Frankenstorm: What is the role of climate change?

Sandy the Superstorm and her water vapor. 
Video via NOAA; hat tip to Andrew Revkin.


[First, check out this hurricane crisis map Google developed, complete with updated information on the storm's status and effects and even shelter location info.]

I’ve seen this question crop up a lot over the last few days–it’s a natural one, I’d think, given promises of more frequent extreme weather events in association with human-driven global climate shifts: What is the role of climate change, if any, in Sandy the Frankenstorm, currently bearing down and flooding the US northeast after having killed dozens in the Caribbean on her way to US shores?

Lucky for people like me who couldn’t begin to answer this question, people like Andrew Revkin at the New York Times have gathered the resources for us. Of course, the first take-home is the usual one: Nothing is straightforward here. As Revkin writes:

While the echo of Frankenstein in that Twitter moniker can imply this is a human-created meteorological monster, it’s just not that simple.

He gets into the “not simple” parts of things and cites some data (with links!) and then has been providing useful and insightful updates from meteorological experts. What it comes down to is, Sure, there’s a littla the global climate change at play here–it’s happening and it’s global, so it’s going to have some influence. But also at play are typical or at least not-wildly-unimaginable variations of weather patterns that just happen to be converging right now, right there. So a single weather event is just an anecdote in the climate context and doesn’t necessarily stand as a reflection of an entire climate pattern. These patterns can emerge with warming or with cooling–and they have, over long time frames. Revkin writes:

But there remains far too much natural variability in the frequency and potency of rare and powerful storms — on time scales from decades to centuries — to go beyond pointing to this event being consistent with what’s projected on a human-heated planet.

In other words, this Frankstorm really is a monster built of parts–convergence of typical weather patterns and heavily populated places, roughly pieced together to some extent by human-driven climate change and animated on live radar. But Sandy the Frankenstorm is likely no more exemplary of the dire future some think it represents than poor Frankenstein’s monster himself was an exemplar of humanity.

By Emily Willingham

The opinions expressed in this post do not necessarily conflict with or represent those of the DXS editors or contributors.

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FYI: For updates on this sort of analysis and what’s happening with Sandy in real time, the folks at Boing Boing tweeted this list of recommended people to follow on Twitter.

Update 2:30 ET: Check out this beautiful, mesmerizing, and scary wind map, made with data on surface winds from a national database.


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

mouselarge

Parenting paranoia comes in different forms

It could be Andrew Wakefield or a brain-hijacking microbe.

by Meredith Swett Walker

I’m a scientist, but I’ve learned that when we become parents, paranoia can trump the powers of rational analysis I’ve so carefully nurtured and developed. For some parents, media-whipped fears about vaccines take front and center in the anxiety lineup. For me, a brain-infecting microbe that makes mice hang around cats is at the top of my parenting paranoia list.

Parenting requires making many, many choices. Some seem inconsequential, like whether your child will wear overalls or sweatpants, pigtails or a pixie cut. But other choices have to do with health issues such as circumcision, immunization, and breast milk vs. formula – just a few in an endless list. For geeks like me, the first impulse is to research each issue, make a choice, and prepare an argument for anyone who questions the decision (and believe me, someone will.) My response usually goes something like this: “Well, recent studies have shown that yada yada yada…” Then I pat myself on the back for being so informed and making such a well-reasoned decision.

My process ran into trouble, though, when my relationship with a university and its online library access ended. What happens when you can’t get your hands on peer-reviewed scientific journal articles? One consolation should be that we live in the “Information Age.” Surely, Google, a fast internet connection, and an overwhelming flood of information should lead to what we need to make well-reasoned, science-based parenting choices. Surely.

Maybe not. A friend recently shared with me an article from the open-access (i.e., free) online journal PLoS: “Why Most Biomedical Findings Echoed by Newspapers Turn Out to be False: The Case of Attention Deficit Hyperactivity Disorder.”  The gist is that the news media preferentially cover initial findings described in the most prominent scientific journals. The key word there is initial. No initial result is going to be the final word in science, and all results require confirmation from other researchers repeating or extending the experiments. Sadly, in practice, many of the follow-up studies don’t get published in the most prominent journals because they are not “a big scoop.” Yet they often show that the initial, Big Headline Finding was overblown or even incorrect.

That brings me to an example that really pushes my buttons — childhood immunizations. In 1998, Andrew Wakefield and colleagues published a study in the prominent British medical journal the Lancet. The paper examined a hypothesized association between the MMR (measles, mumps, rubella) vaccine and autism, but the authors used fairly moderate language in their conclusions. But then, Wakefield participated in a press conference about the paper and asserted in much stronger language that the MMR combined vaccine and autism were linked and that parents should turn to single shots for measles, mumps, and rubella. The news media ate it up.

The scientific community immediately pointed out a number of glaring flaws in the study, and subsequent investigations over the next decade failed to reproduce or confirm the results. But it was too late. The popular media and celebrities like Jenny McCarthy had already done the damage. Parents were terrified, vaccination rates dropped, and deadly measles and whooping cough outbreaks starting cropping up.

Yes, the news media covered subsequent studies reporting no link between vaccines and autism, but let’s face it: Science is slow, and news is fast. In the interval, scary information takes root. The Lancet retracted the article 12 years after its publication, and in 2011, British investigative journalist Brian Deer demonstrated that Wakefield actively falsified data. Still, to this day, vaccination rates have not fully recovered, and many parents remain misinformed and concerned about vaccinating their children. Indeed, the Wakefield debacle has been directly blamed for a huge and ongoing measles outbreak in Wales.

I could haz Toxoplasmodium in my poop, so be careful.

I could haz Toxoplasmodium in my poop, so be careful.

Admittedly, the MMR case is an extreme example but also a good one of how a single initial study and the ensuing media hysteria can have a huge effect on parents — and on children’s health.

And we all have our trigger points for fear. One (of the many) things in our family tree is schizophrenia. A member of our extended family developed schizophrenia as an adolescent and has never recovered. Schizophrenia can run in families, so my two children have up to a 4% chance of developing this disorder compared to the 1.1% chance of someone without close relatives who have it.

So along comes my March 2012 issue of The Atlantic featuring “How Your Cat Is Making You Crazy” by Kathleen MacAuliffe. I would have found this article fascinating even if schizophrenia weren’t a concern. Its subject is a parasite called Toxoplasmosis gondii, which usually cycles through two hosts: cats and rodents. Toxo, as I’ll call this beast, starts life as an egg in a cat, is pooped out, and then gets picked up by a new cat. How does it get into a new cat? Cats, unlike dogs, are pretty fastidious and don’t tend to eat or otherwise mess around with cat poop. So Toxo gets itself into a less fastidious but tasty morsel like a mouse, instead, making its way into the cat when the mouse becomes dinner.

That seems simple enough, but there’s more. Toxo infection ups the odds of a mouse–cat encounter by hijacking the mouse’s brain and changing its behavior. The mouse’s activity level increases (cats love to chase fast-moving objects), and the rodent might become less wary in exposed areas and even attracted to the smell of cats. Watch these videos, and you’ll see how the infected mice move faster and wander into unknown spaces, seemingly without fear, as you can see in this video and this one.

The trouble for humans is that we also can pick up Toxo through contact with cat poop or eating undercooked meat or unwashed veggies from a garden where cats poop. Becoming infected with Toxo during pregnancy can be very harmful to a fetus, so pregnant women have long been warned off cleaning kitty litter boxes. But healthy, non-pregnant adults infected with Toxo weren’t thought to experience any detrimental effects — until recently. According to MacAuliffe’s article, which focuses on the work of Czech biologist Jaroslav Flegr, Toxo might alter human behavior, too, in mouse-like ways, such as reducing fearfulness. In most people, these purported behavioral shifts are probably very subtle and unremarkable. But Flegr suggests that in some people, Toxo infection serves as the trigger for mental illness, including schizophrenia.

Schizophrenia likely develops because of interactions between genes and the environment. Having risk gene variants isn’t a guarantee a person will develop schizophrenia, and it can arise in people without those risk variants. The list of potential environmental triggers is long and includes childhood stress, prenatal undernutrition, drug abuse, and …  infections with microbes like Toxo.

Reading this article set me off on a tear of worrying. We have a cat, but I wasn’t worried about her. She is an indoor cat (we love birds), and there is a very low incidence of Toxo infections in indoor cats. But we have outdoor cats and feral cats in our neighborhood. They sometimes hang out in our yard, where my kids like to play in the dirt and eat things out of the garden, including the dirt itself. Oh, poop.

I took to Google and researched cat traps and repellents and how to get kids to wash their hands. I laid awake at night for hours strategizing about how to keep my home and yard Toxo free. And then I realized, even if I managed to exclude all cats from my yard and the totally impossible feat of getting my children (ages 1 and 2) to wash their hands before they touched their faces or food every time, I was still doomed to failure. My kids would go to friend’s houses and play in their Toxo-infested yards.  Or they might already have encountered Toxo anyway.

Toxo was something I couldn’t control, and I needed to let it go. At our next check-up, I talked to our pediatrician about it, who had never heard about the potential Toxo–schizophrenia link. She graciously concealed her “Oh, Lord, another parent with a loony theory” reaction and calmed me down. As she put it, my only real option to prevent Toxo infection was to never allow my children to play outdoors or in the dirt, and the detrimental effects of that were likely far greater than the risk of schizophrenia, Toxo or no Toxo.

And she also reminded me of what I already knew and should have remembered: These findings about Toxo are initial findings.

As a scientist, I know that the schizophrenia–Toxo link needs more study. A lot more study. As a parent, well … yeah. I still worry, and no lack of replication or confirmation is likely to stop me.

[Image credits: cat on this page by Sasan Geranmehr under Creative Commons 3.o license; mouse under same license.] Continue reading

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.”

On Parenting, Science, and Trust

The following was originally posted over at The Mother Geek (RIP) in January of this year.  The guest author is Alice Callahan, who is a research scientist turned stay-at-home mom. She lives in Eugene, Oregon, with her husband and 14-month-old daughter. Alice writes about the science of parenting, as well as her adventures in mothering, at scienceofmom.com.  You can also find Alice on Twitter.
Via Creative Commons

Having a PhD in science makes my job as a mother easier – but maybe not in the ways that you might expect.

My PhD is in Nutrition, so you would think that getting my kid to eat well would come easy for me. Unfortunately, that has not been the case.  I’ve logged more than two years of postdoc research on fetal programming – how the uterine environment affects outcomes in babies. You might think that this helped me to do everything right during my pregnancy. Instead, I think it just led to more worry about all of the ways I might be damaging my unborn child. Stress! Sugar! BPA! Lab chemical exposure! OMG! More stress!
Sure, I have more knowledge than the average mother. Sometimes that is helpful.  And sometimes it is not. And knowing how to do a literature search to try to answer my parenting questions often leads to further sleep deprivation as I slog through Pubmed hits and come out on the other side with more confusion. Sometimes my drive to find scientific answers for my parenting questions just distracts me from my instinct – not that my maternal instinct is all that amazing, but I do know my baby better than anyone else in the world.
So how does being a scientist make parenting easier for me? As a scientist mother, I trust other scientists. And I trust doctors. I even trust government agencies, which bring together the best scientists and doctors in a field to review the research and make recommendations for the good of public health.
I trust scientists and doctors, because I have worked side-by-side with them for a decade, andI know that they are not only knowledgeable,but by and large, they are overwhelmingly good people. At some point, you have to trust someone.


I trust scientists and doctors.   

I trust scientists, because I know that the vast majority of them are just underpaid nerds who are really passionate about what they do. They are driven by the desire to find the truth about a question and they work, day in and day out, in that pursuit.  In addition, I know that scientists don’t always agree, so when there is a general consensus among the majority of scientists about something, such as vaccine safety or global warming, I feel confident in that conclusion.
Contrary to many claims on the Internet, scientists are not in bed with Big Pharma, conspiring make millions at the expense of your child’s health. They are in bed with their husbands and wives, probably chatting about their latest failed cell culture experiment.
I also trust science because I understand the peer review process all too well. Although it has its flaws and as maddening as it is when I am the one being reviewed, I have confidence that the peer review process is highly effective at weeding out the kooks and pseudoscientists and the conflicts of interest. (Unfortunately, there are a few kooky psuedoscientists out there with serious conflicts of interest, and it just so happens that one of them managed to publish fraudulent research linking the MMR vaccine and autism. Many studies have since shown that such a link does not exist, but it took 12 years for Andrew Wakefield’s Lancet paper to be retracted. How many dollars have been spent and how many people made sick or worse in the continuing fallout and confusion about this public health scare? When the peer review system fails, it can be truly devastating.)
I trust doctors because I know that most of them are, first and foremost, humanitarians at heart, especially those that have chosen to work in primary care. I know how hard doctors work to become competent in the vast ocean of information about pathologies of the human body. I know how seriously they take their responsibility of our health.
I especially trust pediatricians. They have chosen one of the lowest-paid specialties simply because they love working with kids. I know that every pediatrician, at some point during her training or career, has likely cared for a child who was dying of a disease that could have been prevented by vaccination, and that memory haunts her as she faces parents afraid of vaccinating their children. Doctors are not conspiring against us. They want to help us make the best choices for our children, more than anything in the world.
Because I trust scientists and doctors, I didn’t question the CDC’s vaccination schedule. I didn’t pore over vaccine research or agonize about the decision to vaccinate my child. Instead, I trusted that the committees of experts at the CDC and AAP carefully make the best recommendations possible based on the data available.
Maybe that is naïve. Maybe I am a lazy mother for not trying to become a vaccine expert before I allowed those first needles to enter my daughter’s thigh. Maybe. But I also think it would be naïve for me to think that I could become an expert on vaccinations, that I could know and understand the field better than the committees of scientists and doctors who have made this their life’s work.
I know how much work it took me to become an expert on one or two corners of nutrition and fetal physiology. It took thousands of hours of reading textbooks and journal articles, sitting in lectures, attending conferences, and struggling at the lab bench before I started to feel even a little bit comfortable calling myself an expert in any field. So I think it is naïve for a parent to think that she can become an expert on vaccines by spending some time on the Internet, reading questionable sources, almost all of which have some agenda. I accept that I can’t know everything, and I have enough faith in humanity that I trust others who know more than me.

It is not that I don’t question scientists and doctors. I do. For example, I recognize that government agencies and medical organizations often have a lag time for adopting the latest science into their recommendations. I recognize that tradition, culture, politics, and economics all influence those recommendations, and they are not without fault.
I certainly question my doctors, because I know they are each fallible human beings, and they can’t know everything. I brought a stack of journal articles to my OB to convince her to delay cord clamping at my delivery. I did so much research on infant iron nutrition and came to my daughter’s 9-month checkup with so many questions that my pediatrician looked me in the eye and said, “You’re worried enough for both of us about BabyC’s iron.” Although I question my doctors, I also trust that they are adept at discerning fake science from real science. If I bring my doctor the sources I am using to inform my questions or concerns, she should be able to judge whether or not they are trustworthy and have a real discussion with me about factors that I may not have considered.
In truth, I do follow the vaccine debate closely, but not because I wonder if I am doing the right thing by vaccinating my child. I follow the vaccine debate out of interest for how misinformation can explode in a way that creates a public health crisis. I find myself increasingly concerned about the low rate of vaccination in my own community. I worry for the newborns in our town who have not yet had a chance to be vaccinated and for the individuals who cannot be vaccinated due to health conditions. I am starting to feel like I have a responsibility to share accurate information with mothers and fathers struggling with the decision of whether or not to vaccinate, because misinformation is doing real harm.

It is good to question our parenting decisions and in doing so, become more educated about them. However, as a scientist, I’m happy to defer to other scientists about some of the biggest parenting decisions I have faced. I am grateful for their decades of research forming the foundation of our understanding of child health and for the good-hearted doctors who care for my family. They have made my job as a mother a lot easier. I can spend less time worrying and more time playing with my daughter and soaking up the time with her as she grows up way too fast.

Thanks, science, for making it easier to be a mom.


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