Headlights and beads on a string


A line of cars and their headlights: a reminder of higher DNA organization.
(Source)
by Jeanne Garbarino, DXS biology editor

My commute can often cut through some interesting scenery, leading me to occupy myself by staring through the windows. However, it was only the other night that I noticed the highway running parallel to the train. It was packed with cars as New Yorkers were fleeing to their homes in order to brace for the imminent blizzard.  Needless to say, the road traffic moved at a snail’s pace. 

My vision of the highway and all of the beaming headlights reminded me of when I was a kid, stuck in traffic as a passenger in the back seat of my parents’ car. I would try to take my mind off of my seemingly infinite confinement by pretending that the glowing headlights coming toward our car were diamonds, strung up on the most amazing necklace ever made. Truly extravagant beads on a string.  But, seeing that sight again no longer conjured up thoughts of priceless neckwear. Instead, these brightly lit “beads on a string” immediately reminded me of one thing and one thing only: the cellular organization of DNA.  (Talk about science on the brain.)    

In addition to my (sad?) association of consecutive headlights with DNA organization, this imagery also summoned previously dormant areas of my brain, bringing to my current consciousness pictures of my college genetics professor and her lessons on DNA packaging. All of a sudden, I was thinking about histones, chromatin, and solenoids, which are all terms to describe the higher organizational structures of DNA.

Actual “beads on a string,” aka DNA being organized for packaging.
Because we’ve been able to capture images of these structures using microscopes, the “beads on a string” analogy is the classic description used by scientists and teachers to talk about how DNA is packaged in our cells. It essentially describes an elegant solution that has evolved to keep DNA both compact and easily accessible. To fully appreciate this, one must consider the scale of this molecular machinery. If placed end-to-end, the DNA found in a single human cell would be approximately 2 meters (6.6 feet) in length. Now imagine having to package the DNA into a compartment within the cell, called the nucleus, that is so small it can only be visualized with the aid of a microscope. Put another way, this is equivalent of packaging 40km (or 24 miles) of super fine thread into something the size of a tennis ball. 
How is it possible to do this in such a way that prevents the DNA from becoming a tangled mess while still allowing the cellular machinery to easily access the important information kept in our genetic code? The answer starts with the enlistment of specialized proteins called histones.  A length of DNA will wrap around a histone core (1.75 times to be exact; equivalent to 146 base pairs), essentially giving the illusion of a “bead” with each bead separated by a short, linear segment of DNA approximately 60 base pairs long, called a “linker.” Together, one bead plus its neighboring linker sequence is called a nucleosome. When examined on a microscope, the serial organization of each nucleosome unit resembles “beads on a string” and, hence, the analogy has been forever implanted in my mind.
(Source)
More appropriately termed chromatin, the “beads on a string” is only the first level of organization required for DNA packaging with our cells. Chromatin can be further condensed into higher-order structures accomplished by interactions formed between nucleosomes. What has helped me to understand this process is the following: Imagine you have a long, thin stick, around which you begin to tightly wrap a chromatin fiber.  Then, after all of the chromatin has been spiraled around the stick, you slide the stick out leaving a tube-like structure. The tube, which is held together through the interactions formed between nucleosomes, is called a solenoid. The solenoid can be further condensed by looping, ultimately resulting in a super tight and compact packaging of DNA.  

The hierarchy of DNA organization.  Source.

So, will the next time you see headlights in traffic make you think of DNA organization?  For my sake, I sure hope so!     

For more information, check out this video:

Also, check out this interactive site from HHMI.      

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

Double Xpressions: Jennifer Canale, the self-proclaimed "Flamboyant Scientist"

Jennifer Canale is a Senior Microbiologist for the United States Food and Drug Administration (FDA) in Queens, NY, as well as an adjunct microbiology lecturer for City University of NY (York College and College of Staten Island).  Jennifer is also passionate about promoting women in science and leads an annual women in science event at the FDA as a means to promote awareness about gender discrimination in the workplace.

[DXS] First, can you give me a quick overview of what your scientific background is and your current connection to science?

 

[JC] I have always been interested in science, and since most of my family worked in Bellvue Hospital, I was very comfortable around people in lab coats.  In the early seventies, at the age of 5, I announced to my grandfather, the X-ray technician, and his brothers (my great uncles) that I wanted to become a doctor, specifically a doctor that delivers babies.
My grandfather was proud and my uncles were dismayed. My uncle Joe said to me, “Jennifer, you mean a nurse like your cousin Joanie, right?” My cousin Joan applied to Medical School in the sixties and the same group of uncles convinced her that her fiancé, Warren, wouldn’t wait 4 years to get married and it was more lady-like to be a nurse. Today she is a retired left-handed OR nurse that specializes in cracking open chests for cardiac surgery, not so lady-like after all. So in an attempt to not have a repeat of Joanie, my grandfather jumped to my defense against his brothers and said that ‘she can be a doctor if she wanted to be’, and, furthermore, his niece Joanie was smarter and more capable than most of the doctors he worked with and shouldn’t have had to take orders from them.
My uncles agreed that there was no question of the intellectual prowess possessed by both Joanie and myself, and their reluctance came out of concern for me.  They worked in the hospital, too, and saw how male doctors would abuse the female ones and make their lives more difficult because they didn’t want to allow girls in the all-boys club. “Do you want our baby – our most precious blood – to have to fight her whole life for this? What about the family – how will she find a husband and bring us more children if she sticks her nose in a book the rest of her life?”  These arguments sounded a lot better when they were stated in Sicilian. Back then, the concept of ‘women can have it all’ – work and family – was not the norm like it is today.
My grandfather came back with his final answers to them. I was his granddaughter, I looked just like him, I was a fighter just like him, and this is America and she will be what she wants to be, ‘End of Story’. My uncles agreed that I was his granddaughter, I looked just like him, and I was a stubborn mule just like him, so he was probably right and they would pray for me and secretly hope I would change my mind.
Now this all transpired in front of me in a combination of English and Sicilian while I stood there in my denim overalls with a Tweety Bird patch. I was listening, and since I was only beginning to learn Sicilian, I only caught a couple of words: blood, children, book, change, and I misunderstood the word for fighter as “afraid.” I added to my grandfather’s “end of story” remark that I was not afraid of blood, I can learn how to deliver children from a book, and questioned why they wanted me to change- those overalls were my favorite!
My family was supportive to a point, but when I asked for an erector set for Christmas, I got a Barbie town house. When I wanted to go camping with the Girl Scouts, I was sent to dance school (but, much to my amazement, I enjoyed that until I was 17).  My parents started giving in around 3rdgrade, and I got the panda bear-shaped calculator I wanted, as well as the robot toy 2XL featuring the 8-track tape. My mom would beg me to watch Little House On the Prairie, but I preferred Star Trek (the original Kirk version), Lost in Space (Danger Will Robinson), and Land of the Lost. Of course this was all my dad’s fault according to mom – he was the sci-fi guy, but he always said, “Jen was born this way!”
My parents eventually gave up, and my uncles kept praying for that change of mind, but I spent the late seventies and early eighties winning science fairs with experiments my Uncle Ben, the electrician, rigged for me. They thought there was hope for me to be more “lady-like” in 1984 when I started high school and wanted to try out for the cheerleading squad, but the teachers advised me that “the cheer squad” was no place for an “honor student” like me. So it was off to advanced placement Biology and Chemistry, and by graduation in 1988, I was accepted to the pre-med program at NYU. 
I graduated from NYU with honors, and my parents got me two presents: my name in diamonds and a stethoscope. My grandfather bought me a set of crisp white lab coats and gloated to his brothers with a cigar in his mouth. Apparently a bet was made amongst them and from hence forward they had to call me “doctoressa,” the hybrid feminized version of doctor in Italian.
The NYU pre-med was highly competitive – a constant process of elimination from 500 students (1:3, female:male) down to only 109 of  us actually completing the program. The men thought it was strategic to flirt with the girls and convince us that we shouldn’t become doctors but instead should marry them. The guy that told me that got a punch in the stomach – in the name of the other women that worked. It was also apparent that many were planting the seeds of doubt in the pre-med females, stating that if we became doctors, then we wouldn’t be able to have a family.  In essence, we were being told that we would be giving up the chance to have children. You had to go against your “true female nature” to breed and nurture and (instead) become a selfish and testosterone-like human to make it in this field. That was the nail in the coffin for a lot of the women in my program. The most brutal tactic and final blow to confidence was when I heard someone say that “only the ugly girls become doctors because no man would want them.” 
In the nineties – halfway through college – I did change my mind, and my uncles were dancing in the streets. They thought I met a nice boy in college and I was going to settle down, give them more kids, and make sauce and meatballs on a Sunday like the good Paesana I was supposed to be. I announced I didn’t want to be an MD anymore, I wanted to be a PhD, instead. I wanted to be a SCIENTIST, do research, and maybe teach in a university.  A “Scientista”-“Professoressa” “Aiuta Dio” (which means help us god)! Back to church and the rosary beads. When I got my master’s degree in microbiology, the family was just convinced I liked to collect graduation hats.
There was a feeling among my family members that science was a “boy thing,” and my cousins teased me as a result.  They considered me a nerd and less feminine than my other girl cousins. I was told that I would never get married and have kids because I am a bookworm. Even in the mid-’90s, I had friends that told me not to tell guys that I was a scientist because they wouldn’t ask me out. I was kind of cute and only told a guy the truth about my profession if we got serious. As an experiment, I told one guy I met that I was a scientist and he said I looked too sexy to be that smart – and then he walked away.
I met discrimination on both sides of the stereotypical coin, in academia and in the work force. I was told when I was interviewing for graduate schools (and then for science jobs) that I had several strikes against me. First, strike one, my thick Staten Island/ Brooklyn accent supposedly made me sound less intelligent. My mentor in graduate school, Dr. Mark Albano, said to tell people to kiss your  “you know what” because as long as I could discuss topics like “molecular genetics” who cares how it sounds. Besides he found my accent endearing, especially because it made boring topics sound more interesting.

Strike two was my long hair.  I was told that my long hair was not practical in a scientific environment, and if I looked too glamorous on interviews I would not be taken seriously. I put my hair in a bun and toned down my make-up, but I didn’t cut it.  Apparently, I looked too feminine, especially given my major curves, and even my power suits could not hide that. Women at the time were dressing very masculine (think early Miranda on Sex in the City) to compete with men for jobs. When I got the interview for my first job with Dr. Moretti in the Reproductive Immunology Lab at St. Vincent’s Medical Center in Staten Island, I remember wearing a black and white houndstooth print sheath dress with a matching short suit jacket, accessorized with pearls.  Dr. Moretti said I was like Rosalind Franklin and Jackie Kennedy all rolled up into one, with a side order of cannoli.  

 

The early 2000s arrived, and attitudes toward science changed. Shows like CSI became wildly popular. Science fiction movies about transforming robots became blockbusters. People began to use technology in their everyday lives, such as smart phones, tablets, and car navigation systems, and it suddenly became “cool.”  I met my husband in 1999, and since I really was into him, I told him the truth about being a “microbiologist” from the start.  He said, and I quote, “Wow, your smart, sexy, and Sicilian – it’s like I hit the Lotto!”
My wedding was the most joyful event in our family’s history because most of them thought that would never happen.  I still get teased by my family when I give a long, drawn out scientific explanation of something or when I bake and make exact measurements of ingredients with my Pyrex bakeware with both the ounces and metric conversions. My husband responds for me and says “he learns something new everyday and hopes that our son becomes a nerd just like his mommy.” 
So now I have it all: I am a female scientist, a wife, and a mother, even though others didn’t think that would be possible.  But I always knew it would happen. I understood and forgave my uncles because I knew that they wanted to protect me, not hinder me. As for all my doubters I regularly take Dr. Albano’s advise and tell them to kiss my “you know what!”


Even my current supervisor, Maureen Coakley, recently told me in an interview that I am an “anomaly,” meaning that I am a flamboyant scientist. That was one of the best compliments I ever received. I am who I am, and that is why my playlist on my iPhone has the “Big Bang Theory Theme Song” followed by “I’m sexy and I know it!”
Times have changed. Perceptions have altered in a good way, but not entirely. Lesson learned from both academia and the school of life is that some people will get you and some people won’t. If they don’t, don’t take it personally because it is their loss and their ignorance. Some people see the person, and some see the stereotype. All you can do is try to educate them in an attempt to bust the stereotype. The only perception that matters is how you perceive yourself and use that perception as a means to become the woman that you were meant to be.
[DXS] What ways do you express yourself creatively that may not have a single thing to do with science?   
[JC]Ever since planning my wedding in 2004, I have been interested in event planning.  I have a knack at coordinating events, which I do as part of my collateral duties at FDA, where I have served as the Women’s Program Coordinator for the past 9 years.  People call me the ”Fun Fairy” because I can be very creative and take any topic, put a different and interesting spin on it, and present it to a group in very entertaining ways. My creativity is driven by my intellectualism, and I incorporate that into something fun and memorable. I always make little inexpensive favors – buy them to give out to my audience – that are”theme oriented,” and they keep them as a reminder of the event.
The people I work with have whole collections of these favors, and they remember what each one stands for. For instance, the Women’s History Month theme for one year was “Our History is Our Strength.”  Before planning this event, I had attended at NYU the Satellite Summit of National Women’s Conference hosted by Maria Shriver (then 1st Lady of California) and the First Lady, Michelle Obama. So I thought I would highlight the contributions of the First Ladies to US history. I found an educational video on the history of the First Ladies, did a presentation on the Satellite Summit, and even had a fashion show featuring of reproductions of Jacqueline Kennedy jewelry collection (my favorite first lady). I used the symbol of a “Cameo” to represent the first ladies, and so I made a huge paper one with beads on tulle on my bulletin board with pictures of the first ladies around it and gave out cameo bracelets that I made from gluing plastic cameo buttons on ribbon. Everyone still has a cameo on their desk at work, occasionally conjuring up memories of my First Ladies event.
[DXS] Do you find that your scientific background informs your creativity, even though what you do may not specifically be scientific? 

[JC]My entire life is influenced by, or even revolves around, “Science.”  I love science fiction movies, books, comic books, etc.  Any inspiration I get for any of my creative projects always has some root in something “science-related.” I also think that my background in science helps make my visions come to life. Even the smallest details like the stemware I chose for my wedding was a Mikasa pattern that resembled a DNA double helix, or a hexagonal candleholder that looked like a benzene ring (at least it did to me!).  Another example comes from my Women’s Program, when the theme was “Writing Women Back Into History.” So I found a book called The Women of Apollo, which gave the untold story of the women engineers who had critical contributions to the Apollo Space programs.  For me, all roads lead back to science.  

 

[DXS] Have you encountered situations in which your expression of yourself outside the bounds of science has led to people viewing you differently–either more positively or more negatively?  
[JC]I have experienced both negative and positive views by others when I am expressing my self creatively. On one hand, there were people that associate planning events with a negative stereotype of being a “party-girl” or “bimbo” type that cares more about the “girly fun” stuff than the serious business of science. On the other hand, there have been people who constantly praise me for presenting science-related topics in entertaining ways. The latter view me as a “flamboyant scientist” who shares her knowledge in an interesting manner.  In this life you will never please everyone; only seek to please yourself and your loved ones because those are the only opinions that matter.
[DXS] Have you found that your non-science expression of creativity/activity/etc. has in any way informed your understanding of science or how you may talk about it or present it to others?   
[JC]In planning these events, I have come up with a formula of sorts to create a successful soirée.  Of course, this formula is an entire science in itself. I have to consider things like timing, lighting, printed materials (programs, table cards, menus, etc.) and a gamut of other things that involve an understanding of science. I am a biologist with a minor in chemistry, but the more I do these events, the more I get into things like astronomy (for a celestial-themed wedding, for instance).  I mention lighting, which seems so simple, because it is actually quite complicated – getting the right reflections and materials to use (i.e.- LEDs, wax candles vs. battery operated, the limitations of pyrotechnics in party venues) is critical. Even in doing crafts for favors and printed materials, like event programs, I’ve learned different scientific techniques, such the right kind of bonding agent to use to attach ribbons, charms, or vinyl decorations, or even the use of edible ink in printers to make fondant or wafer decorations to put on cupcakes or cakes. It is a continuous learning experience.
[DXS] How comfortable are you expressing your femininity and in what ways? How does this expression influence people’s perception of you in, say, a scientifically oriented context?   
[JC]I am comfortable with expressing my femininity in the way I dress and conduct myself in any setting.  Although, many years ago, I was advised to dress in suits and tailored shirts similar to a man and wear neutral make-up or none at all if I wanted to be taken seriously in the scientific world, I went against the grain. I am a curvy girl, and there is no hiding my femininity. So I embrace it. I wore suits, but nothing drab – always something like a red or purple skirt suit with heels. I adhere to work environment rules like no open toe shoes in the lab, which is a safety concern, but I do not downplay my female attributes to fit in, or to present a more palatable image to my scientific peers. I do not concern myself with people’s perceptions of me based on my looks because once I “speak” and “communicate” scientific concepts, there is no question of my prowess. I am what I am, and that is a female scientist, and I pride myself in being a “stereotype buster.” 
[DXS] Do you think that the combination of your non-science creativity and scientific-related activity shifts people’s perspectives or ideas about what a scientist or science communicator is? If you’re aware of such an influence, in what way, if any, do you use it to (for example) reach a different corner of your audience or present science in a different sort of way?  

[JC]I think that being the “flamboyant scientist” works in my favor, and as a science communicator, it is effective all aspects of my life. As an adjunct professor, my students often thank me for making science fun and understandable. As a scientist, my colleagues and interns find my training methods to be memorable and actually increase their understanding of the job. As the Women’s Program Coordinator at the FDA, I create unforgettable events that people look forward to and learn a lot from. As a wife, mother, daughter, aunt, cousin, and friend, I am the “Fun Fairy” (pictured with wings and a lab coat), and their lovable nerdy girl. 
I feel my true gift is being able to communicate science.  My mentor in graduate school always told me I had the talent of taking complicated scientific ideas and expressing them in a way that anyone could understand. I have some ideas brewing involving science books for children and teens, and I would like to explore these avenues in order to share this gift with others. I would also like to get involved in maybe writing for popular science publications, if given the opportunity.
[DXS] If you had something you could say to the younger you about the role of expression and creativity in your chosen career path, what would you say?  
[JC]I would say be true to yourself. Whatever path you take career-wise, always remember that is could be something you will be doing the rest of your life. Yes, there are financial considerations to make, but if you do not have that creative outlet incorporated into your career, then you will be miserable. I am the happiest at work when I am planning a Women’s Program alongside doing experiments or going to my second job as a professor at York College. You need the creativity to keep the blood flowing. Where would science be without creativity? Find what your talent is and what makes you happy, and then apply it to your career.  That is the secret to success.

From spiders to breast cancer: Leslie Brunetta talks candidly about her cancer diagnosis, treatment, and follow-up

According to Leslie Brunetta, she now has much more hair than she had last July.
We became aware of Leslie Brunetta because of her book, Spider Silk: Evolution and 400 Million Years of Spinning, Waiting, Snagging, and Mating, co-authored with Catherine L. Craig. Thanks to a piece Leslie wrote for the Concord Monitor (and excerpted here), we also learned that she is a breast cancer survivor. Leslie agreed to an interview about her experience, and in her emailed responses, she candidly talks about her diagnosis, treatment, and follow-up for her cancers, plural: She was diagnosed simultaneously with two types of breast cancer. 
DXS: In your Concord Monitor piece, you describe the link between an understanding of the way evolution happens and some of the advances in modern medicine. What led you to grasp the link between the two?

LB: I think, because I’m not a scientist (I’m an English major), a lot of things that scientists think are obvious strike me as revelations. I somehow had never realized that the search for what would turn out to be DNA began with trying to explain how, in line with the theory of evolution by natural selection, variation arises and traits are passed from generation to generation. As I was figuring out what each chapter in Spider Silk would be about, I tried to think about the questions non-biologists like me would still have about evolution when they got to that point in the book. By the time we got past dragline silk, I realized that we had so far fleshed out the ways that silk proteins could and have evolved at the genetic level. But that explanation probably wouldn’t answer readers’ questions about how, for example, abdominal spinnerets—which are unique to spiders—might have evolved: the evolution of silk is easier to untangle than the evolution of body parts, which is why we focused on it in the first place.

I decided I wanted to write a chapter on “evo-devo,” evolutionary developmental biology, partly because there was a cool genetic study on the development of spinnerets that showed they’ve evolved from limbs. Fortunately, my co-author, Cay Craig, and editor at Yale, Jean Thomson Black, okayed the idea, because that chapter wasn’t in the original proposal. Writing that chapter, I learned why it took so long—nearly a century—to get from Darwin and Mendel to Watson and Crick and then so long again to get to where we are today. If we non-scientists understand something scientific, it’s often how it works, not how a whole string of people over the course of decades building on each other’s work discovered how it works. I knew evolution was the accumulation of gene changes, but, until I wrote that chapter, it hadn’t occurred to me that people began to look for genes because they wanted to understand evolution.

So that was all in the spider part of my life. Then, a few months into the cancer part of my life, I was offered a test called Oncotype DX, which would look at genetic markers in my tumor cells to develop a risk profile that could help me decide whether I should have chemotherapy plus tamoxifen or just tamoxifen. The results turned out to be moot in my case because I had a number of positive lymph nodes, although it was reassuring to find out that the cancer was considered low risk for recurrence. But still—the idea that a genetic test could let some women avoid chemo without taking on extra risk, that’s huge. No one would want to go through chemo if it wasn’t necessary. So by then I was thinking, “Thank you, Darwin!”

And then, coincidentally, the presidential primary season was heating up, and there were a number of serious candidates (well, serious in the sense that they had enough backing to get into the debates) who proudly declared that they had no time for the theory of evolution. And year after year these stupid anti-evolution bills are introduced in various state legislatures. While I was lying on the couch hanging out in the days after chemo sessions, I started thinking, “So, given that you don’t give any credence to Darwin and his ideas, would you refuse on principle to take the Oncotype test or gene-based therapies like Gleevec or Herceptin if you had cancer or if someone in your family had cancer? Somehow I don’t think so.” That argument is not going to convince hard-core denialists (nothing will), but maybe the cognitive dissonance in connection with something as concrete as cancer will make some people who waver want to find out more.

DXS: You mention having been diagnosed with two different forms of cancer, one in each breast. Can you say what each kind was and, if possible, how they differed?

LB: Yes, I unfortunately turned out to be an “interesting” case. This is one arena where, if you possibly can, you want to avoid being interesting. At first it seemed that I had a tiny lesion that was an invasive ductal carcinoma (IDC) and that I would “just” need a lumpectomy and radiation. Luckily for me, the doctor reading my mammogram is known as an eagle eye, and she saw a few things that—given the positive finding from the biopsy—concerned her. She recommended an MRI. In fact, even though I switched to another hospital for my surgery, she sent emails there saying I should have an MRI. That turned up “concerning” spots in both breasts, which led to more biopsies, which revealed multiple tiny cancerous lesions. The only reasonable option was then a double mastectomy.

The lesions in the right breast were IDCs. About 70% of breast cancers are diagnosed as IDCs. Those cancers start with the cells lining the milk ducts. The ones in the left breast were invasive lobular carcinomas (ILCs), which start in the lobules at the end of the milk ducts. Only about 10% of breast cancers are ILCs.

Oncologists hate lobular cancer. Unlike ductal cancers, which form as clumps of cells, lobular cancers form as single-file ribbons of cells. The tissue around ductal cancer cells reacts to those cells, which is why someone may feel a lump—she’s (or he’s) not feeling the cancer itself but the inflammation of the tissue around it. And because the cells clump, they show up more readily on mammograms. Not so lobular cancers. They mostly don’t give rise to lumps and they’re hard to spot on mammograms. They snake their way through tissue for quite a while without bothering anything.

In my case, this explains why last spring felt like an unremitting downhill slide. Every time someone looked deeper, they found something worse. It turned out that on my left side, the lobular side, I had multiple positive lymph nodes, which was why I needed not just chemo but also radiation (which usually isn’t given after a mastectomy). That was the side that didn’t even show up much on the mammogram. On the right side, the ductal side, which provoked the initial suspicions, my nodes were clear. I want to write about this soon, because I want to find out more about it. I’ve only recently gotten to the place emotionally where I think I can deal with reading the research papers as opposed to more general information. By the way, the resource that most helped us better understand what my doctors were talking about was Dr. Susan Love’s Breast Book.  It was invaluable as we made our way through this process, although it turned out that I had very few decisions to make because there was usually only one good option.   

DXS: As part of your treatment, you had a double mastectomy. One of our goals with this interview is to tell women what some of these experiences with treatment are like. If you’re comfortable doing so, could you tell us a little bit about what a double mastectomy entails and what you do after one in practical terms?

LB: A mastectomy is a strange operation. In a way, it’s more of an emotional and psychological experience than a physical experience. My surgeon, who was fantastic, is a man, and when we discussed the need for the mastectomies he said that I would be surprised at how little pain would be involved and how quick the healing would be. Even though I trusted him a lot by then, my reaction was pretty much, “Like you would know, right?” But he did know. When you think about it, it’s fairly non-invasive surgery. Unless the cancer has spread to the surrounding area, which doesn’t happen very often now due to early detection, no muscle or bone is removed. (Until relatively recently, surgeons removed the major muscle in the chest wall, and sometimes even bone, because they believed it would cut the risk of recurrence. That meant that many women lost function in their arm and also experienced back problems.) None of your organs are touched. They don’t go into your abdominal cavity. Also, until recently, they removed a whole clump of underarm lymph nodes when they did lumpectomies or mastectomies. Now they usually remove just a “sentinel node,” because they know that it will give them a fairly reliable indicator of whether the cancer has spread to the other nodes. That also makes the surgery less traumatic than it used to be.

I opted not to have reconstruction. Reconstruction is a good choice for many women, but I didn’t see many benefits for me and I didn’t like the idea of a more complicated surgery. My surgery was only about two hours. I don’t remember any pain at all afterwards, and my husband says I never complained of any. I was in the hospital for just one night. By the next day, I was on ibuprofen only. The bandages came off two days after the surgery.

That’s shocking, to see your breasts gone and replaced by thin red lines, no matter how well you’ve prepared yourself. It made the cancer seem much more real in some way than it had seemed before. In comparison, the physical recovery from the surgery was fairly minor because I had no infections or complications. There were drains in place for about 10 days to collect serum, which would otherwise collect under the skin, and my husband dealt with emptying them twice a day and measuring the amount. I had to sleep on my back, propped up, because of where the drains were placed, high up on my sides, and I never really got used to that. It was a real relief to have the drains removed.

My surgeon told me to start doing stretching exercises with my arms right away, and that’s really important. I got my full range of motion back within a couple of months. But even though I had my surgery last March, I’ve noticed lately that if I don’t stretch fully, like in yoga, things tighten up. That may be because of the radiation, though, because it’s only on my left side. Things are never quite the same as they were before the surgery, though. Because I did have to have the axillary nodes out on my left side, my lymph system is disrupted. I haven’t had any real problems with lymphedema yet, and I may never, but in the early months I noticed that my hands would swell if I’d been walking around a lot, and I’d have to elevate them to get them to drain back. That rarely happens now. But I’ve been told I need to wear a compression sleeve if I fly because the change in air pressure can cause lymph to collect. Also, I’m supposed to protect my hands and arms from cuts as much as possible. It seems to me that small nicks on my fingers take longer to heal than they used to. So even though most of the time it seems like it’s all over, I guess in those purely mechanical ways it’s never over. It’s not just that you no longer have breasts, it’s also that nerves and lymph channels and bits of tissue are also missing or moved around.

The bigger question is how one deals with now lacking breasts. I’ve decided not to wear prostheses. I can get away with it because I was small breasted, I dress in relatively loose clothes anyway, and I’ve gained confidence over time that no one notices or cares and I care less now if they do notice. But getting that self-confidence took quite a while. Obviously, it has an effect on my sex life, but we have a strong bond and it’s just become a piece of that bond. The biggest thing is that it’s always a bit of a shock when I catch sight of myself naked in a mirror because it’s a reminder that I’ve had cancer and there’s no getting around the fact that that sucks.    

DXS: My mother-in-law completed radiation and chemo for breast cancer last year, and if I remember correctly, she had to go frequently for a period of weeks for radiation. Was that you experience? Can you describe for our readers what the time investment was like and what the process was like?

LB: I went for radiation 5 days a week for about 7 weeks. Three days a week, I’d usually be in and out of the hospital within 45 minutes. One day a week, I met with the radiology oncologist and a nurse to debrief, which was also a form of emotional therapy for me. And one day a week, they laid on a chair massage, and the nurse/massage therapist who gave the massage was great to talk to, so that was more therapy. Radiation was easy compared to chemo. Some people experience skin burning and fatigue, but I was lucky that I didn’t experience either. Because I’m a freelancer, the time investment wasn’t a burden for me. I’m also lucky living where I live, because I could walk to the hospital. It was a pleasant 3-mile round-trip walk, and I think the walking helped me a lot physically and mentally.
DXS: And now to the chemo. My interest in interviewing you about your experience began with a reference you made on Twitter to “chemo brain,” and of course, after reading your evolution-medical advances piece. Can you tell us a little about what the process of receiving chemotherapy is like? How long does it take? How frequently (I know this varies, but your experience)?
LB: Because of my age (I was considered young, which was always nice to hear) and state of general good health, my oncologist put me on a dose-dense AC-T schedule. This meant going for treatment every two weeks over the course of 16 weeks—8 treatment sessions. At the first 4 sessions, I was given Adriamycin and Cytoxan (AC), and the last 4 sessions I was given Taxol (T). The idea behind giving multiple drugs and giving them frequently is that they all attack cancer cells in different ways and—it goes back to evolution—by attacking them frequently and hard on different fronts, you’re trying to avoid selecting for a population that’s resistant to one or more of the drugs. They can give the drugs every two weeks to a lot of patients now because they’ve got drugs to boost the production of white blood cells, which the cancer drugs suppress. After most chemo sessions, I went back the next day for a shot of one of these drugs, Neulasta.

The chemo clinic was, bizarrely, a very relaxing place. The nurses who work there were fantastic, and the nurse assigned to me, Kathy, was always interesting to talk with. She had a great sense of humor, and she was also interested in the science behind everything we were doing, so if I ever had questions she didn’t have ready answers for, she’d find out for me. A lot of patients were there at the same time, but we each had a private space. You’d sit in a big reclining chair. They had TVs and DVDs, but I usually used it as an opportunity to read. My husband sat through the first session with me, and a close friend who had chemo for breast cancer 15 years ago sat through a few other sessions, but once I got used to it, I was comfortable being there alone. Because of the nurses, it never felt lonely.

I’d arrive and settle in. Kathy would take blood for testing red and white blood counts and, I think, liver function and some other things, and she’d insert a needle and start a saline drip while we waited for the results. I’ve always had large veins, so I opted to have the drugs administered through my arm rather than having a port implanted in my chest. Over the course of three to four hours, she’d change the IV bags. Some of the bags were drugs to protect against nausea, so I’d start to feel kind of fuzzy—I don’t think I retained a whole lot of what I read there! The Adriamycin was bright orange; they call it the Red Devil, because it can chew up your veins—sometimes it felt like it was burning but Kathy could stop that by slowing the drip. Otherwise, it was fairly uneventful. I’d have snacks and usually ate lunch while still hooked up.

I was lucky I never had any reactions to any of the drugs, so actually getting the chemo was a surprisingly pleasant experience just because of the atmosphere. On the one hand, you’re aware of all these people around you struggling with cancer and you know things aren’t going well for some of them, so it’s heartbreaking, and also makes you consider, sometimes fearfully, your own future no matter how well you’re trying to brace yourself up. But at the same time, the people working there are so positive, but not in a Pollyannaish-false way, that they helped me as I tried to stay positive. The social worker stopped in with each patient every session, and she was fantastic—I could talk out any problems or fears I had with her, and that helped a huge amount.

DXS: Would you be able to run us through a timeline of the physical effects of chemotherapy after an infusion? How long does it take before it hits hardest? My mother-in-law told me that her biggest craving, when she could eat, was for carb-heavy foods like mashed potatoes and for soups, like vegetable soup. What was your experience with that?

LB: My biggest fear when I first learned I would need chemo was nausea. My oncologist told us that they had nausea so well controlled that over the past few years, she had only had one or two patients who had experienced it. As with the surgeon’s prediction about mastectomy pain, this turned out to be true: I never had even a single moment of nausea.

But there were all sorts of other effects. For the first few days after a session, the most salient effects were actually from the mix of drugs I took to stave off nausea. I generally felt pretty fuzzy, but not necessarily sleepy—part of the mix was steroids, so you’re a little hyped. There’s no way I’d feel safe driving on those days, for example. I’d sleep well the first three nights because I took Ativan, which has an anti-nausea effect. But except for those days, my sleep was really disrupted. Partly that’s because, I’m guessing, the chemo hits certain cells in your brain and partly it’s because you get thrown into chemical menopause, so there were a lot of night hot flashes. Even though I’d already started into menopause, this chemo menopause was a lot more intense and included all the symptoms regularly associated with menopause.

By the end of the first session, I was feeling pretty joyful because it was much less bad than I had thought it would be. By the second week in the two-week cycle, I felt relatively normal. But even though it never got awful, the effects started to accumulate. My hair started to fall out the morning I was going to an award ceremony for Spider Silk. It was ok at the ceremony, but we shaved it off that night. I decided not to wear a wig. First, it was the summer, and it would have been hot. Second, I usually have close to a buzz cut, and I can’t imagine anyone would make a wig that would look anything like my hair. My kids’ attitude was that everyone would know something was wrong anyway, so I should just be bald, and that helped a lot. But it’s hard to see in people’s eyes multiple times a day their realization that you’re in a pretty bad place. Also, it’s not just your head hair that goes. So do your eyebrows, your eyelashes, your pubic hair, and most of the tiny hairs all over your skin. And as your skin cells are affected by the chemo (the chemo hits all fast-reproducing cells), your skin itself gets more sensitive and then is not protected by those tiny hairs. I remember a lot of itching. And strange things like my head sticking to my yoga mat and my reading glasses sticking to the side of my head instead of sliding over my ears.

I never lost my appetite, but I did have food cravings during the AC cycles. I wanted sushi and seaweed salad, of all things. And steak. My sense of taste went dull, so I also wanted things that tasted strong and had crunch. I stopped drinking coffee and alcohol, partly because of the sleep issues but partly because it didn’t taste very good anyway. I drank loads of water on the advice of the oncologist, the nurses, and my acupuncturist, and I think that helped a lot.

During the second cycle, I developed a fever. That was scary. I was warned that if I ever developed a fever, I should call the oncologist immediately, no matter the time of day or day of week. The problem is that your immune response is knocked down by the chemo, so what would normally be a small bacterial infection has the potential to rage out of control. I was lucky. We figured out that the source of infection was a hemorrhoid—the Adriamycin was beginning to chew into my digestive tract, a well-known side effect. (Having to pay constant attention to yet another usually private part of the body just seemed totally unfair by this point.) Oral antibiotics took care of it, which was great because I avoided having to go into the hospital and all the risks entailed with getting heavy-duty IV antibiotic treatment. And we were also able to keep on schedule with the chemo regimen, which is what you hope for.

After that, I became even more careful about avoiding infection, so I avoided public places even more than I had been. I’m very close to a couple of toddlers, and I couldn’t see them for weeks because they were in one of those toddler constant-viral stages, and I really missed them.

The Taxol seems to be much less harsh than the AC regimen, so a lot of these side effects started to ease off a bit by the second 8 weeks, which was certainly a relief.

I was lucky that I didn’t really have mouth sores or some of the other side effects. Some of this is, I think, just because besides the cancer I don’t have any other health issues. Some of it is because my husband took over everything and I don’t have a regular job, so I had the luxury of concentrating on doing what my body needed. I tried to walk every day, and I slept when I needed to, ate when and what I needed to, and went to yoga class when my immune system was ok. I also went to acupuncture every week. I know the science is iffy on that, but I think it helped me with the side effects, even if it was the placebo effect at work (I’m a big fan of the placebo effect). We also both had extraordinary emotional support from many friends and knew we could call lots of people if we needed anything. That’s huge when you’re in this kind of situation.

Currently, I’m still dealing with some minor joint pains, mostly in my wrists and feet. I wasn’t expecting this problem, but my oncologist says it’s not uncommon: they think it’s because your immune system has to re-find its proper level of function, and it can go into overdrive and set up inflammation in the joints. That’s gradually easing off, though.

Most people don’t have it as easy as I did in terms of the medical, financial, and emotional resources I had to draw on. I’m very mindful of that and very grateful.

DXS: You say that you had “few terrible side effects” and a “very cushy home situation.” I’m sure any woman would like to at least be able to experience the latter while dealing with a full-body chemical attack. What were some factors that made it “cushy” that women might be able to talk to their families or caregivers about replicating for them?

LB: As I’ve said, some of it is just circumstance. For example, my kids were old enough to be pretty self-sufficient and old enough to understand what was going on, which meant both that they needed very little from me in terms of care and also that they were less scared than they might have been if they were younger. My husband happens to be both very competent (more competent than I am) around the house and very giving. I live in Cambridge, MA, where I could actually make choices about where I wanted to be treated at each phase and know I’d get excellent, humane care and where none of the facilities I went to was more than about 20 minutes away.

Some things that women might have some control over and that their families might help nudge them toward:

  • Find doctors you trust. Ask a lot of questions and make sure you understand the answers. But don’t get hung up on survival or recurrence statistics. There’s no way to know for sure what your individual outcome will be. Go for the treatment that you and your doctors believe will give you the best chance, and then assume as much as possible that your outcome will be good.
  • Make sure you talk regularly with a social worker or other therapist who specializes in dealing with breast cancer patients. If you have fears or worries that you don’t want to talk to your partner or family about, here’s where you’ll get lots of help.
  • Find compatible friends who have also had cancer to talk to. I had friends who showed me their mastectomy scars, who showed me their reconstructions, who told me about their experiences with chemo and radiation, who told me about what life after treatment was like (is still like decades later…). And none of them told me, “You should…” They all just told me what was hard for them and what worked for them and let me figure out what worked for me. Brilliant.
  • Try to get some exercise even if you don’t feel like it. It was often when I felt least like moving around that a short walk made me feel remarkably better. But I would forget that, so my husband would remind me. Ask someone to walk with you if you’re feeling weak. Getting your circulation going seems to help the body process the chemo drugs and the waste products they create. For the same reason, drink lots of water.
  • Watch funny movies together. Laughter makes a huge difference.
  • Pamper yourself as much as possible. Let people take care of you and help as much as they’re willing. But don’t be afraid to say no to anything that you don’t want or that’s too much.

Family members and caregivers should also take care of themselves by making some time for themselves and talking to social workers or therapists if they feel the need. It’s a big, awful string of events for everyone involved, not just the patient.

DXS: In the midst of all of this, you seem to have written a fascinating book about spiders and their webs. Were you able to work while undergoing your treatments? Were there times that were better than others for attending to work? Could work be a sort of occupational therapy, when it was possible for you to do it, to keep you engaged?

LB: The book had been published about 6 months before my diagnosis. The whole cancer thing really interfered not with the writing, but with my efforts to publicize it. I had started to build toward a series of readings and had to abandon that effort. I had also started a proposal for a new book and had to put that aside. I had one radio interview in the middle of chemo, which was kind of daunting but I knew I couldn’t pass up the opportunity, and when I listen to it now, I can hear my voice sounds kind of shaky. It went well, but I was exhausted afterwards. Also invigorated, though—it made me feel like I hadn’t disappeared into the cancer. I had two streams of writing going on, both of which were therapeutic. I sent email updates about the cancer treatment to a group of friends—that was definitely psychological therapy. I also tried to keep the Spider Silk blog up to date by summarizing related research papers and other spider silk news—that was intellectual therapy. I just worked on them when I felt I wanted to. The second week of every cycle my head was usually reasonably clear.

I don’t really know whether I have chemo brain. I notice a lot of names-and-other-proper-nouns drop. But whether that’s from the chemo per se, or from the hormone changes associated with the chemically induced menopause, or just from emotional overload and intellectual distraction, I don’t know. I find that I’m thinking more clearly week by week.

DXS: What is the plan for your continued follow-up? How long will it last, what is the frequency of visits, sorts of tests, etc.?

LB: I’m on tamoxifen and I’ll be on that for probably two years and then either stay on that or go onto an aromatase inhibitor [Ed. note: these drugs block production of estrogen and are used for estrogen-sensitive cancers.] for another three years. I’ll see one of the cancer doctors every three months for at least a year, I think. They’ll ask me questions and do a physical exam and take blood samples to test for tumor markers. At some point the visits go to every six months.

For self-care, I’m exercising more, trying to lose some weight, and eating even better than I was before.

DXS: Last…if you’re comfortable detailing it…what led to your diagnosis in the first place?

LB: My breast cancer was uncovered by my annual mammogram. I’ve worried about cancer, as I suppose most people do. But I never really worried about breast cancer. My mother has 10 sisters and neither she nor any of them ever had breast cancer. I have about 20 older female cousins—I was 50 when I was diagnosed last year–and as far as I know none of them have had breast cancer. I took birth control pills for less than a year decades ago. Never smoked. Light drinker. Not overweight. Light exerciser. I breastfed both kids, although not for a full year. Never took replacement hormones. Never worked in a dangerous environment. Never had suspicious mammograms before. So on paper, I was at very low risk as far as I can figure out. After I finished intensive treatment, I was tested for BRCA1 and BRCA2 (because mutations there are associated with cancer in both breasts) and no mutations were found. Unless or until some new genetic markers are found and one of them applies to me, I think we’ll never know why I got breast cancer, other than the fact that I’ve lived long enough to get cancer. There was no lump. Even between the suspicious mammogram and ultrasound and the biopsy, none of the doctors examining me could feel a lump or anything irregular. It was a year ago this week that I got the news that the first biopsy was positive. In some ways, because I feel really good now, it’s hard to believe that this year ever happened. But in other ways, the shock of it is still with me and with the whole family. Things are good for now, though, and although I feel very unlucky that this happened in the first place, I feel extremely lucky with the medical care I received and the support I got from family and friends and especially my husband.
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Leslie Brunetta’s articles and essays have appeared in the New York Times, Technology Review, and the Sewanee Review as well as on NPR and elsewhere. She is co-author, with Catherine L. Craig, of Spider Silk: Evolution and 400 Million Years of Spinning, Waiting, Snagging, and Mating (Yale University Press).

Double Xpression: Debbie Berebichez, PhD Physicist

Deborah is the first Mexican woman to graduate with a physics PhD from Stanford University. She is a physicist, author, and media personality whose initiatives to popularize science have impacted thousands of people around the world. Her passion is to popularize science and motivate young minds to think analytically about the world. This has led her to pioneer learning initiatives in schools and universities in Mexico, Africa, the US and Israel. She is a frequent public speaker and has been recognized by numerous media outlets such as Oprah, CNN, WSJ, TED, DLD, WIRED, Martha Stewart, City of Ideas, Dr. Oz Show, Celebrity Scientist and others. She regularly appears as a science expert on different international TV networks; currently she is the TV host of National Geographic’s “Humanly Impossible” show. And she will appear on the Discovery Channel’s upcoming show ‘You’ve Been Warned.’  You can find Deborah on Twitter, or on her blog, Science With Debbie.  You can also find Deborah telling her story for The Story Collider.



DXS: First, can you give me a quick overview of what your scientific background is and your current connection to science?

I grew up in Mexico City in a fairly conservative community, and as a child, I was discouraged from doing and studying science.  My parents, family, and peers would all ask, “oh, why don’t you study a more feminine career?” Although I was pretty good in school, I wasn’t exactly a math wizard.  I used to say that I loved philosophy and physics – because philosophy was a deep discipline of asking questions about the world.  And physics studied the world itself.   
It was clear when I was born that my personality was was quite different to the one of my mom.  When I was growing up, my mom was scared because she didn’t know what to do with this little girl that was smart and always asking questions.  She is not a naturally curious person, so she kept trying to tame down my curiosity and kept telling me not to tell boys that I was interested in math and science because I would never find a husband.  According to her, the life goal for a girl was to find a husband, have kids, and that’s it.  Women didn’t have to have a career.  (Not that there is anything wrong with not having a career.)  My high school teachers and counselors were not so different and encouraged me to go into philosophy or literature, not into math or physics.  And my friends in school told me I literally had to be an out of the world genius to be able to study physics.      
Given the circumstances, I started studying philosophy in Mexico.  There were some classes with logic, and some with a little bit more math, and those were the ones I just devoured!  And, at the same time – secretly – I was reading the biographies of scientists.  For some bizarre reason, I was hugely attracted to their life stories.  I didn’t have any family members, or anyone else for that matter, that had pursued a career in science, so I didn’t have a mentor or a role model.  I felt an extreme kinship with Tycho Brahe, who in the late 1500’s was locked in a tower, doing all of these calculations for years, hated by everyone in the town.  Go figure! I felt some kinship with these scientists.   But I didn’t have the courage nor the means to switch majors.  I did confess that I wanted to study another area (physics), but in Mexico one cannot study two majors. So, I studied philosophy for two years.

In the middle of it, I felt way too curious about science and I decided to apply to schools in the US.  It was hard at the time because college in Mexico was a lot cheaper than in the states.  At the private school where I was attending, my tuition was about $5,000 per year.  If I were to come to the US, I would be looking at costs exceeding $35,000 per year. I couldn’t really ask my dad to help me with that price tag so I started to apply everywhere and anywhere that had scholarship opportunities.

I ended up getting a letter from Brandeis 

University saying that they would let me take this advanced placement test and write an essay, which, if I did well, would give me a full scholarship.  I received a full Wien Scholarship and was to continue studying philosophy in the US.  This was probably the nicest thing that has ever happened to me because it opened the path of opportunity.

Brandeis transformed me as a person – I saw females doing science!  But, the bravado moment that changed my life was a very general course called Astronomy 101.  The teaching assistant, Roopesh, was a very sweet man from India and he saw that my eyes would just light up when I was in that class – I was much more curious than the random student that was just taking it to fulfill some requirement.   
At the end of that year, Roopesh and I 

were walking around Harvard Square and stopped to sit under a tree.  I started to tell him, with tears in my eyes, that I just don’t want to die without trying.  What I meant by that is I don’t want to die without trying to do physics.  Everyone’s questioning of my decision made me question my actual ability.  Everyone telling me ‘no’ hampered my development.  I mean, I was good at math, but I definitely didn’t have the same background as all the kids coming in with advanced math and physics courses. 
 

I told Roopesh that I don’t even remember how to solve the equation (a+b)2 – even my algebra was rusty!  But, he believed in me and went back to his professor and told him my story.  This professor decided to meet with me and ends up telling me about someone who had done this sort of thing in the past.  His name was Ed Witten and he went on to become the father of string theory.  

He said “Witten had switched from history to physics, and I will let you try too.”  With that, he handed me a book on vector calculus called ‘Div, Grad and Curl’ and told me that If I could master it in three months by the end of the summer, they would let me switch my major to physics and also let me bypass the first two years of course work.  This would allow me to graduate by the time my scholarship ran out.        
I have never in my life experienced the level of scientific passion condensed into such a short amount of time and I am jealous of the person I was that summer.  I had so much perseverance and focus.  I don’t think I can ever reproduce that intensity again.  From the moment I woke up to the moment I went to sleep, and even in my dreams, I only thought about physics. Roopesh, who became my mentor for the summer, taught me.  

I always wanted to pay Roopesh for his tutoring, but he would never accept any money.  He told me that when he was growing up in the mountains of Darjeeling in India, there was this old man who would climb up to his home and teach him and his sisters English, the musical instrument Tabla, and math.  Roopesh’s father always wanted to pay the old man for his tutoring, but the man always declined.  The man said that the only way he could ever pay him back was if Roopesh did the same thing with someone else in the world.  And by mentoring me, Roopesh fulfilled his payment to the old man.  
Out of that, that became a seed for my physics journey and purpose.  It is now my life’s mission to do the same for other people in the world – especially women – who feel attracted to science but feel trapped.  They for some reason, whether it is social, financial, etc., just can’t find the way toward science.  That is the motivation that dictates my actions.
I was able to pull it off and graduated Brandeis Summa Cum Laude with highest honors in physics and philosophy. I went back to Mexico afterwards to figure out what to do next and to spend some time with my family. At the same time, I did a master’s degree in physics at the largest university in Mexico UNAM.  My curiosity for physics didn’t diminish and in 1998, I randomly applied to two physics PhD programs in the US.  I applied very, very late, but, fortunately, I won a merit-based full scholarship from the Mexican government who provided me with funding, which made it easier for me.    


Because I loved biophysics, I did a search on who was doing this line of research.  I came across Steven Chu, who is currently the secretary of energy.  At the time I was applying, he was at Stanford and was one of the first to manipulate a single strand of DNA with his ‘optical tweezers.’  To me, his story was fascinating!  Without really knowing who he was other than what I found on the web, I wrote him an email asking him if I could work in his lab.  Had I known who he was – that he had just won the Nobel prize in 1997 – I would have been too intimidated.  


I was admitted to Stanford and was invited to work with Dr. Chu, but after two years I decided to switch labs.  As expected, it was a very challenging environment and having only studied two years of physics at Brandeis, I wasn’t as prepared as most of the other students.  I struggled for the first two years.  Everyone worked so extremely hard at Stanford and there I was, struggling to be the best, but, in the beginning, I couldn’t even be average.

Fast forward four years.  I had worked my butt off and ended up becoming the first Mexican woman to graduate with a PhD in physics from Stanford.  It was the best day of my life – I kept thinking that I was so blessed to have my parents live to see this!  It was so moving, I was crying so much and I couldn’t believe what had happened.  My friends had flown in from all over the world to be with me.  It was amazing. 

When people hear what I do, they – especially teenage girls – feel intimidated.  But, when they hear the whole story, their tune changes.  I tell them that I know what it is like to not understand something.  I was not the kind of person where comprehension of my science came naturally.  But I did it.  And if I can do it, anyone can do it!  My story can be inspirational to someone who comes from a background completely lacking in science because they, like me, can reach their goal. 
DXS: What ways do you express yourself creatively that may not have a single thing to do with science?

I was always a very curious girl growing up. I had a lot of interests, one of which being theatre.  I wanted to be an actress when I was young, but my father didn’t let me pursue that as a career, which was probably a good idea.  But, during high school, I went to an after school drama program.  I wrote my own plays – three of them – and performed one of them.  I was in heaven when I was on stage. 

In NY, I have tried to do a little bit of that.  Of course, I’ve never done any big roles, but I will be an extra in a film, or if there is a small production being made in Spanish, I will play a part.  It doesn’t matter how big the role is – I just love doing something creative and getting into a character. 

DXS: What types of productions and/or films have you done?

I don’t think I would come up in the credits as an extra, but I did a movie with Simon Pegg, Kirsten Dunst and Megan Fox in the movie “How to lose Friends and Alienate People.” It was a very, very fun film!  In theatre, Jean Genet, who is a French playwright, has a play called The Maids, and I was the madame.   

DXS: Do you find that your scientific background informs your creativity, even though what you do may not specifically be scientific?

Debbie talking to the TEDYouth audience about waves.

I have a concept that I call “physics glasses.”  And what I mean by that is, for me, physics is not a subject that you just teach in a complex way in a classroom.  Rather, physics is something that is related to everyday life.  From the moment you wake up, you can just put on your physics glasses.  It is a mode of thinking – it is a way where although reality can be very rich and diverse, physics goes very deep and it abstracts commonalities, general principles that apply to many things.  To give you an example, I asked the kids in the audience of my TEDYouth talk, “what do the sun, the ocean, and a symphony orchestra have in common?”  When just looking at them on the surface, there isn’t much in common.  I mean, they are all beautiful things but they are not obviously related.  But, to a physicist, they are all waves.   You have sound waves, light waves, and water waves and you can interchange many of the concepts in physics to explain all three.



Where most of us see the world with our eyes through light waves, other might see the world differently.  Take, for example, my friend Juan, who is blind.  He “sees” the world with sound waves – he senses sound as it bounces off the objects around him.  Through this, he can bike, play basketball, and do a load of activities using sound as a guide.  This is one of my favorite analogies because, really, physics “infects” the way I see the world. 

Deborah the Physicist model

To give you a more specific example in the creativity realm, when I got to NY, I felt really un-feminine.  When I was studying physics, I felt that if I was even slightly feminine, I wouldn’t be respected.  It didn’t help that some of the other women in the physics program at Stanford were more of a “guys girl,” always wearing a baseball cap and t-shirts.  Now, since I am Latin, I first showed up wearing a skirt to class, but I quickly learned to dress down.  Looking feminine would assure that no one would talk to me in class.



So, when I got to NY, I had an explosion.  I wanted to know what it was like to express myself as a woman and my friend suggested that I do some modeling.  So I did.  It was a brief, lasting about a year.  But during that time, my friend, who was a designer from Mexico, asked me to work with her and I wrote and did some videos about the physics of fashion, which also included the physics of high heels video.  


Some people could consider fashion to be superficial, but not me.  I love fashion and color.  But, other scientists generally looked down upon you for liking this sort of thing.   This fueled my desire to prove to everyone that there actually is science everywhere, including fashion, and that they shouldn’t be snobs about it.  There is complex science in how different materials work, how they interact with the environment and you can prove to the women, like my mother and friends back home who think that science has nothing to do with their everyday lives, that it has EVERYTHING to do with it.   So I talked about a Newtonian theory for color – how to pick the right color for you based on how much light the color would reflect on that day, etc.  

DXS: Like a more sophisticated version of colors based on your “season?”

DB: Exactly! 

I also did pieces on the materials, including some of the newest engineering accomplishments with fabric.  For example, I hooked up with a woman and helped her to design a fashionable and very scientific coat.  It ended up costing $11,000, but it was made up of nano fibers and it had a patch in it that could detect the temperature and the probability of rain.  Based on this probability, it could change permeability of the fabric.  It was a very light coat that was comfortable in nice weather, but when it would rain, it would become impermeable to water once it detected a high probability of rain, transforming into a raincoat.

DXS: That’s incredible!  I wish it wasn’t $11,000!

DB:  Yeah, that’s usually the problems with these technologies.  They are often so novel, but one day I’m sure we can figure out how to make things like this scalable.

Science is very much what guides my thinking when I am being creative and I wish I had more time to do creative things while being influenced by a scientific mindset.

DXS: It is so cool that physics has such an incredible overlap with everyday living.  Like, when we take a shower, I want to know “how is the water getting pumped from the ground or through pipes and make its way out of the showerhead?”  But, as a biochemist, I often find it hard to relate everyday things to biochemistry, but I would like to!

DB: Its funny that you say that.  When I try to teach girls that the worst thing they can do is memorize.  Critical thinking is so important and they shouldn’t take anything at face value, and they should even question teachers and authoritative figures in their lives.  Always ask: what goes into making this?  Why is this here?  Why is it this way and not another?  Constantly ask questions.  That s the gift that physics will give you. 

DXS: Have you encountered situations in which your expression of yourself outside the bounds of science has led to people viewing you differently–either more positively or more negatively?

Without saying I am a scientist, I can tell you that people have come up to me and told me that before they even hear me speak, they think I am dumb.  They are usually surprised that I am smart!  I think it is because I am bubbly and friendly and that often makes an impression as being unintelligent.  For them it seems that if a woman is intelligent, she is very cold and distant and serious.  


I’ve met a lot of physicists, and yes, some of them do tend to be that way, often as a reaction to how others treat them.  Or, people would say to me that, because I am Latin, my cultural identity comes across as being warm and the last thing they’d expect me to be into was something as cold as physics.  So yeah, I have definitely been judged so many times!  


It even happens in my current job on Wall Street, especially with my male peers.  When there are off site client meetings, I’m often accompanied by my male sales colleague.  Sales people are generally required to know less about the complexities behind our risk models compared to someone on a more research-oriented role, like me and he will bring me along to these sales meetings in case the potential client has more sophisticated questions that go beyond what he can comfortably answer.  Many times upon meeting the clients for the first time they think that I am the sales person, there to be the smiling face to sell them something, and that he is the risk modeler.  They always direct their mathematical questions to him. 
It came to a point where I became so annoyed that I decided to stop caring.  Now, my sales colleague goes out for drinks with the clients and I know that I am going to be invisible. So I don’t go anymore. I know that I am always going to struggle to get the full intellectual respect in that industry – it will always be a challenge.

DXS: Have you found that your non-science expression of creativity/activity/etc. has in any way informed your understanding of science or how you may talk about it or present it to others?

Yes, absolutely.  For example in Mexico, unlike the US, you absolutely have to do an honors thesis project as an undergrad in science.  Because I had already studied philosophy for four years, I wanted to do a thesis project in philosophy.  But I also wanted to do one in physics.  I recall that back in 1997, when you presented a dissertation in front of the physics community, if you had any power point, forget it.  You would be immediately be called dumb or not a good physicist.  Because, who takes the time to do something fancy!  If you had any color in your presentation, forget it!  


So, literally, the smartest students in physics were people who didn’t really communicate that well, or didn’t really speak English that well, or just didn’t really make an effort.  Their slides were on those overhead projector things with those rolls of plastic sheets, and most of their talks were so confusing and couldn’t be interpreted!  But they were respected!  It was just assumed that if the formula looked complex, they were probably right. 
So what I did was completely different.  I infused my talk with my spiciness and color.  I did an artwork of liquid crystals, which was my research at Brandeis.  Liquid crystals are little cigar-shaped molecules that actually make up the screen of your laptop.  If you pass an electric field through them, they all orient themselves and that is how we can use them for displays in our laptops and TVs. 

I colored these cigar-shaped molecules with purples and reds and greens, and I tried to explain it at the most basic level. This is because of one my philosophy professors in Mexico, who told me that if you cannot explain what you do to your grandmother or 6 year old niece, you don’t understand what you are doing – I loved it!  


And I said to myself that I shouldn’t care what they think.  I pretty much expected to not gain a lot of respect from the physics department, but it had the opposite effect!  I actually had one of the professors from that department come up to me and tell me that he had never really understood what a liquid crystal looked like or what it really was!  He said that “finally I understand [liquid crystals] because of your drawing.  Thank you!”  It was incredible!  


To see the effect on people and from then on, I bounced up in down, I made jokes, I put in creativity.  It doesn’t always have a great effect on very serious audiences, but the younger generation is definitely appreciative.  When it keeps going well, you gain confidence.  And, for me, I even started wearing high heels to the next talk.  When someone commented about my attire, I would counter, hey I have a PhD!

DXS: How comfortable are you expressing your femininity and in what ways? How does this expression influence people’s perception of you in, say, a scientifically oriented context?

This question is deep and a little bit of a struggle at the moment.  This is because I still have that fear – when I arrived in NY, I did that short stint in modeling and I expressed myself and I would dress very creatively – just like my other girlfriends who were not scientists.  But I did feel a little bit of a backlash.  By that I mean that I would post a photo of myself on Facebook or something like that.  They were pretty pictures, not at all seductive or provocative, and my high school mates, usually male, would write me saying: “I always knew you as a serious person and you have achieved so many things – I am just telling you for your own good that this can really damage your image.”  That made me reply with “so you’re telling me that being smart is actually kind of a bummer?”  That actually means that I have to dress very differently from what other women wear for the rest of my life? 

I remember feeling very upset about all of that.  I think that not being taken seriously is still a little bit of a fear of and I think my website has damaged my serious image a little bit.  As a scientist, I was very secluded from the outside world.  I didn’t have a lot of friends when I moved here, but I did know an amazing and powerful woman who happened to be the CEO of Blip TV.  She was insisting that I do videos!  So she invited me to her place and showed me how to do video.  Being the quick woman that she was, she asked me to make up a name for myself on the spot.  When I didn’t answer, she instantly coined “The Science Babe” for me.  I was like, sure, what a cool idea! 

It was kind of a cute name, but because English is not my first language, I don’t always understand some of the cultural connotations associated with some English words.  A few months later, I started to get a few emails from mothers who were upset that I was using my looks.  They would say things like “Are you saying that women have to be in the kitchen or wear short skirts  to be scientists?”  I would answer that no, that was not it at all.  I would further explain that I was trying to change the definition of “babe.”  If you are smart, if you are empowered, you will be a babe no matter how you look.  I am trying to shift what people think of when they think “scientist.”

I don’t feel quite successful with The Science Babe.  It seems like there are quite a few people, especially some from the older generation, who say that they’d love to introduce me to fancy science organizations but are worried that the name “the science babe” will make it difficult.  Also, I had the BBC wanted to talk to me about doing a TV show in NY, and then they said but there’s so much bad stuff out there about you!  And I was like, what do you mean?  They answered “All these things with the “science babe” brand…”

It doesn’t happen all the time, but some people are really critical about the science babe theme, citing that its way too feminine.  Other female scientists that haven’t gone that route have perhaps discounted my seriousness about science.  They assume that what I am doing is not really that important because I do focus on the science everyday life, which is simpler, and it is too much color and too much vivaciousness for our field.  I feel like my femininity has decreased over the last few years because I’ve been too nervous about not being taken seriously.  It s almost like the balance tipped the other way. I feel like perhaps I’ve feminized things to a fault and now I want to appear more serious.  So, I am changing my website to “Science With Debbie” because I really felt the backlash.

It is a struggle to find the balance between being able to express my femininity and presenting myself in a way that people will take me seriously.  In a way, I wish I had a little more courage to not care that much about what people have to say about the science babe but, unfortunately, agents have told me that if I don’t go to the “dumbed down version of femininity” I would get better speaking engagements.  Being feminine has literally affected my career, and it’s because of other people’s perceptions.  I’m never going to be bland, but I will try to change things so I am more serious

DXS: Do you think that the combination of your non-science creativity and scientific-related activity shifts people’s perspectives or ideas about what a scientist or science communicator is? If you’re aware of such an influence, in what way, if any, do you use it to (for example) reach a different corner of your audience or present science in a different sort of way?

The fact that I am approachable and pretty down to earth has allowed me to reach corners of society that more distant and fancy scientists would never even consider. For instance, I am going to a small university to give a talk.  Some of my friends ask why I even bother, especially considering that this insitution is not the most renowned university.  But, I feel the opposite – it is these corners that need the influence the most!  Similarly, when I go to Hispanic high schools, many of the mothers have never seen a scientist.  And there I am, a scientist from Mexico, speaking to them and their kids.  It is that powerful combination of being a smart and warm female that can be shocking, which is cool.

In line with this, there was an experiment where women were asked to draw a female scientist.  Most drew a plain, relatively unattractive woman.  Immediately when you break that mold, it has an incredible effect.  People say, “Hey! She kind of looks like me and she dresses like me.  Maybe I can do science too!”  Some girls are afraid that by being smart, boys won’t talk to them.  My femininity allows me to be a voice in a field that has tended to isolate themselves from the public, which is bad. Some of my colleagues have become a little snobbish.  The fact that I have serious credentials (PhD and 2 postdocs) shows that I had to work like crazy – looks and personality can only go so far.  It s hard work that gets you there! Serious science communication has a lot of math and problem solving in order to explain things accurately to the public. So I still feel like I am doing science!

   

   

Double Xpression: Karyn Traphagen, co-founder of ScienceOnline

Hanging out with Al.

Karyn Traphagen is the Executive Director of ScienceOnline Inc., a non-profit organization representing a diverse science community that cultivates conversations both online and face-to-face. At face-to-face events, including a perennially popular signature conference in North Carolina, ScienceOnline encourages creativity, collaborations, connections, and fun. Through social media, the ScienceOnline community listens, supports, shares, recommends, and reaches out. ScienceOnline also develops tools such as ScienceSeeker news river and curates The Open Lab, an annual anthology of the best science writing on the web.

Karyn previously taught physics at the high school, undergraduate and graduate levels. As a teacher, she sought to connect the science of the curriculum with the everyday life of her students and to instill lifelong skills for learning. Karyn completed graduate work at the University of Virginia and also studied at the University of Stellenbosch (South Africa). She has trained physics teachers through the University of Virginia’s Physics department and traveled to South Sudan to conduct professional development training for local teachers. She has more than 10 years of experience developing and teaching online courses.

In addition to her science work, Karyn maintains a freelance graphic design studio. Her latest project was a work on Ancient Near Eastern royal inscriptions.

Karyn lives in Durham, North Carolina, and she encourages readers wherever they are to Stay Curious at her blog. Connect with her on Twitter or Google+. You can also follow ScienceOnline on Twitter and Google+.  [Editor's note: Karyn is also an official ADK46er, which is pretty incredible.]



DXS: First, can you give me a quick overview of what your scientific background is and your current connection to science?

Karyn enjoys creating art with…LEGOS!

I remember one of my favorite childhood gifts was a chemistry set and a microscope. My mother was a great role model. She left a job as a chemist to get married and raise a family, but she always instilled in me the attitude that if I was interested in any subject, I could learn it and do it. I always accepted a challenge.

Although I attended excellent public schools, I had to overcome some significant challenges. Our family was one of the only ones in our town designated as eligible for the new free lunch program, and I started high school when Title IX was passed (go ahead, do the math). This was an exciting time for girls in school–but not just for sports (our legacy to our 8thgrade class was a change in our public (!) school policy to allow girls to wear jeans).

I was thrilled to be the one of two females on our Math League squad and to have access to advanced science courses and labs in high school. It seems I always took a circuitous route though. I helped change the rules so that I could graduate in 3 years. I was very fortunate to have lots of opportunities after graduation (including being recruited for the first female class at West Point). But then, I took on other responsibilities and went back to school later to finish my degrees.

In addition to research, I have taught high school physics and physical science, undergrad physics (I especially liked the Physics for Non-Science majors!), and helped to develop a degree program in the university physics department for high school physics teachers. I’ve led sailing trips in the Bahamas for biology students and I’ve been trained by the American Meteorological Society to use live data in classrooms. I’ve even been a programmer. Obviously I’m interested in too many things for my own good.

Currently, I am the Executive Director of ScienceOnline, a non-profit organization that facilitates discussion about science through online networks and face-to-face events. We welcome all to the conversation – scientists, journalists, librarians, educators, students, and anyone interested in engaging in science. Four words that help to define ScienceOnline are: Connections, conversations, collaborations, and community. We also develop projects that work to connect scientists and their research to the public. I’m thrilled to be representing this thriving community, and I enjoy working with so many talented, brilliant, and fun people.

Karyn has traveled to South Sudan to conduct professional development training for local teachers.

DXS: What ways do you express yourself creatively that may not have a single thing to do with science?

I have an insatiable thirst to learn and try new things, which has resulted in a string of very diverse jobs. Over the years my creative activities (and jobs) have included medieval calligraphy, art, photography, mathematics (I count this as creative), LEGO creations, graphic design, garment creation, gardening, construction projects, violin/guitar (as musician and also instructor), studying ancient languages and writing systems (both real and created).

On the surface, many people think these are not “science-y” but really, they are all about science. Seeing that connection is something I love to introduce people to. My science career has included research that helps create more bio-fidelic crash test dummies (I worked with cadavers–this makes for great party stories), meteorology, high school physics teacher, and university physics instructor. I used to think that people would think I was flighty or unable to commit to a project. Now I see the benefits of having been successful at so many different skills and fields of study. The key was seeing how they all tapped into my curiosity and creativity.

DXS: Do you find that your scientific background informs your creativity, even though what you do may not specifically be scientific?

Definitely. Paying attention to the details of the world gives me opportunity to see beauty, symmetry, order, and chaos in unusual places. I am thrilled by the macro and the micro vision of our universe and lives (which is why I continue to study other fields of science in addition to physics). These are not only realms to explore with experiments, but to experience emotionally and to communicate creatively. I have learned to appreciate the details in science and that carries over into the art, photography, design, and construction projects that I may spend time on. Even my tattoo (snow crystals) reflects both beauty and science (and a lot of personal meaning too!)

DXS: Have you encountered situations in which your expression of yourself outside the bounds of science has led to people viewing you differently–either more positively or more negatively?

I think that sometimes the more conventional creative side of my life makes me seem more “human” and approachable. When non-science people ask what I do, I don’t usually start with “physics” in the answer because that often is hard for people to relate to and the conversation dies. But if they get to know some things I am interested in or the diversity of things I’ve created, and THEN learn about my science background, they are more likely to perceive me as more than a physics geek. At that point they feel more comfortable asking questions about science.

On the other hand, some of my science colleagues in the physics department saw those other activities as something that took me away from time that could be spent on physics. Even if they thought my non-science activities might be amazing they minimized their value. Thinking back now, maybe this is why I keep so much of what I do to myself and it takes time to draw out of me all the things that I have had the joy of learning and doing.

I think there is a geek aspect to many of the things I like to do. They don’t completely overlap with the same brand of geekiness though. It’s just that you align yourself with a community that is very engaged in a certain niche. A tribe if you will. Some of these tribes don’t understand each other very well, so I sometimes feel like an ambassador of the various communities I am a member of.

DXS: Have you found that your non-science expression of creativity/activity/etc. has in any way informed your understanding of science or how you may talk about it or present it to others?

Karyn collecting water samples in Molokai, Hawaii

Yes, I used to focus more on the narrow aspects of my field. Now I try to see interconnectedness—not only with other fields of science, but more broadly with day-to-day life. My “non-science” expressions are really gateways into understanding the science better or being willing to think more creatively about how to solve a research problem. Bottom line: I always want to stay curious. We don’t value curiosity enough. I think curiosity undergirds creativity. Curiosity doesn’t just beget science questions. We also have to ask, “What would happen if I mixed these colors together?” or “How small can I write with this pen nib and ink?” or “What kind of effects can I create in this photograph by changing the lens?”

DXS: How comfortable are you expressing your femininity and in what ways? How does this expression influence people’s perception of you in, say, a scientifically oriented context?

I really tried to think about this carefully. In the physics department at the university where I worked, my main concern was not the fact that I was in the minority (or that there were more men’s rooms in the building), but that the lab was freezing and I needed to keep warmer layers at work to survive! Basically, the lab protocols determined what kind of clothing and shoes I could wear, how I kept my hair (out of the way!) etc. I never felt those things were anything particularly against being feminine, but I didn’t go out of my way to wear makeup or dress special.

On the other hand, I do think that female visitors and students who dressed more feminine were definitely treated differently. I desperately wanted to be valued for my ideas and work ethic and not what I looked like or which bathroom I used, so I was probably more affected by others attitudes than I realize(d).

Probably the most feminine thing I’ve ever done was to have children and show my priority for them (I realize that there are fathers who do this too, so it may be more a parent thing than a feminine thing, but in the society I live in, it is still the mothers who bear the lion’s share of the responsibility for child-rearing). I had colleagues who could not understand some choices I made because of family. They felt I was wasting my potential (whatever that means!).

Now that I am not in a lab and don’t have small children at home, I alternate between tomboy and professional attire. I do like that it is easier to create a more feminine professional wardrobe these days.

I find it odd that women are complimented for their appearance more than men. I don’t think people realize how out-of-balance this is. I try to notice and mention men’s clothing and appearance as a small step toward equalizing that.

DXS: Do you think that the combination of your non-science creativity and scientific-related activity shifts people’s perspectives or ideas about what a scientist or science communicator is? If you’re aware of such an influence, in what way, if any, do you use it to (for example) reach a different corner of your audience or present science in a different sort of way?

I think that getting the attention of whatever audience you are addressing is paramount. You may have something wonderful to share, but if you don’t have their attention, it will fall to the ground. I want to develop a relationship with people in order to get them to trust me, believe me, and be interested in what I have to say. Dispensing information is not enough.

The manner in which I communicate makes all the difference in how the person will engage the topic. To do this, I need to listen first and understand who my audience is. Using creativity, I will then try to connect with each person or audience in a way that I hope will best bring them along the journey I have experienced. Some people will want to know more specific details, others will want to know how it affects their lives, and still others will challenge and question my thoughts and methods.

Using visual arts (e.g. fine arts, video, etc) can be as important as a data chart. As long as the conversation continues, then I have been successful in communicating. My goal is to make someone (whether a researcher or a teenager) so interested that they will take on a search for more information on their own. That’s really how we learn and retain best—to explore something we have invested our own time in.

I also use a variety of outlets for communication. There are definitely important and different roles for journals, conference presentations, Twitter, blogs, Google+, etc. These diverse outlets are just as important as creative ways of presenting material. Again, you must always be aware of your audience. I would use a museum’s Twitter account to communicate differently than I would my regular account.

DXS: If you had something you could say to the younger you about the role of expression and creativity in your chosen career path, what would you say?

Knowing myself, I’m not so sure that the younger me would listen to any advice I would give! In some ways, going through the experiences is what made me who I am and there are no short cuts for that. However, there are definitely things that would have been great to learn earlier on.

So, I would tell the younger me not to try to keep creative interests and career objectives separate or think that they have to be at odds with each other. They don’t need to be in competition for your attention. Creativity, job skills, life experiences, and responsibilities can interweave. You will not only be more content, but probably more productive in all your endeavors.

I would also tell her that “no” is not a dirty word and that it is ok to be selective in how you spend your time.