Why don’t more girls get the HPV vaccine??

Double X Science is pleased to be able to repost, with permission, this important piece courtesy of author Kate Prengaman and her Xylem blog, focused on spreading science and new ideas.

Imagine if there was a vaccine that could prevent cancer. Everyone would want it, right?
Surprisingly, no. There IS a vaccine to prevent cervical cancer, which, according to the CDC, affects about 12,000 women every year. Unlike most cancers, cervical cancer is caused by a sexually transmitted virus, Human Papillomavirus, also known as HPV. The virus can cause abnormal cell growth in the cervix, which can turn cancerous. The vaccine, approved in 2006, works against many common strains of HPV.
The vaccine is recommended for girls ages 11-12, and also provided to women up through their early twenties.  The goal is to protect girls long before they are ever sexually active, so that they never contract HPV in the first place. As of 2011, the vaccine is also recommended for adolescent boys.
Contracting HPV is so common that more than half of all sexually active men and women in the United States will become infected with HPV at some point in their lives. According to a CDC factsheet on the HPV vaccine, “about 20 million Americans are currently affected, and 6 million more are infected every year.” In most people, HPV infections never lead to symptoms but the virus can cause development of cervical cancer and, more rarely, cancers of the vagina and anus, as well as genital warts. Furthermore, men can develop cancer from HPV. The virus is transmitted through skin to skin contact, which reduces the efficacy of condoms at preventing the spread of this disease.

Yet, despite the dangers associated with HPV, only 33.9% of American girls, ages 13-17, reported to the CDC in 2010 that they had been fully vaccinated (3 doses) against HPV.  When I mapped the state by state rates of vaccination, I found a dramatic distribution, from only 19% of girls in Idaho to nearly 60% in South Dakota and Rhode Island.

Map created by Kate Prengaman
Much of the resistance to vaccinating adolescent girls against cancer-causing HPV comes from  many people who are uncomfortable with or resistant to the fact that adolescent girls will grow up and have sex. I expected to see a strong correlation between states with Abstinence-only sex education and low vaccination rates, but the pattern in the map is weaker than I had anticipated. I also considered that the cost of the vaccines might play a role, although if they are not covered by a family’s health insurance, there are federal programs in place to subsidize the cost. There’s also some correlation there, but again, not as strong as you see, for example, when mapping teenage birthrates.
Map created by Kate Prengaman
Clearly, the pink map, lovely as it is, does not provide an answer for why more adolescent girls are not receiving the HPV vaccine. There is an unfortunate anti-vaccination movement in this country, with people choosing not to protect their kids from dangerous diseases because of unfounded fears that vaccines can cause autism, among other things. Last fall, Michelle Bachmann even used a presidential debate to stir up more fears that the HPV vaccines could cause mental disabilities, a enormous error that the medical community quickly tried to correct.
The truth is that these vaccines are safe. The truth is that HPV is really common, and it can cause cancer, and if you ever have sex, you have a good chance of getting it. Why aren’t more parents of adolescents taking the lead on protecting their kids’ future health?  If you have any ideas for other factors that might explain the patterns of vaccination, let me know in the comments and I  will try adding to my map.  Thanks!

About the guest author:

Kate Prengaman is a science writer and outdoor enthusiast currently based in Madison, WI. Formerly a botanist, Kate is pursuing her masters in science journalism at UW, reading and writing as much as possible.  She loves talking to people, telling stories, finding adventures,  geeking out over wildflowers, and eating delicious things. She blogs at Xylem

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.
Carbohydrates

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.

Proteins

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

Blog of the Week: Context and Variation


This week’s Blog of the Week is Context and Variation, part of the Scientific American blog network. The blog author, Kate Clancy, is an assistant professor of anthropology at the University of Illinois, where she studies evolutionary medicine of women’s reproductive physiology, otherwise known as ladybusiness. Clancy writes about how human behavior evolved and is evolving and is also a vocal but thoughtful advocate for women in the sciences. That makes her sound stuffy and high-falutin’, so I’ll also add that she’s a baddass roller derby player who recently sustained a second black eye during play. She rolls under the nom d’derby of Anthrobrawlogist. If you don’t love that–and how could you not?–you’ll love that she’s a mother of a young child, struggling like many mothers do to figure out how to balance work, life, parenting, and play, some of which all happen at the same time.


Highlights from her blog



Honestly, every post has something on offer for the ladybusiness crowd. Go forth and read.

You can follow Kate Clancy on Twitter: @kateclancy



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The fantastic image at the top is from the Context and Variation banner and is the work of Jacqueline Dillard.

On this Father’s Day, let’s remember the allofathers, too

A big brother, practicing the art of allofathering.

By Emily Willingham, DXS managing editor

On Mother’s Day, scientist and blogger Kate Clancy wrote an excellent post at Scientific American about allomothers, the people in your circle of friends and family who support mothers in their mothering. In thanking the allomothers in her life, Clancy included in that list her husband because men can be allomothers, too. Although this site is called Double X because we want to bring evidence-based science–and yes, some snark–to women, tomorrow is Father’s Day. So today, we’re shifting into XY gear and talking about allofathers. 

We all have or had fathers. Some for better, some for worse, some we may never have even seen. Many of us also have had other men in our lives who participated in a father role or who supported our fathers in the same way that Clancy writes about supporting mothers. The funny thing is, a Google search on “allofathers” confuses Google so badly that it actually declines to do that search and instead offers a search on “allomothers.” When you force it to search “allofather,” you get only three pages of scanty hits, some of which reference a more general “alloparenting.”

Why no love for the allofathers, Google? Fathers these days need allo support as much as mothers, or at least, the fathers I know do. As Paul Raeburn writes in this Father’s Day piece:

The grindingly slow recovery of the economy is making it hard for fathers to earn enough to help support their families. Those who do have jobs are working more hours, taking time away from checkers and family dinners. In many families, both parents are working, leaving less time for fathers and partners to work on their relationships with each other.

He notes that fathers these days thrive in a habitat that allows the time with family, time to do things other than make a living wage, although that remains an important feature of fatherhood and a key goal of every father I know. In fact, that emphasis means that my spouse–who is also the father of my children–is at work right now, on Saturday, after already putting in overtime through the week. Indeed, he may have to work tomorrow, on Father’s Day, and is looking at a midnight deadline Monday night. There will be no games of chess with Dad this weekend. 

The work is difficult enough and in a trying environment. And pushing against this need to work hard and keep a job is also a desire to have the kind of family time those of us in the United States have come to expect on weekends, particularly when we work salaried weekday jobs that ostensibly promise weekends off. That means that on top of the anxiety associated with stacking 20 or 30 extra hours onto a 40-hour work week to meet a tough deadline, my husband and my children’s father also feels angst about this inability to be a part of our family time. These are first-world problems, I realize, but that doesn’t make them any less real for us and our children.

So I’m allofathering for him. Yes, I’m the mother, but I’m also supporting my husband’s fathering role, in part by doing things that assure him that we’re all OK, and in part by doing things with our sons that people might think of as stereotypically “dad” activities: fishing, baseball, football, soccer, hiking. But I also have taken on the things he usually does around the house, like emptying the dishwasher Every Single Time, vacuuming, and doing the laundry. Bless the man, he usually does all the laundry. But I do miss the other allofathers in our lives.

We no longer live a stone’s throw or a short-ish drive from our extended family, but when we did and still when we visit, the allofathers are abundant. My children have uncles who take them fishing, monitor group infighting among nine cousins, catch snakes with them, play football and soccer with them, and take them on hikes and (fruitless) dove hunting. My husband does his share of allofathering for their children, reading books and playing with the youngest, making dinners, and serving as an ever-necessary playground monitor. And my children have a grandfather who builds things in his shop for them, closely monitors their BB gun target practice, wanders for hours with them in nearby woods to find animal bones, and patiently acknowledges every single mystifying LEGO construction and rambling imaginary story surrounding it.   

All of these alloparents expand the parenting and support and safety net for my children. They are the village raising my sons, and my children trust them implicitly. These allofathers summon up reserves of energy they probably didn’t know they had and in spending this time with their nephews or grandchildren, they add layers of complexity and different insights from father figures that my children wouldn’t otherwise have. They also model for children like my sons the many roles a man can have through life.

As humans, we fit several features of species that engage in this extra-parental parenting, including typically having a single offspring at a time, a relatively small number of offspring over a lifetime, and an extended period of parental investment, and being part of a highly social species with tight family bonds. It may be that as our culture evolves so that the father role expands into what was previously considered maternal territory, we need to more closely consider allofathers as well as allomothers. These factors that characterize us as an alloparenting species can add up to benefits and greater success for mothers and fathers and children alike. At any rate, I know that’s been the case in our family.

When I was growing up, I had four grandmothers and four grandfathers. Half of them were “step” grandparents, obviously, but I loved the fact that I had all of these grandparents, blissfully unaware in my childhood of the fractures and angst that had led to their presence in my life. Among these step-grandparents was the man who married my mother’s mother. They met over square-dancing, he a handsome architect, she a tiny, fiery single mother who could sew some kick-ass square-dancing outfits.

Through various unanticipated turns in Life’s do-se-do, after marrying my grandmother, this man one day became father to two of my cousins. From their early childhoods, he has been their father, even though for the rest of us cousins, he was our step-grandfather. Along with my grandmother, he committed himself to rearing them and being their parent, and today, in part thanks to his steady, calm presence, they are successful, happily married parents themselves. Without his stabilizing influence, their paths might have been much less straightforward. 

While what my step-grandfather did crossed over from alloparenting to being an actual father, my own children have a step-grandfather of their own who, I think, epitomizes allofathering. When we visit, he has a ready store of caps available for all the cap guns he buys them by the dozen (if you think there are a lot of guns in this post, there are; it’s Texas). He actually builds–builds–go carts and other motorized vehicles to take them buzzing around the large property where he and my mother live and maintains a fleet of bicycles for them to ride. He will drop anything to run a quick errand just because one of the youngest generation expresses a wish for a certain treat or toy. Ask him to make you an ax from a stick and a rock, and he’ll do it masterfully. He attends every volleyball, baseball, or basketball game my niece and nephew have and has simply been a steady and much-loved allofather figure in the lives of all of the youngest generation in our family.

When I think of men like these who enter into lives already structured around complex family interactions and who take on without comment or resentment the care and loving of the children in that family, I wonder if I could be as kind or selfless. Of course, I hope that I could. These little people are, after all, children, and they need love and support and classic grandparental spoiling and an understanding that parenting and parental love come in different forms and different ways of expression. To all the allofathers in my life, I–and my children–are extremely grateful. To all the fathers and allofathers out there, happy Father’s Day. And may I say, I think you all warrant more Google hits. 


***Special thanks to Kate Clancy for her post on allomothers and to Paul Raeburn for his post about the role of fathers today, which certainly drove my thinking about this topic.***

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

Miscarriage: When a beginning is not a beginning

The “Pregnant Woman” statue
at Ireland Park, Toronto, by Rowan Gillespie

Photo credit: Benson Kua.
[Editor's note: We are pleased to be able to run this post by Dr. Kate Clancy that first appeared at Clancy's Scientific American blog, the wonderful Context and Variation. Clancy is an Assistant Professor of Anthropology at the University of Illinois. She studies the evolutionary medicine of women’s reproductive physiology, and blogs about her field, the evolution of human behavior and issues for women in science. You can follow her on Twitter--which we strongly recommend, particularly if you're interested in human behavior, evolutionary medicine, and ladybusiness--@KateClancy.]
Over the course of my training to become a biological anthropologist with a specialty in women’s reproductive ecology and life history theory, or ladybusiness expert, I have learned a lot about miscarriage. Only it wasn’t miscarriage, it was spontaneous abortion. Except that some didn’t like the term spontaneous abortion and used intrauterine mortality (Wood, 1994). Or fetal loss. Fetal loss is probably the most common.
There is also pregnancy loss (Holman and Wood, 2001). You can use that term, too. Oh, or a Continue reading

Friday Roundup: Jane Austen’s arsenic poisoning, breastfeeding and bones, dog bites that trigger pregnancy, and a cranky crab

Jane Austen. Engraving via Wikimedia Commons, in the U.S. public domain.

Curious about how climate has changed over the long term–the very, very long term? This video from the National Oceanic and Atmospheric Administration puts it all into perspective:


  • Jane Austen poisoned by arsenicA mystery author claims that all signs point to arsenic poisoning as the cause of Jane Austen’s death. The rationales that treatments with arsenic may have been fatal are plausible, but how about the idea that it was…murder?
  • Peanut butter recalled for Salmonella concerns, but no illnesses reported.
  • In other recall news, Kotex tampons also have been recalled for bacterial contamination. Please read.
  • You may have heard that when women spend a lot of time together, their cycles synchronize. You may have heard wrong, and Kate Clancy tells us why.
  • Birth control: Not just about sex. According to a report, many, many women use birth control for reasons having nothing to do with…birth control.
  • This just in: Girls can be engineers, too.
  • Chilling trauma patients to save them. Trauma surgeons may be turning to deep chilling their patients to stop their bleeding to death before livesaving surgery can be completed. 

If you found the climate change video depressing, how about some astronauts falling down on the moon? Watching smart courageous people fall over is always entertaining, right?

  • Bones and breastfeeding fads. Would you consider giving your baby pap, “a mixture of flour or bread crumbs cooked in milk or water, or a bread broth called panada, or milk flavoured with spices, sugar, or eggs? These bones tell the story of breastfeeding practices before our time.
  • Ever wondered why smells–like baking cookies or a pinewood fire in the grate–are so evocative and memory stirring? Here’s why.
  • Perhaps you’ve heard about fecal transplants–they are exactly what they sound like–and thought, “Ewwww.” The thing is, they seem to work, but as Maryn McKenna writes, they are not easy to come by.
  • Rick Perry’s debate brain freeze: Parents, you know this happens to you, too, just not on national television. In a presidential debate.
  • In the downer category, orangutans in Indonesia killed by the hundreds every year.
  • Remember when ketchup became a vegetable in the Reagan years? Now Congress wants to add pizza sauce to that category. Someone should tell Congress that there are no do-overs on a healthy childhood.
  • For your “Weirdest News of the Day” reading: People in this village genuinely believe that a dog bite can trigger pregnancy–in men or women–with puppies. It is mass hysteria.
  • Have you been reading confusing and conflicting information about the HPV vaccineHere’s a piece that clears all of that up. 

And finally, we give you this crab because it made us laugh. And laugh. Feel free to suggest captions.

The sperm don’t care how they got there, Rep. Akin

17 c. rendition of human inside sperm.
Public domain in US.
[Trigger warning: frank language about sexual assault]
By Emily Willingham
By now, you’ve probably heard the phrase: legitimate rape. As oxymoronic and moronic as it seems, a Missouri congressman and member of the House Science, Space, and Technology committee used this term to argue that women who experience “legitimate rape” likely can’t become pregnant because their bodies “shut that whole thing down.”
If his words and ideas sound archaic, it’s because they are. Welcome to the 13th century, Congressman Todd Akin. It’s possible that this idea that a woman couldn’t become pregnant because of rape arose around that time, at least as part of the UK legal code. People once thought that a woman couldn’t conceive unless she enjoyed herself during the conception–i.e., had an orgasm–so if a rape resulted in pregnancy, the woman must somehow have been having a good time. Ergo, ’twas not a rape. This Guardian piece expands on that history but doesn’t get into why such a concept lingers into the 21st century. A lot of that lingering has to do with a strong desire on the part of some in US political circles to make a rape-related pregnancy the woman’s fault so that she must suffer the consequences. Those consequences, of course, are to be denied abortion access, to carry a pregnancy to term, and to bring a child of rape into the world.
This idea that pregnancy could determine whether or not a rape occurred was still alive and kicking in 20th century US politics, so Akin’s comments, as remarkably magic-based and unscientific as they are, are still not that shocking to some groups. In 1995, another Republican member of the House, Henry Aldridge, made a very similar observation, saying that women can’t get pregnant from rape because “the juices don’t flow, the body functions don’t work.” A year after Aldridge made those comments, a paper published in a US gynecology journal reported that pregnancies from rape occur “with significant frequency.” That frequency at the time was an estimated 32,101 pregnancies resulting from rape in a single year. In other words, the “body functions” did work, and “that whole thing” did not shut down in 32,000 cases in one year alone.
Consider that current estimates are that 1 out of every 6 women in the United States will be a victim of completed or attempted rape in her lifetime and that by the close of the 20th century, almost 18 million women were walking around having experienced either an attempted or a completed rape. The standard expectation for pregnancy rates, whether from an act of violence (rape) or mutually agreed, unprotected intercourse, is about 5%.
In his comments, Akin used the phrase “legitimate rape.” He joins with his colleague of 17 years ago in ignorance about human reproduction. But he also joins legions of people with a history stretching back hundreds of years, people who blamed women for everything having to do with sex and human reproduction. In the medieval world, if a woman bore a daughter and not a son, that was her fault. If she made a man so hot blooded that he forced himself on her, that was her fault for being so attractive, not his for being a rapist. In Akin’s world, in Aldridge’s world, a woman doesn’t need abortion access or a morning after pill to prevent a pregnancy following rape because the determinant of whether or not the rape was “legitimate” is whether or not she becomes pregnant. And the woman, you see, in the Akin/Aldridge cosmos, can “shut that whole thing down” and keep “bodily functions” from working if the rape was, you know, a real, legit-type rape.
In addition to quick primer on human reproduction, I’m offering here a couple of quick points about rape.
Rape is usually an act of violence or power. It is not just an act of sex. It uses sex as a weapon, as though it were a gun or a billy club. It is an act of violence or power against another person without that person’s consent. Nine out of ten rape victims are female. There is not a category of “not legitimate” rape. Sexual violence inflicted without consent is rape. Period.
The thing is, sperm don’t care how they get inside a vagina. They may arrive by turkey baster, catheter, penile delivery, or other creative mechanisms. Any rancher involved in livestock reproduction can tell you that violating a mammal with an object that delivers sperm is no obstacle to impregnating said mammal, no matter how stressed or unwilling the mammal may be.
Akin and Aldridge aren’t the first politicians to manifest a sad lack of understanding of the female body and of human reproduction. Mitt Romney himself has provoked a few howls thanks to his ignorance about birth control, leading Rachel Maddow to offer up a primer on female anatomy for the fellas out there. 
Here’s my own quick primer. About the female: The human female takes some time producing a ready egg for fertilization. That time is often quoted as 28 days, but it varies quite a bit. When the egg is ready, it leaves the ovary and begins a journey down the fallopian tube (also called the oviduct) to the uterus. During its brief sojourn in the fallopian tube, if the egg encounters sperm, fertilization likely will take place. If the egg shows up in the fallopian tube and sperm are already there, hanging out, fertilization is also a strong possibility. In other words, if the egg is around at the same time as the sperm, regardless of how the sperm got there, fertilization can–and often will–happen. The fertilized egg will then continue the journey to the uterus, where implantation into the wall of the uterus happens. Again, if a fertilized egg shows up, the uterine wall doesn’t care how it got fertilized in the first place.
Now to the human male. With ejaculation, a man releases between 40 and 150 million sperm. If ejaculated into the vagina, these sperm immediately begin their short lifetime journey toward the fallopian tube. Some can arrive there in as little as 30 minutes. A woman who has been raped could well already be carrying a fertilized egg by the time authorities begin taking her report. Sperm can live up to three days, at least, possibly as long as five days, hanging out around the fallopian tube. So if an egg isn’t there at the time a rape occurs, if the woman releases one in the days following, she can still become pregnant. Again, the fallopian tubes and ovaries do not care how the sperm got there, legitimately or otherwise.
Although Akin talks about “legitimate rape,” what he and Aldridge and so many other men truly are seeking to do is a twofold burdening of women for having the temerity to experience and report rape. If a woman becomes pregnant because of a rape, you see, then it was not rape. Point one. Point two, because of point one, a woman who reports a rape but becomes pregnant was really engaged in a willing sexual act and therefore must bear–literally–the consequences and, yes, punishment of engaging in that act. She must carry a pregnancy to term. She cannot have access to morning after pills or abortion to prevent or end a rape-related pregnancy because if she’s pregnant, it wasn’t rape, and if she’s pregnant, well, that’s totally her fault for not having her body “stop juices” and “shut that whole thing down.” Got that?
Get this: If you’re a woman who has just been raped, among the many other considerations you deserve, you deserve a morning after pill as part of your rape treatment, if you so desire. Because the hormones in the pills can prevent the impending release of an egg, among other things, create an inhospitable uterine environment for pregnancy, this series of pills can block the implantation of a fertilized egg in the uterine wall** they can save you the added pain, burden, and anguish of a pregnancy resulting from a rape. That, Srs. Akin and Aldridge, is the only established way to “shut that whole thing down,” and it’s a right that every single woman should have.

**A commenter has alerted us (thank you!) to information that came out in June regarding FDA claims about implantation prevention with the morning after pill, which may not be accurate. More on that here and here (NYT). Planned Parenthood cites the IUD as a form of emergency contraception that presumably would prevent implantation. 
These views are the opinion of the author and do not necessarily reflect or disagree with those of the DXS editorial team.

Related links worth reading (updated 8/21/12)

  • io9 breaks down more of the data about rapes and pregnancies, including information about why mammals don’t tend to engage in sperm selection
  • David Kroll notes the problem with having Akin on the House sci and tech committee
  • At the New Statesman, what people really mean when they talk about “legitimate rape”
  • Jezebel’s guide to “legitimate rape”
  • Kate Clancy puts rape stats in context and discusses why pre-eclampsia is not a mechanism for “shutting that whole thing down”
  • Melanie Tannenbaum lays it out and talks about the “Just-world fallacy” that drives thinking like Akin’s 

 

Giving girls…and science…their due

Respecting both is key to bringing girls into the sciences.

By Susan E. Matthews

When deciding what college to attend, I wouldn’t even consider an all-girls school, despite my mother’s encouragement. I refused to believe that my life had been even a little bit different because I was a girl — though years later as a woman in science, I’ve rethought that assumption.

I knew that my mom had to do gymnastics while the boys in her elementary PE classes had played basketball. I also knew that in her first job, as a computer scientist for a small company, she had been asked to answer the phones when they were between secretaries because she was the only woman in the office. As far as I was concerned, this sort of discrimination was a thing of the past, not something affecting my life. I felt like I was in the clear.

But we are not quite in the clear. We may value girls more, but there are still gaps. One of those gaps exists in the sciences — itself an area that we do not value nearly enough. While I did go to a co-ed school, studied science, and worked in a biogeochemistry lab, I’m in the minority. In 2009–2010, women represented less than a quarter of all students in secondary or post-secondary education studying STEM (science, technology, engineering, and math) topics nationally. This disparity has led to great debate over the reasons for the discrepancy. In early February, in a piece addressing the validity of recent findings, two researchers wrote in the Guardian that to resolve this issue, we could continue to insist that young women make up the difference themselves, by finding their own mentors and paving their own way. But beyond individual industry, we can change our institutions. As Chris Chambers and Kate Clancy argue:

The broader societal constraints that lead so few girls to consider themselves “science people” by middle school derive not from whether we push them into science, but what we value in girls as a culture Continue reading