels directly between Earth and the Sun, blocking a tiny amount of light. Astronomers in different locations timed the crossing of Venus across the Sun’s disc, and by comparing their numbers, were able to determine the distance between Earth and the Sun. With that distance in hand, they were able to calibrate the size of the entire Solar System. The 1769 observation was an international scientific effort (to use modern language), and while the results weren’t as good as the astronomers of the day had hoped, they still agreed with modern measurements.

Today we use a variety of techniques to measure distances, including radar ranging (bouncing radio waves off planets and timing the round trip), so we don’t have to wait for Venus transits anymore—which is good, since they aren’t common! The last Venus transit was in 2004, but the previous one before that was in 1882, and the next one will be in 2117. I got up very early in the morning on June 8, 2004, joining some fellow astronomy enthusiasts at the Rutgers observatory, where we took the photo you see at the top of the post.

The seemingly odd intervals between transits are because Earth’s and Venus’ orbits around the Sun don’t lie in the same plane. If you draw Earth’s orbit as an ellipse on a sheet of cardboard, and Venus’ orbit on another sheet of cardboard, they need to overlap in a small X pattern, as shown in the picture. The only times Venus will transit is when both Earth and Venus are on the same side of the Sun, and only when they are in the region where the cardboard pieces overlap. The angle (3.5°) in the picture is correct, but I’ve exaggerated the size of the Sun and the sizes of the “transit zones”; in truth, even though the Sun is huge compared to Earth, it’s not that big on the sky. If you do the real calculation, you find that Venus transits happen roughly twice per century, and those two events are separated by 8 years. It’s a rare and wonderful event!

Viewing the Transit

If you want to view the Venus transit, the first thing you should do is see if it will be visible where you live. (Hopefully the weather will cooperate too! Such is the life of an astronomer.) In Richmond, Virginia (where I live), the transit begins around 6 PM. If you’re in the area, the Science Museum of Virginia is hosting a free viewing on the lawn; many other cities and towns have similar events.

A common sense warning: please don’t look directly at the Sun! However, you don’t need fancy equipment or a big observatory to witness the transit. Two weeks ago, I observed the solar eclipse using nothing but a microwave macaroni-and-cheese container. By piercing a hole in the bottom of the tub, I created a simple pinhole camera. A small and kind of fuzzy image of the eclipse appeared on a piece of paper, which I photographed. (Obviously you can do better if you have better equipment—I happened to be far from home during the eclipse and used what I had on hand.) A piece of cardboard covered in aluminum foil with a small hole works better, and you can project the image right onto the sidewalk, the side of a building, or another screen.

If you have a pair of binoculars that use glass lenses (since plastic will melt), point the larger lens toward the Sun and the smaller lens onto a flat surface. (Again, don’t look through the binoculars if you value your eyeballs!) If you have a telescope with a mirror or glass lenses, you can also project the image onto a flat surface, or create a sun funnel. There are a lot of ways to view the Sun if the ones I mention don’t appeal to you.

As a word of caution: the Venus transit won’t look as impressive as a solar eclipse, since Venus is a lot farther away than the Moon. It will appear to be a small round shadow on the Sun’s disc. The thrill (for me at least) lies in the knowledge: you are viewing a planet not much smaller than Earth as it crosses between us and our home star! If it isn’t enough these events are rare, think of how significant it is to catch a glimpse of the sheer size of our Solar System, in a way we don’t usually get to see. And always, always remember to ask the question: “how do we know?”

Further Reading

If you want to know more about transits and why they are still scientifically important today, try these links:

Happy Venus-watching!

To Everything (Turn Turn Turn) There is a Season

Today – June 20 – is the northern Summer Solstice, sometimes known as the Northern Solstice, “first day of summer”, or Midsummer’s Day, depending on where you live. It’s the longest day and shortest night of the year in the northern hemisphere (where I live), though exactly howlong or short depends on how far north you live. And of course in the southern hemisphere, today is is the shortest day and longest night, since the seasons are reversed.
The secret to the solstice and to Earth’s seasons in general involves the tilt of Earth’s axis. Our planet orbits the Sun in an elliptical path, which you can draw on a flat piece of paper: it doesn’t move “up” or “down”, but stays in a single plane known as the ecliptic. (The name “ecliptic”, as you might guess, is related to the word “eclipse”, since ancient astronomers determined eclipses of the Moon and Sun could only occur at certain places in the sky.) Earth’s axis is tilted compared to the ecliptic, and the axis points more or less in the same direction, wherever the planet is in its orbit. The axis points almost directly at Polaris, the North Star, which is why that star is a good navigational guide for those in the northern hemisphere: no matter what time of year, it’s always in the same spot in the sky. Other stars rise and set as Earth rotates, but not Polaris. (Unfortunately, there isn’t a South Star.)
As you can see from the diagram above, during about half the year, the North Pole points more toward the Sun, while it points more away for the rest of the year. Where I live, the Sun will never be directly overhead, even at noon. The farthest north that will ever happen is a special latitude known as the Tropic of Cancer – and the northern Summer Solstice is the day that occurs. On the northern Winter Solstice, which happens on December 21 or 22, the Sun is directly overhead at noon at the latitude of the Tropic of Capricorn.
Now we can see why summers are hot! In summer, the Sun rises earlier, sets later, and reaches a higher point in the sky. Those things combined mean extra sunlight, heating up the air and the ground longer. We can also see why I put “first day of summer” in quotes: the Solstice is the apex of the process, but the increase in daylight and temperatures begins long before June 20 (at least every place I’ve lived). The Midsummer’s Day festival, celebrated throughout northern Europe, acknowledges that; Shakespeare’s play A Midsummer Night’s Dream may have been written for the English version of the festival (though from what I can tell, the historical evidence is scant).
Similarly, during winter the Sun’s light comes in at a steeper angle and days are shorter, so the time for the ground to warm is greatly reduced. The northern Winter Solstice (also known as the Southern Solstice, “first day of winter”, Midwinter’s Day, or Yule) is the shortest day and longest night of the year in the northern hemisphere. On that day, the North Pole points as far away from the Sun as it ever does. We also have the reason the tropics are warm all year around: they receive about the same amount of sunlight during both summer and winter.
Approximately halfway between the solstices, the Sun appears directly overhead at noon at the Equator. On those days, everywhere on Earth gets about 12 hours of daylight and 12 hours of night. These days are the equinoxes, meaning “equal night”. (The spell to extinguish light in the Harry Potter books is “nox”, for what it’s worth. Yes, I remember such things. I’m still waiting for my “accio!” summoning spell, though.) The two days are known as the Vernal(or spring) and the Autumnal (or autumn) Equinox, again based on the seasons in the northern hemisphere. From an astronomical point of view, Earth’s “solar year” is marked between successive vernal equinoxes. (A second measurement of the year, known as the sidereal year, is measured with respect to the stars. These two year measurements are almost, but not quite, the same length!)
Now let’s put all of this together in a movie! (For some reason, the Sun – which was a gently glowing lamp in my original simulation – came out looking flat and boring in the final movie. I guess I still have more to learn about creating three-dimensional animations.) For best results, please view this full-screen.

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

As Seen on TV! Age Your Wine in 10 Seconds!!!!

Old, old wine. (Source)

Anyone who watches TV, reads magazines, or flips through catalogs has seen some interesting products. Maybe they seem plausible to you, maybe they don’t. However, a little investigation shows they are based less on science and well…actually working, and more on wishful thinking. At worst they’re actual con-jobs, designed to separate you from your money as efficiently as possible (which I guess is a certain standard of success).

As a result, we at Double X Science are starting a new series: “As Seen on TV!” In these features, we’ll look at some of the products shilled on talk shows and infomercials, items lurking between the articles you read in magazines, or things you might find on the shelves of the stores where you shop.

Our first entry is one I spotted in SkyMall, the catalog you (if you’re like me) read if you forget to bring a book on an airplane. Where else can you find dog water bowls shaped like toilets or sports chairs built deliberately too large for anyone, so you look tiny sitting in them? While the catalog is full of impractical items (to put it mildly), some of them go beyond that into the realm of…imagination. Yeah, I’ll call it that. It avoids potential lawsuits.

It’s the Aging Accelerator! With Magnets!

Here’s the idea: depending on which device you buy, you insert either a glass or a bottle of wine, and within 10 seconds! it ages the wine, with the unspoken assumption that this is desirable. (It also evidently works for whiskey, but I’ll skip that discussion in the current article.) Now, anything that promises to drastically alter something within 10 seconds! is probably suspicious to begin with, but that’s the part I’m going to leave alone. After all, magnets do work quickly, so if the device does what it claims to do, it’s quite possible that 10 seconds will be enough time for the magic to happen.

Well, it seems like magic to me. I went to a winery last weekend, and spoke to one of the vintners there (yup, that’s the name for ’em). She told me that not all wines should be aged, and the reason has to do both with the way wine is made and how it is stored.

First, not all wine should be aged! All wines actually go bad over time, including many of the usual types you may see in the store. That time may be pretty long, but you don’t want to just buy any bottle, stick it in your basement, and wait 20 years to drink it – most of them won’t taste good. According to my source, the days are gone where you might buy bottles of wine and put them in a cellar for your children. (Who has a wine cellar now anyway? I live in a second-floor apartment!) Basically, my source tells me to ask an expert if you have any doubts, but basically all wine is sold today in a drinkable state – no aging is necessary or even wanted. (I can’t endorse it, but Wikipedia has a list of wines that can be aged, and possible ranges.) Earth’s magnetic field has nothing to do with the aging process, whatever the ad says.

Second, the reason some wines age better than others has to do with their chemistry: how much sugar is in the grapes and how much tannin content they have. Red wines typically are higher in tannins because the skins are thrown in with the flesh of the fruit – and tannins act as a preservative. Sugar also acts as a preservative, but it’s not as effective, so white wines (lower in tannins, higher in sugar) don’t keep as well.

The point I’m trying to make is that wine aging isn’t mysterious, either why it happens or how. I don’t have the “Aging Accelerator” package in front of me, so I can’t tell you if they give advice on which wines to put in it and which ones to avoid, but the picture shows both reds and whites. So let’s turn to the way the device is supposed to work: magnetism.

They certainly have one thing right: neodymium magnets are very strong! (Neodymium is one of the “rare earth” elements, found near the bottom of the periodic table, so sometimes you’ll see them referred to as “rare earth magnets”.) When I’ve used neodymium magnets for various experiments, two of them attracting each other pinched my fingers hard enough to create blood blisters.

Admittedly magnets can seem mysterious: understanding exactly how they work requires looking at electrons and atoms, which might seem a little out of the ordinary. However, challenging isn’t the same thing as magical, but some people seem to think that magnets are capable of all sorts of feats, from curing arthritis to – yes – aging wine.

How magnets actually work could be the topic of an “Everyday Science” post, but in brief: the way a material responds to a magnet is called its magnetic susceptibility. Some materials, like neodymium, are very susceptible, but most things aren’t, including the human body. (Some organisms such as pigeons use Earth’s magnetic field to navigate, but exactly how they do it is still not known.) I couldn’t find any particular data on the magnetic susceptibility of tannins or other molecules in wine, but my feeling is it’s not large. Tannins are big biological molecules – think DNA or proteins – and those don’t tend to be magnetic.

But here’s the deal: suppose tannins are magnetic. Why then would exposing them to a magnetic field age the wine? Simply putting a strong magnet near your wine would merely rearrange the molecules inside the liquid – it’s like stirring it, in other words. Obviously stirring something can change the way it tastes, since it can mix sediments in, but that’s not the same thing as aging.

So, let’s wrap up: why should we be suspicious of paying $60 or $100 for an “Aging Accelerator”?
  • The concept misuses a well-understood physical principle – magnetism. Just because someone doesn’t understand how it works doesn’t mean it can perform miracles.
  • The aging process is chemical, and we understand how that works – it involves tannins, sugars, and other molecules. There are no secrets, in other words, and nothing simple to make your wine taste better.
  • Basically, if it sounds like a magic trick, it probably is – but its main result will be to magic money out of your pocket.
We’ll see these kinds of rules repeated throughout the series!

Stay tuned for further installments of “As Seen on TV!”

By DXS Physics Editor Matthew Francis 

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DXS Op-Ed: How birth control can save the world

By DXS Biology Editor Jeanne Garbarino

Over the last few months, the concept of birth control has been under great scrutiny in the American eye.  Many politicians have been discussing it’s “moral” implications, and whether institutions or organizations should have the right to deny insurance coverage for hormonal contraception if it does not fall within the confines of their belief systems.  And while American women have narrowly escaped legislation that would impede their reproductive health and freedom, politicians, mostly men, feel it necessary to make misinformed or even completely false statements about birth control. 

For some strange reason, there is this erroneous idea that birth control is not a matter of health, but rather a means by which a woman can engage in careless and frequent sexual activity, with a man, and without the consequences of pregnancy.  It’s clear that the picture these politicians are trying to paint is that of debauchery and immorality, which, of course, is a departure from the puritanical integrity they embody.  But, rather than focus on this utter nonsense, I would prefer to highlight the significant impact birth control will have on the future of our civilization and our planet.

The human population has grown steadily since the beginning of our species.  However, the rate of growth began to skyrocket after the industrial revolution, and our population has actually doubled over the last 50 years, reaching 7 the billion mark in March of this year.  This is an astounding statistic since it took until 1804 – around 50,000 years – to reach our first billion. 

World Population: 1800 – 2100 (Wikimedia Commons)

What makes these numbers really scary is the concept of carrying capacity, which is an ecological term used to describe the maximum number of individual members of a species that a certain habitat can support.  In this case, the species is human and that certain habitat is planet earth. 

Here’s the thing: the availability of our resources will not match the rate of population growth.  Given our current technologies, there is only so much food we can grow, only so much water we can drink, only so much space we can inhabit, only so much waste we can safely rid, only so much energy we can harness.  There will be a point that the human population will hit its carrying capacity on earth, and when it does, the chances of widespread famine will be great, and the delineation between the developing world and the developed world will be no longer.  

Given this very serious issue, Britain’s Royal Society has recently convened to discuss the future of the human population and on April 26th, 2012, and published their findings in the People and the Planet Report [PDF].  For me, key findingnumber three struck a cord:

Reproductive health and voluntary family planning programmes urgently require political leadership and financial commitment, both nationally and internationally. This is needed to continue the downward trajectory of fertility rates, especially in countries where the unmet need for contraception is high. (emphasis theirs)

Political leadership and financial commitment – Did you see that, American politicians??  For those of you who are unnecessarily waging war on women’s reproductive rights, its time to get your giant heads out of your collective asses and realize the implications of legislation that would go against ensuring both the continued success of our species and the health of our planet.  It is time to stop spending money on these regressive and oppressive campaigns guised under the false pretense of “religious freedom” and start making a financial commitment to the women (and by association, men) who live in our nation.

To drive this point even further, here is another excerpt from the People and the Planet Report (my favorite bit, found in Box 2.5 on page 33):

Women bear the main physical burden of reproduction: pregnancy, breastfeeding and childcare. They also bear the main responsibility for contraception as most methods are designed for their use. Men, it may be argued, reap the benefits of children without incurring an equal share of the cost. It follows that women may be more favourable to the idea of small families and family planning than their partners but unable to express their inclinations in male-dominated systems. Such views received international endorsement in the Program of Action resulting from the UN conference on population in 1994. Paragraph 4.1 states that “improving the status of women is essential for the long-term success of population programs”.

We currently live in a nation where 99% of women who are of reproductive age have used some form of birth control at least once.  And when it comes to hormonal contraception, over 80% of sexually active women aged 15-44 have relied on “the pill” as a means to prevent unwanted pregnancies.  This has contributed to an average of two births per American woman, which is considered to be the replacement rate for a population.  Compare this number to countries where birth control and reproductive education is scarce – countries like Niger (7.52 births per woman) or Afghanistan (5.64 births per woman) – and one can see the impact of family planning through contraception.  Furthermore, it has been well documented that women in developed worlds who are provided with the means to control their fertility are more empowered and their families are healthier.   

While our situation in the US is significantly better compared to underdeveloped nations where rape and the cultural devaluing of women is commonplace, we still have a responsibility to uphold – a responsibility that would undoubtedly increase the quality of life for women (and men), as well as contribute to the overall health of the human population.  Why would we want to go backwards and remove the ability of a woman to decide when, if ever, she would like to reproduce? 

Having access to birth control empowers women and allows them to make greater contributions to society.  And because contraception is primarily the responsibility of a woman, our society needs to ensure that birth control, reproductive education, and family planning resources are readily available to EVERYONE.

The United Nations predicts that the ten-billionth person will be born around 2050.  Will we continue to fight this ridiculous fight against women’s rights or will we redirect our collective energy to developing technologies that will help our species and planet better cope with the increasing demands associated with a steadily rising population?  Let’s stop allowing stupidity to prevail and let’s start doing the right thing: making sure that birth control is readily available to any woman who wishes to use it.  Because, now more than ever, it is clear that birth control will save the world.   

Note: In my readings for this article, I came across a wonderful resource for anyone interested in learning more about human fertility and population growth.  Through the wonders of the internet, Academic Earth is offering a free (!) online course called Global Population Growth, given by Yale University professor Robert Wyman. 

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