As I sit and type this in my study, I can hear my cats crashing around the living room, which is around the corner from me. There’s a wall between us, so I can’t see them or shoot them with my water pistol (which I would be tempted to do if they were in the same room, before they knock over something fragile). So, just like in my earlier post on mirrors, we’ll start with a question: why can I hear my cats around the corner, but not see them? Both sound and light are waves, but the way we perceive those waves are very different. I don’t just mean the organs we use – eyes and ears do have major biological differences – but how the characteristics of those waves differ. We perceive differences in light through color, and differences in sound through pitch, but in the end these characteristics mean the same thing: they’re a measure of how big the wave is. The technical term for this is its wavelength: the distance it takes for a wave to start repeating itself. For visible light, red has the longest wavelength, while violet has the shortest. In between you get the other colors of the rainbow, and if you mix them all together you get white light. Visible light wavelengths are between 400 and 700 nanometers, which is smaller than bacteria (which themselves are smaller than cells in our bodies)! Wavelengths smaller than 400 nanometers get into ultraviolet, X-ray, and gamma-ray territory; wavelengths greater than 700 nanometers comprise infrared, microwaves, and radio waves. For sound, the situation is a little messier, since our ears respond to frequency, not wavelength. The specific wavelength of sound depends on the temperature and humidity of the air, but if we assume dry room-temperature air, a low-pitched sound has a wavelength of about 17 meters and high-pitched sounds have wavelengths around 2 centimeters. That’s a big range, and not all those sounds will travel around corners. Shorter wavelengths are ultrasound, which are probably most familiar for tracking the health of fetuses: these sound waves can penetrate or reflect off tissue, and by measuring the waves that bounce back, doctors can track blood flow and other developmental processes inside your body. (X-rays go right through soft tissues, so they’re better for looking at bones.) Longer wavelengths are infrasound; animals like elephants use these very low-pitched sounds for communication across long distances. When a wave meets an opening like a door, it can experience something known as diffraction: the wave passing through the opening spreads out on the other side. However, the wave doesn’t just come through the center of the door: it makes a bunch of waves along the length of the opening, and those waves actually interfere with each other. The wider the door, the more of these new waves are made. The image to the right shows the interference pattern from a red laser shining through a very narrow opening (smaller than a millimeter). The central maximum is where most of the light coming through the opening ends up, but you also have dark spots where the light interferes and cancels out. The secondary spots on either side of the maximum are much less bright, and you also get tertiary and smaller spots that are fainter still. You get the same pattern for sound, though for obvious reasons I can’t show you a picture of it! The only difference is you exchange brightness for loudness, and dark spots for places where the sound is silenced. The width and intensity (brightness or loudness) of the spots depend on the ratio of the wavelength to the size of the opening. If the wavelength is bigger than the opening, there isn’t diffraction; if the wavelength is about the size of the opening, then you get strong diffraction, and the central maximum is a lot wider than the opening. If the wavelength is much smaller than the opening, then the central maximum is quite small, and since the secondaries, tertiaries, and so forth are fainter still, the pattern may be hard to detect. So there’s our answer! A typical doorway is around a meter wide (a little less, usually), so sound with its relatively large wavelengths will create a big central maximum and sufficiently-loud secondaries. That can be enough to hear even if you aren’t in a straight line with the hooligan cats in the other room. A corner is just a very wide doorway, so everything I’ve said about doorways carries over to them too. Visible light has very small wavelengths, so while you do get light diffraction through doorways, you’d need a microscope to see the pattern! If you have a strong light shining through the door, you’ll get a nice rectangular blaze of light on the opposite wall, but it’s not much bigger than the door, and doesn’t go around corners. However, if you have a cell phone or a cordless phone, the signal from those definitely can go around corners: those are based on microwaves or radio waves, which have much larger wavelengths than visible light. Similarly, elephants communicate via infrasound over huge distances because rocks, trees, and other obstacles are smaller than the wavelengths they use, so the sound just diffracts right around them. Very handy! Tigers use roars to establish territories, and since they live in dense forests, again infrasound lets their growls travel around the trees easily. (We humans may not hear the infrasound part of the roar, but we can definitely feel it. The lowest notes from large pipe organs or tubas are below our normal hearing range, but they still can contribute to the overall sensation of a musical piece.) There is one place where diffraction does play a role in our vision: our eyes themselves. Doorways are too big for diffraction, but the pupil in a human eye is about 2 millimeters across, varying depending on whether we’re in a bright or dark place. The size of the central maximum of light cast on our retina is part of what determines how well we see. Diffraction also is why radio telescopes need to be very large, but why an ordinary visible light telescope you might have doesn’t need to be huge – yet the larger it is, the more clearly you’ll be able to see distant planets and galaxies. The telescope is like a big window, so you want to match the size of the window to the wavelength of the light you’re viewing. Now if you’ll excuse me, I need to go make sure my cats haven’t wrecked the living room.
The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.
The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.
Big Molecules with Small Building Blocks
The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.
We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.
You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.
When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.
Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.
The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.
Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.
On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.
The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!
If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.
The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?
If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.
In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.
Sugar and Fuel
A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.
Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.
Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.
Polysaccharides: Fuel and Form
Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.
Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.
Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.
Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.
The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.
Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.
The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.
That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.
These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.
Lipids: The Fatty Trifecta
Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.
Fats: the Good, the Bad, the Neutral
Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?
Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows. Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.
Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.
Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.
Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.
The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.
You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.
In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.
A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.
Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.
Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.
Phospholipids: An Abundant Fat
You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.
Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.
There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.
Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.
The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.
Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.
Steroids: Here to Pump You Up?
Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.
But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.
Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.
Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.
As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.
Levels of Structure
Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.
For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.
This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.
Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.
The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.
In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.
A Plethora of Purposes
What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.
As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.
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.
It’s that time of the year in the U.S. – when we blow up pretty bombs in celebration of the approval of the Declaration of Independence, declaring the independence from the Kingdom of Great Britain. Around this time of year, there is no dearth of articles about the chemistry of fireworks, but the chemistry editor here could not let her secret love of this topic pass by.
What is an explosive? An explosive is a combination of materials that when reacted produce an abundance of light, sound, heat, and pressure. A firework encompasses all 4 of those: we are familiar with the light – the whole reason we view fireworks, we are familiar with the sound – the boom that follows especially large displays, we are familiar with the pressure if we are close enough – that’s the force that pushes into you and the “shock wave” pictured in movies after large explosions; and we are familiar with the heat – ever held a sparkler?
There are three main types of explosives: chemical, nuclear, and mechanical. The bulk of this post will focus on chemical explosives with a short bit about nuclear and mechanical.
If we start at the beginning – well, we’ll skip to the “accepted” first explosive – black powder. Black powder, also called gun powder and the precursor to fireworks, is coined a chemical explosive. Chemical explosions generally fall into a specific classification of chemical reactions called oxidation.
The earliest definition of oxidation was the addition of the element oxygen to a compound, also called combustion. Due to limits of this definition, it was later changed to be the loss of electrons from an element (within a compound.) The original definition can easily be shown in terms of explosives. The simple mixing of hydrogen and oxygen with the addition of just a bit of heat, will form water in an explosive display:
2H2 + O2 –> 2H2O
The little flame used to catalyze the reaction in the video is actually much more energy than is necessary to cause this reaction to occur, but it’s difficult to get an even littler source of heat and safely demonstrate this reaction. You might also note a lot more energy comes out of that reaction once started in terms of light and heat and sound. I’ve been the one lighting that reaction in a demo without both ears plugged and I couldn’t hear out of one ear for the rest of the lecture.
If we focus on the loss of electrons version of oxidation, we get specific colors. This is what the flame video by The Fabulab focused on in their entry for Alan Alda’s Flame Challenge. I direct your attention to 1:08 and the discussion of electrons.
Metals are the simplest example (and most used) example of oxidation as the loss of electrons and the color change associated. Because some electrons are lost, we now have a different set of electrons changing energy and a different color appears.
From here, it is easy to see how fireworks fall into this category of explosives. Fireworks are always being further refined to produce a specific set of light and sound. For a bit more information, this video gets fairly specific.
The vast majority of explosives in use today are considered chemical explosives. This covers a range of materials, including the aforementioned black powder and fireworks, nitroglycerin, dynamite, plastic explosives (C4 for Mythbusters and sci-fi television show fans), and the ones with water now restricting the amount of water one is allowed to bring onto an airplane in the U.S.
Another type of explosive is a nuclearexplosive. The energy in these explosives come from a nuclear reaction. Wikipedia differentiates types of nuclear explosions into stellar and man-made. Another way to differentiate nuclear reactions is by fission and fusion. The explosions at the heart of stars fall under nuclear fusion and are called stellar nucleosynthesis.
Nuclear fusion is the process of forcing 2 atoms into 1 new, larger atom. The CNO cycle, diagrammed here, is one of the nuclear fusion reactions occurring in stellar nucleosynthesis.
Nuclear fission is the process involved in nuclear weapons.
Nuclear fission is the process of dividing an atom into 2 or more smaller atoms. In both nuclear fusion and nuclear fission processes, specific types of radiation are emitted because the new atoms produced do not have the same energy as the starting material. The radiation emitted in these reactions is not just from a change of electrons but from a change from the nucleus of the atom. This emission of radiation is part of the light and heat from the sun and the light and heat of a nuclear bomb.
The third and last type of explosive I will cover is a mechanicalexplosive. These explosions occur as a purely physical process, but can then incite a chemical explosion. Mechanical explosions occur due to a sudden release of a build up of pressure. A specific kind of these explosions are under conditions where a liquid is pressurized in a vessel and a rupture brings it above its boiling point, called a boiling liquid expanding vapor explosion, BLEVE. Steam powered trains were sometimes damaged by these type of explosions. An explosion of a water heater falls into this category. Mechanical explosions are the rarest and perhaps least covered types of explosives.
Water heater explosion by the Mythbusters.
These views are the opinion of the author and do not necessarily either reflect or disagree with those of the DXS editorial team.
Dolphins have been trained to mimic people, but the fellow in this recording apparently picked up human-sounding lingo on his own. Researchers describe his acquisition as self taught. According to this BBC story, the way the white whale pulls it off isn’t easy–he had to really work at it in a pretty un-beluga-like way to get his voice so much lower than the normal beluga vocalization. You can listen to the typical beluga talk, which sounds like a dyspeptic piglet trapped by a creaky door here. It sounds. Ed Yong at Not Exactly Rocket Science tells us these whales are sometimes called “sea canaries” but that they usually sound like children in the distance.
To me, this human mimicry sounds like nothing as much as men on a fishing boat, hollering at each other over the wind, just as they might sound to ears underwater. In fact, the way the researchers found NOC, according to the BBC story, was when a diver surfaced, thinking he’d heard someone tell him to get out.
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 waswas 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?”
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 undergradin 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!
Today’s post is long. It’s long because it involves the winding path that science can take from ignition to exploding into the public view… and how the twists and turns in that path can result in a skewed representation and understanding of the science. Read the whole thing. It focuses on an example that involves autism–which seems to pop up in skewed representations every day–but certainly this path from science to you, the consumer, happens with scientific information in general. The author is Jess, who blogged this originally at “Don’t Mind the Mess” and graciously gave us permission to reproduce it here. Jess, an attorney with a B.S. in biochemistry, parent of an autistic child and brand new baby, and self-described “Twitter fiend,” tweets as @JessicaEsquire.
I am putting my foot down.
As the parent of an autistic child I hear a lot about vaccines and about half a million other things that people think cause autism.
I’m hyperaware of the attention autism gets in the media. So I know about the CDC’s new stats on autism rates. I know about the debate on whether the increase in autism is due to more awareness and diagnosis or more actual occurrences. (Personally, I find the former to be a serious factor, though who’s to say how much.) And I see all the articles that come out week after week about the millions of things that are linked to autism.
There’s a recurring problem here. Valuable research is done. Research is disseminated. Information is reported. Articles are read. Findings are spread. What starts in a lab ends up in a Facebook status. What starts as truth ends up as mistruth in something like a child’s game of telephone. Along the way, piece by piece, truth fades away in favor of headlines and pageviews and gossip.
It’s getting just plain stupid. I’m starting to suspect these articles have nothing to do with serious research but with a search for traffic and hype, an attempt to ride the wave of a trendy topic as concerned parents read every horror story they can find.
A particularly egregious one came up recently. This one doesn’t just cite some random correlation. This one is just plain making things up. The problems here just pile one on top of the other. So let’s consider it piece by piece, a case study in how real research becomes misinformation.
Part One: Research
It starts with scientists. It starts with research. They write up their findings and publish them in a peer-reviewed scientific journal. In this case there are several papers published over a few years about chemicals and their link to brain development. They cover a wide variety of issues and present a wide variety of conclusions. All of them suggest further study.
Maybe they have bad methodology or use statistics incorrectly. Only a few people would ever know the difference. That’s not my concern today. Bad science is one thing, but bad information on good science is another. So let’s assume we have good, solid science in this research.
Part Two: The Conference
Scientists and researchers with similar interests get together and discuss their findings. It’s not that difference from any other conference. There are panels and presentations.
Part Three: The Op-Ed
Next, a group that works on environmental hazards for children publishes a paper. Not a research study but an op-ed in a peer-reviewed journal. In this op-ed they review the conference from Part Two and encourage the study of environmental factors and their relationship to neurodevelopment disorders. Autism is one of many neuro-ish disorders and is mentioned by name in the piece and its title. It’s unclear to me why they zero in on autism. They have a couple vague pieces of evidence that are autism-specific, but the vast majority of what they’re looking at has never been demonstrated to have any kind of relationship to autism, not even a correlation.
Problem #1 is the unnecessary autism name-checking. Problem #2 is much worse, it’s the list of 10 chemicals they suggest for future study. The list itself isn’t a bad idea, I guess. They’re suggesting places for potential research, which certainly needs to be done. But it does reek a little bit of the kind of thing magazines do, you know what I mean, 10 Ways To Get Your Guy All Fired Up! and such. Still, it’s their prerogative.
So let’s examine their evidence for these suggestions. They cite at least one paper for each of these chemicals. I checked them all. The vast majority of them have never shown any connection to Autism (or even ADHD, another diagnosis they name-check). In fact, many of them show that with exposure to these chemicals, the outcome differentials between exposure and non-exposure is 5 IQ points.
FIVE IQ POINTS. Statistically significant? Perhaps. Practically important for a parent? No.
IQ itself is a strange and vague thing. And 5 points isn’t going to move your super-genius down to the level of an average person They’d still be a super-genius. And adding 5 points to someone with severe deficits isn’t going to make them average, either. It’s hard to imagine what difference you’d see between two people whose IQ’s are 5 points apart.
Such statistical differences may well be a sign to warrant further study. And they may be a sign that these chemicals affect neurological development. But it’s getting a bit ahead of ourselves to say they are suspected of being tied to autism. Many of these papers are in areas of research that are just beginning. Many of them involve homogeneous groups (for example, all the participants are Mexican-American migrant workers) which makes issues of genetics and heredity very difficult to account for. Many involve parents self-reporting by filling out surveys rather than having the children examined by professionals.
Let’s be fair. These are the very beginnings of research. You’ll need to do all sorts of rigorous testing and consideration to make real connections. Of course more research is needed. And it’s important that we keep that in mind as we move forward.
(Though, of course, no one else will.)
Part Four: The Press Release
The op-ed is about publicity so it’s the beginning of the problem. But it gets worse.A press release comes out with the list of ten chemicals and already the twisting starts. These are chemicals suggested for further research, but suddenly they’re a ”List of the Top Ten Toxic Chemicals Suspected to Cause Autism and Learning Disabilities.” This, unsurprisingly, is the headline you’ll see all over the internet when news organizations report on the press release. Already it’s turned from suggestions for research into a watchlist.
It gets worse. The press release has this second headline:
The editorial was published alongside four other papers — each suggesting a link between toxic chemicals and autism.
No, actually that’s not at all accurate.
Let’s start with the first paper, which examines the possibility of a connection between maternal smoking and autism. What’s their conclusion?
The primary analyses indicated a slightly inverse association with all ASDs[.]
What does that mean? Among the autistic kids vs. regular kids, there was actually LESS maternal smoking in the autism group. The paper does point out that when it comes to “subgroups,” for instance high-functioning ASD or Asperger’s, there may be a possibly positive relationship. But there are so many caveats I can’t even get to them all. Let’s just take this one:
The ASD subgroup variables were imperfect, relying on the child’s access to evaluation services and the documentation by a myriad of community providers, rather than direct clinical observation.
This means that when they’re saying some groups of ASD kids may have this relationship, they didn’t actually classify these kids. They never saw these kids. They’re relying on data collected by other people. Not even by a consistent set of people. It comes from 11 different states and who knows how many providers. Who’s to say how accurate any of it is. And who’s to say whether these kids are correctly classified at their particular place on the spectrum.
So take all that with a whole jar full of salt and you’re still looking at, overall, no connection with smoking. If anything, the data would indicate smoking has LESS autism rather than more.
After this there are 2 papers on the same chemical. One of them does not contain the word “autism” anywhere. (One of its references has it, but nowhere does it appear in the text of their paper.) The second paper is better. It focuses on the chemical’s effects in particular processes which have been linked to autism. This is very micro-scale science, there are no people involved, just cells and chemicals. It’s important research, but there’s a long stretch between cellular interactions and a person’s diagnosis. It didn’t involve any analysis with autistic individuals. This is certainly the most useful paper of the bunch by a long shot, but it still just sets the stage for further research.
The fourth paper is a review. That means it asserts no new information but summarizes the research on a particular issue, specifically pesticides and autism. Technically I suppose it does assert a link, but none of this is new information.
So I think we’ve pretty much destroyed the headline in that press release. There were not 4 articles suggesting a connection between chemicals and autism.
Is it likely that the writers who take this press release and write articles on it are going to read the papers it cites? Are they going to realize that what they’re saying isn’t actually true? They should. Of course they should. But they don’t.
This list has chemicals suspected of being tied to neurological development. And we should just leave it at that. It’s not that they shouldn’t be studied. They should. But we shouldn’t be throwing out buzzwords like ADHD and Autism when the research doesn’t show any firm data.
Part Five: News Articles
This is a process, though. First research, then op-ed, then press release and finally news articles. So what’s the headline of our news article? “Top 10 Chemicals Most Likely to Cause Autism and Learning Disabilities.” Guilty of serious fearmongering, no? A more accurate title may be: Researchers propose list of chemicals potentially tied to neurological development for further study. But I doubt anyone’s going to write that.
The article itself, to be fair, is full of caveats. The reasons for the increase in autism are “controversial.” There is a “gap in the science.” But then you get a sentence like this:
But clearly, there is more to the story than simply genetics, as the increases are far too rapid to be of purely genetic origin.
Clearly? Clearly says who? What source says it’s too rapid? The author certainly isn’t a reliable source. She is Robyn O’Brien, a writer for Prevention who posted this article. Her scientific credentials are nonexistent. She is a former financial analyst who now writes about the food industry. She has an MBA, and her undergraduate was in French and Spanish.
Full disclosure: I have a B.S. in Biochemistry, but I feel I’m unqualified to write this article. I’d much rather it be written by someone with a PhD. I’m married to a PhD, which has given me a lot more exposure to science since leaving school, but I fully acknowledge that I shouldn’t be the one doing this. I know how to read a scientific article and examine its conclusions, but I certainly am not someone who can tell you if their methods and analysis are correct.
But I’m talking because there aren’t enough people talking about it. Because the PhD’s aren’t generally science writers. They are scientists. They write about their research in journals, not in the newspaper. And certainly not on a blog for a healthy living magazine.
The author goes on to restate the inaccurate subheadline of the press release verbatim.
In the end she suggests things like buying organic produce, opening your windows and buying BPA-free products.
This is part 5 of our process, but it’s where many of us start. Many of us will only read this article and not the press release or the op-ed or the research papers. Most of us aren’t qualified to do so, all we have is this article. Well, we have that and what other people tell us. Which leads us to our next step.
Part Six: Readers
The article is frustrating, but I can only get so mad. She is saying what the scientists told her to say. She has even included some cautionary language. The problem is that when writing for laymen, you have to be careful.
And with AUTISM? You have to be really careful. Just for you I’m going to venture into the comments to this article to show you how people have responded.
–How about we quit injecting our kids with aluminum, formaldehyde and the rest of the toxic stew that they call vaccines — we bypass every natural defense our bodies have (skin, saliva, stomach acid) to put these things directly in the blood stream.
–Thank you Robyn for always providing sound information to continue guiding our decisions.
–What about heavy metals like Arsenic that are trapped in soils that our “organic” brown rice is growing in to be made into brown rice syrup to sweeten organic foods and baby formula? Not to mention the reports coming in regarding the radiation and contamination from Fukushimi that has reached the west coast an is spreading across this country in the produce and even the pollen…
–Unvaccinated children are some of the healthiest little people on the planet. As far as the Autism link, who really knows but why risk it.
–Thank you for this information. It confirms to me that we should keep doing what we are doing. It also helps me to enforce our no shoes policy in our home. Some people are so disrespectful and just don’t take them off and I hate to sound like a nag and ask even though they already know its what we prefer.
Thankfully there are some people in there who take the writer to task, but how is a reader to trust any one commenter over another? You have no way of knowing from a comment what someone’s experiences or qualifications are.
There’s a reason we need responsible scientific reporting. I’m all for the open dissemination of information, but I’m also aware of what happens when people read something they don’t understand.
I encountered this FB conversation the other day. Usually I overlook such things but I could not help myself. I jumped in. I tried hard to be polite and present facts. When all that was over, no one was convinced. The response?
Enough articles on vaccines and people are scared even without evidence. Enough headlines and people don’t bother reading articles. It doesn’t matter how much is retracted or debunked, the damage is done.
We need responsible science reporting. We need responsible reporting, period. I’ve seen plenty of lazy articles on Supreme Court opinions that lead me to read the opinion myself only to realize that they’ve stated the conclusions all wrong.
I don’t want to go on all day, but I do feel like it’s important for us to put our foot down and demand better.
We aren’t all scientists. But we can ask for science writers with the appropriate qualifications. We can ask for links and citations in their articles. (I spent quite some time tracking everything down for this post, and luckily I’m relatively familiar with looking up scientific articles online.) We can ask for articles that show failed connections. It doesn’t all have to be “Autism linked to X” there’s plenty of “Autism not linked to Y” that happens in these studies but you never see that, do you?
As for us laymen, we have to find our own trusted experts. Ask your pediatrician. And if your pediatrician’s not qualified (most of them are MD’s but not PhD’s) ask them if they have a trusted source. Track down specialists in Autism with PhD’s and ask them what they think of the research. Find reliable books and articles and spread them to your friends. We can’t necessarily do a lot, but we can do our part to stop the spread of misinformation and demand better.
These views are the opinion of the author and do not necessarily either reflect or disagree with those of the DXS editorial team.