Why a UN ban on thimerosal in vaccines would be a big mistake

By Tara Haelle, Health Editor

[This post appeared previously at Red Wine and Apple Sauce.]

Several articles published in Pediatrics today discuss an issue that could affect the protection of children everywhere from vaccine-preventable diseases. The posts center on a controversy that keeps coming up related to vaccines – the  use of thimerosal in them.

All three Pediatrics articles deal with the same thing: an international treaty drafted by the  United Nation Environmental Program’s  Global Mercury Partnership to reduce mercury pollution and environmental mercury exposure across the world. Great! This is an important and valuable initiative – except for one part. As part of the treaty, the UN wants to ban the use of thimerosal, a mercury-containing preservative, used in vaccines. Not so good. The short version for why? This proposed ban threatens millions of children’s lives across the world, including children in the U.S. and in other developed countries. I’ll get to the long version in a moment.

First, the  World Health Organization and American Academy of Pediatricians (AAP) have already pushed for the thimerosal ban provision to be removed from the UN treaty. But today’s three AAP articles drive the point home. One of these provides some  historical context for why thimerosal was removed from childhood vaccines in the U.S. (as  recommended by the AAP and the U.S. Public Health Services in 1999) and in other high-income countries. The other two emphasize just how important it is – and how ethically essential it is –that the ban not be included in the UN treaty.

Here’s the back story:
A  1997 US FDA review of the mercury content in products revealed that the amount of thimerosal in childhood vaccines could, possibly theoretically, build up to exceed the EPA’s guidelines (but not the FDA’s guidelines or those of the Agency for Toxic Substances Disease Registry) on safe exposure limits for  inorganic mercury, called  methylmercury.

Methylmercury is the neurotoxin you hear about when you’re warned not to eat too much fish ( especially while pregnant). Back in 1999, scientists knew a lot about methylmercury, but they didn’t know much about  ethylmercury, the type in thimerosal. As Dr. Louis Cooper and Dr. Samuel Katz, both involved with the 1999 recommendations,  put it, “the absence of clear data for ethylmercury did not allow any assumption to be made about its safety.”

Meanwhile, debates were raging in Congress about concerns over vaccines and autism, fueled by the now-retracted and  thoroughly debunked (pdf) study by Andrew Wakefield  linking the MMR vaccine to autism. Parents were scared and confused. Media coverage was exacerbating the impression that public health officials weren’t being forthright about vaccine risks.

So, poof! All thimerosal was pulled from childhood vaccines except the multi-dose flu vaccine, since kids getting that would only get amounts below the EPA guidelines for methylmercury (even though, again, thimerosal is ETHYLmercury).

Now fast forward to today. We know a LOT more about ethylmercury: namely, that it’s not as bad as methylmercury and  sails through our bodies a lot more quickly. In fact, methylmercury’s half-life is about  seven times that of ethylmercury, which does not build up in the body like methylmercury does.
“There is no credible scientific evidence that the use of thimerosal in vaccines presents any risk to human health,” writes Dr. Katherine King in one of  today’s Pediatrics articles. Dozens of studies and a massive review at the Institute of Medicine back this up.

Thimerosal in vaccines is not a problem. But what is a problem is thimerosal’s PR image. Again, from one of  today’s AAP articles: “Given the complexity of the science involved in making guidelines, the polarity between vaccine advocates and those believing their children have been harmed, the media’s attraction to controversy, and, in retrospect, inadequate follow-up education about the issues to clinicians and the general public, it is not surprising that the steps taken left misunderstanding and anxiety in the United States and concerns in the global public health community.”

Basically, they’re saying, yea, we kinda screwed up with conveying that thimerosal really IS safe after all. We wanted to be over-cautious before, and we were, and that was good, but now we’ve sorta dropped the ball on following through in letting you know that YOU HAVE NOTHING TO WORRY ABOUT with the ethylmercury in thimerosal. As Dr. Walter Orenstein  today’s AAP articles, “Had the evidence that is available now been available in 1999, the policy reducing thimerosal use would likely have not been implemented. Furthermore, in 2008 the World Health Organization endorsed the use of thimerosal in vaccines.”

But apparently, the WHO’s endorsement can’t overcome thimerosal’s PR image problem in the eyes of the UN. And so the UN is short-sightedly and dangerously trying to ban thimerosal in vaccines.

Well, that just means getting rid of it in flu vaccines (many of which don’t even have thimerosal since they’re single-dose), so what’s the big deal anyway? The big deal is that not all countries got rid of thimerosal in their childhood vaccines. Many high-income countries like the U.S. did – because they could afford to be overly cautious.

But more than 120 middle- and low-income countries – including the developing countries where vaccine-preventable diseases have the highest rates of infection and death –  have continued using thimerosal-containing vaccines because the preservative allows them to make cheaper vaccines that withstand less rigorous storage without compromising safety.

Getting rid of thimerosal would mean overhauling vaccine production and storage in those countries, which the WHO estimates would cost more than  $300 million for vaccines supplied by UNICEF or the Pan American Health Organization alone. As Dr. King argues, “it is banning thimerosal that would cause an injustice to those living in low- and middle-income countries and relying on these vaccines for effective protection against many harmful infectious diseases.”

Why does this matter to people in the U.S. or in other higher income countries? Because we live in a global world. Vaccines with thimerosal are currently used to immunize about  84 million children across the world every year, saving an estimated 1.4 million lives from vaccine-preventable diseases.That also includes lives saved in developed countries, where a future outbreak could potentially be imported from other countries in which a vaccination program may have ceased following a thimerosal ban.

More simply put: If the UN forces the removal of thimerosal from vaccines, then 84 million children risk not getting vaccinated (and/or vaccinated on time) due to delays in vaccine production or due to a shortage of vaccines because of increasing costs. This, in turn, could (and likely would) mean an increase in vaccine-preventable infections, which will, in turn, kill more children worldwide and risk disease carriage to other countries.

Over and beyond the increases in vaccine-preventable infections and deaths throughout the world, a thimerosal ban in vaccines could also still pose problems for developed countries. In an emergency, as Dr. Orenstein and colleagues argue, not being able to manufacture vaccines with thimerosal could endanger lives during an epidemic if it slows down vaccine production. This proposed UN ban – and the necessity of its removal – matters.

Dr. Cooper and Dr. Katz – again, both pediatricians who were closely involved in the original 1999 decision to pull thimerosal out of vaccines – sum it up best: “The World Health Organization recommendation to delete the ban on thimerosal must be heeded or it will cause tremendous damage to current programs to protect all children from death and disability caused by vaccine-preventable diseases.”

How fluorescent lights work: quantum mechanics in the home


We have a tendency to think that “quantum mechanics” is synonymous with “out of the ordinary.” I do that, too, since there’s so much strange to talk about: the blurring of particles and waves, the apparent randomness that drove Einstein crazy, and so forth. It’s easy to forget that quantum mechanics also is an everyday matter. The odds are pretty good you’re reading this post on a computer screen (as opposed to a printout), and possibly the light you’re using is fluorescent.


The three major types of lights you can buy are incandescent bulbs, fluorescent lights (including compact fluorescent lights), and light-emitting diodes. Incandescent bulbs are the “normal” type (though they are becoming less so): They light up when an electric current runs through a thin wire made of tungsten, which heats up. The wattage of an incandescent is a measure of how much power it consumes, and most of that power goes to heat, not light, which is why you can burn your hand if you touch a bulb that’s been on any length of time. Because of the wasteful nature of that kind of bulb, a lot of people have made the switch to compact fluorescent lights (CFLs), which don’t run hot and use a lot less power for the same amount of light. And they work by using quantum mechanics!


Of course even incandescent bulbs are quantum-mechanical underneath: after all, everything Continue reading

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

Striking a balance between health and sustainability: a study inspired by a love for sushi


Sushi for sale (Source)
by Jeanne Garbarino, DXS biology editor

A conservation scientist walks into a [sushi] bar…

You’ve probably heard that eating a diet including fish, especially fatty fish, is good for us. Fish can be a source of high quality, lean protein, and also provide heart-healthy omega-3 fatty acids. However, there are risks associated with eating some types of fish. For instance, fish that are at the top of the food chain or have a long lifespan (or both!) can accumulate high levels of mercury or chemicals called polychlorinated biphenyls (PCBs).  Exposure to high amounts of these compounds could be particularly harmful for pregnant/nursing women or young children.

On the other hand, there is the issue of sustainability. We are seeing a wide-scale collapse of many marine fish populations, which is primarily the result of overfishing.   While there are conservation efforts in place to help consumers make eco-friendly choices, it is not clear if raising consumer awareness is impacting fishing or marine farming practices. Furthermore, many consumers will choose fish based on their nutritional value and safety without really considering ecological consequences.

In an attempt to better educate consumers on both nutrition andsustainability with regard to making the best seafood choices, Leah Gerber, professor of Ecology, Evolution and Environmental Science at Arizona State University, has evaluated current fish “eco-ranking” schemes. In a study recently published (PDF) in Frontiers in Ecology and the Environment, Dr. Gerber provides a model that quantifies both the health benefits and sustainability level of individual fish species.

Interestingly, her group found that fish with the highest health benefits, determined by omega-3 fatty acid content, generally had low mercury levels. Similarly, fish that are unsustainable – meaning that fishing threatens their existence — tended to have higher levels of mercury, and lower omega-3 fatty acid amounts.  Basically, fish populations that are not threatened by overfishing are generally heart healthy and have low mercury. A win-win!

The novel thing about this study is that it is the first to consider multiple types of sustainability rankings as well as health impacts, and Dr. Gerber is taking her message to the streets. It is her hope that she and her colleagues will be able to develop tools so that consumers can easily make seafood choices that are both good for you and good for the environment.

But the coolest thing about this study is that Dr. Gerber is not a ‘fisheries person’, per se.  However, her passion for learning about human impact on the natural environment combined with her love of sushi prompted a closer look at the fishing industries and how to make good choices when it comes to seafood.

This is an excellent example of how a scientist is applying her knowledge to promote science in one of its most relatable forms –- eating!  I mean, we all have to eat, and it is particularly awesome when we can do so in the most educated way possible. Kudos to Dr. Gerber for taking this on since we all benefit from knowing.  

The opinions expressed in this article neither necessarily reflect nor conflict with those of the DXS editorial team.

flu pic resized

25 myths about the flu vaccine debunked

Setting the record straight on the flu vaccine

by Tara Haelle
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Rest in peace, Sally Ride

Photo public domain image, via Wikimedia Commons.

By Matthew Francis, DXS Physics Editor


This week—on Monday, July 23—Sally Ride passed away after a battle with pancreatic cancer. She was 61.


Dr. Ride was a physicist and passionate advocate for STEM education for girls, a position she bolstered through her fame as a former Space Shuttle astronaut. In fact, she was the first American woman in space, and only the third woman worldwide to travel into space. She flew twice aboard the Challenger, first in 1983 and then again in 1984, when she controlled the Shuttle’s robotic arm to deploy a satellite. Later, she served in the investigations after both the Challenger and Columbia disasters, the only person to sit on both committees. After retiring from NASA, she started Sally Ride Science, a company devoted to providing educational materials and classroom presentations to schools, specifically with an eye toward encouraging girls in the fields of science and engineering.


I remember her flights well, as I paid a lot of attention to the space program when I was young. (I also loved the robotic arm on the Shuttle, and wanted a chance to play with it. Now I understand that, while it might resemble a video game, it’s a video game with millions of dollars in equipment at stake. However, I still haven’t gotten over wanting to play with robotic arms. I can admit that, right?) I was the kid who wrote letters to NASA, asking for photos and information about their spacecraft. I have the pictures they sent me in a stack on my desk right now, in fact, and I’m looking at them as I write this post. While the photos themselves predated Dr. Ride’s trips into space (the last group photo in the batch comes from the third flight, STS-3, while she first flew on STS-7), my greatest interest in the Shuttle peaked during her time as as an astronaut.


Much digital ink has been spilled over the revelation about her sexual orientation—her partner in business, writing, and life for the last 27 years was Tam O’Shaughnessy, which was no secret to her family and friends but not widely known beyond. I can’t really blame Dr. Ride for keeping mostly quiet about it. After all, in the 1980s, it could have been grounds for dismissal from NASA; she faced enough sexism as it was. Her very existence as a woman astronaut was symbolic, and even today the default American astronaut is a white, (presumably) heterosexual male. Although the astronaut corps is a lot more diverse than it used to be, NASA’s close ties with the military and its historical homophobia have no doubt made it difficult for any astronaut to acknowledge their sexual identity openly. For Dr. Ride and her primary mission in life to encourage girls in science, I can understand her reluctance to make herself into another symbol. However, that very fact is a sad comment, that being a woman in the public sphere is enough to be considered unusual that she didn’t want to bring her sexual orientation into the picture. (I don’t even presume to call her a lesbian, since human sexual identity is more fluid than many of us like to admit.)


Over the last two days, many people have written eulogies, reminiscences, tributes, and biographies; I’m not sure I can add much to those. Here are some of the best:

  • Nadia Drake’s personal story from her childhood brought tears to my eyes. Similarly, I love astronomer Meg Urry’s tribute.
  • Here’s the big New York Times official obituary, which (as you might expect) is quite good and thorough.
  • While we rightfully celebrate Sally Ride’s accomplishments, let’s face it: the United States was really late in sending women into space. Institutional sexism delayed women astronauts far longer than should be acceptable in any civilized nation, and the locker-room culture at NASA during that era bears a lot of responsibility for the problem. Thirteen women trained to be part of the Mercury program, but were barred from ever flying. I lost a lot of respect for John Glenn when I found out he actively worked against allowing women to fly.
  • Natalie Wolchover at Space.com examines why there aren’t openly gay astronauts in much more detail; here’s another post on a similar personal note, from a lesbian astronomer.
  • An obituary from BuzzFeed, with comments from Ride’s sister, Bear. (Seriously, isn’t it also awesome to have a sister nicknamed “Bear”?)

Please leave your recollections of Sally Ride in the comments.

Bad flu season in full swing, but flu shot still helpful

Bad flu season in full swing, but flu shot still helpful

Source: Wikimedia Commons; credit: CDC.

The flu season that is unfolding is a killer, with influenza having already taken dozens of lives across the United States. Deaths from flu during the flu seasons are actually the norm, ranging from 3000 to 50,000 annually, but this year’s outbreak arrived early and features a strain that is infamous for its virulence. Forty-four states now have met the cutoff for “widespread” flu activity as of this writing, and in hotspots like Boston, MA, cases are 10 times the number from the same time last year. In many areas, hospitals have taken to setting up temporary tent shelters outside the buildings to manage the flood of cases and prevent spread inside the facility. ETA: This USA Today article gives an overview of how clinicians are experiencing this outbreak on the ground. [Update: As of 1/18/13, a total of 48 states are now at widespread status, and 29 children have died. Forty percent of hospitalized children have had no known underlying medical conditions.]

Public health officials from the US Food and Drug Administration and the Centers for Disease Control and Prevention(CDC) are urging people who have not gotten their flu shots to do so, saying that there is still time for the vaccination to work for you against the flu. The most vulnerable population is children, and 18 children have already died in the United States during this year’s season. According to reports, far less than half of the eligible population in the US has gotten a flu vaccination.

People express reluctance to get the flu vaccine for several reasons. Among them are fears that the vaccine contains mercury as part of a preservative, thimerosal, that has been used for years in various immunizations, although it’s been removed from many. For the flu, only vaccines from multidose vials contain this preservative, which is needed to protect the contents from contamination when the vials are opened for repeated use. Single-dose shots and the inhaled Flu Mist do not contain this preservative, which an abundance of studies have shown does not cause harm despite diligent efforts from anti-vaccine organizations to argue otherwise. For more information about this preservative in multidose vials of flu vaccines, the CDC offers a Q&A.

Another source of reluctance is the fact that the flu vaccine, like several other vaccines–or indeed, having the infection itself–is not 100% protective against the illness. In fact, it appears to be about 60% effective in preventing illness, although those who have been vaccinated and do fall ill with the strain included in the vaccine might experience less intense symptoms. The CDC also offers a Q&A addressing why some people who have been vaccinated still catch the flu. My personal feeling is that I’d rather give my children that 60% chance in a rampant flu season with a virulent strain that’s hospitalized tens of thousands than give them no protection at all. Any number of interventions don’t carry a 100% guarantee of effectiveness, but they certainly enhance the favorable odds. My children and I all received the Flu Mist vaccine back in October. ETA: A recent report found that different forms of the vaccine have different levels of effectiveness in different age groups and that the vaccines and vaccine program require improvement. For more information about the report, which concluded as we’ve written here that flu vaccines offer moderate protection and have a good safety profile, please see this post by an epidemiologist.

People also forgo a shot because they think that only people in poor health or with pre-existing conditions are susceptible to the most dreaded outcomes with flu: hospitalization and death. That’s not actually the case. “Influenza” is the name we give to the highly variable viruses that play games of genetic mix-and-match in different species, with results that are unpredictable and rapidly changing. No one’s previous experience with flu will necessarily be predictive of later experiences with the virus. Some flu strains do hit certain populations with specific existing health problems, but other strains kill the young and healthy preferentially. And whether or not you yourself are in perfect health, if you get the flu, you risk passing it along to someone who is not. ETA: For a personal look at who some of those people are, please see the Faces of Influenza site. Some people cannot get a flu shot for medical reasons, and anyone who has had a reaction to a vaccine should obviously consult with their medical professional about vaccines.

A final source of reluctance is that the flu vaccine each year is developed based on educated guesses. No one can predict with certainty which strains will gain the upper hand. As it happens, one strain in circulation this year falls outside of the vaccine target, but medical authorities report that so far, 91% of strains identified in circulation are targets of the vaccine. Because we are talking about influenza and several circulating strains, if you do not get a vaccination, it’s entirely possible for influenza viruses to hit you or your family hard more than once this flu season.

Bottom line? Without a vaccination, you’re 100% exposed no matter what your age, health, diet, exercise routine, or supplement intake. And if you get sick, you’ll endanger everyone you’ve been around and contaminate every place you’ve been. Flu carries innumerable potential and unpredictable outcomes, from complete recovery to death, and hospitalizations this year are extremely high. People with a genuine case of influenza end up floored for days, in body-wide pain, with high fevers and wracking coughs and a risk for pneumonia, hospitalization, and death, sometimes with unpredictable rapid progression. Even for those who don’t end up in the hospital, complete recovery from these deadly and unpredictable viruses typically takes weeks, meaning lost school, lost productivity, lost work, lost wages. Meanwhile, the vaccine cost ranges from free to about 20-40 bucks at various pharmacies.

Here is a basic video explaining some of the complexities of the flu vaccine and its success rate:

The opinions expressed in this article do not necessarily reflect or conflict with those of the DXS editorial team or contributors.

Making Light in Electronics

By DXS Physics Editor Matthew Francis 

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

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

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

The Electrons in the Band

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

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

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

Cars and Roads and Electrons

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

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

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

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

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

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