Frankenstorm: What is the role of climate change?

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

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

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

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

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

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

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

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

By Emily Willingham

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

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

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

Biology Xplainer: Evolution and how it happens

Evolution: a population changes over time
First of all, in the context of science, you should never speak of evolution as a “theory.” There is no theory about whether or not evolution happens. It is a fact.

Scientists have, however, developed tested theories about how evolution happens. Although several proposed and tested processes or mechanisms exist, the most prominent and most studied, talked about, and debated, is Charles Darwin’s idea that the choices of nature guide these changes. The fame and importance of his idea, natural selection, has eclipsed the very real existence of other ways that populations can change over time.

Evolution in the biological sense does not occur in individuals, and the kind of evolution we’re talking about here isn’t about life’s origins. Evolution must happen at least at the populationlevel. In other words, it takes place in a group of existing organisms, members of the same species, often in a defined geographical area.

We never speak of individuals evolving in the biological sense. The population, a group of individuals of the same species, is the smallest unit of life that evolves.

To get to the bottom of what happens when a population changes over time, we must examine what’s happening to the gene combinations of the individuals in that population. The most precise way to talk about evolution in the biological sense is to define it as “a change in the allele frequency of a population over time.” A gene, which contains the code for a protein, can occur in different forms, or alleles. These different versions can mean that the trait associated with that protein can differ among individuals. Thanks to mutations, a gene for a trait can exist in a population in these different forms. It’s like having slightly different recipes for making the same cake, each producing a different version of the cake, except in this case, the “cake” is a protein.
Natural selection: One way evolution happens

Charles Darwin, a smart, thoughtful,
observant man. Via Wikimedia.
Charles Darwin, who didn’t know anything about alleles or even genes (so now you know more than he did on that score), understood from his work and observations that nature makes certain choices, and that often, what nature chooses in specific individuals turns up again in the individuals’ offspring. He realized that these characteristics that nature was choosing must pass to some offspring. This notion of heredity–that a feature encoded in the genes can be transmitted to your children–is inherent now in the theory of natural selection and a natural one for most people to accept. In science, an observable or measurable feature or characteristic is called a phenotype, and the genes that are the code for it are called its genotype. The color of my eyes (brown) is a phenotype, and the alleles of the eye color genes I have are the genotype.

What is nature selecting any individual in a population to do? In the theory of natural selection, nature chooses individuals that fit best into the current environment to pass along their “good-fit” genes, either through reproduction or indirectly through supporting the reproducer. Nature chooses organisms to survive and pass along those good-fit genes, so they have greater fitness.

Fitness is an evolutionary concept related to an organism’s reproductive success, either directly (as a parent) or indirectly (say, as an aunt or cousin). It is measured technically based on the proportion of an individual’s alleles that are represented in the next generation. When we talk about “fitness” and “the fittest,” remember that fittest does not mean strong. It relates more to a literal fit, like a square peg in a square hole, or a red dot against a red background. It doesn’t matter if the peg or dot is strong, just whether or not it fits its environment.

One final consideration before we move onto a synthesis of these ideas about differences, heredity, and reproduction: What would happen if the population were uniformly the same genetically for a trait? Well, when the environment changed, nature would have no choice to make. Without a choice, natural selection cannot happen–there is nothing to select. And the choice has to exist already; it does not typically happen in response to a need that the environment dictates. Usually, the ultimate origin for genetic variation–which underlies this choice–is mutation, or a change in a DNA coding sequence, the instructions for building a protein.

Don’t make the mistake of saying that an organism adapts by mutating in response to the environment. The mutations (the variation) must already be present for nature to make a choice based on the existing environment.

The Modern Synthesis

When Darwin presented his ideas about nature’s choices in an environmental context, he did so in a book with a very long title that begins, On the Origin of Species by Means of Natural Selection. Darwinknew his audience and laid out his argument clearly and well, with one stumbling block: How did all that heredity stuff actually work?

We now know–thanks to a meticulous scientist named Gregor Mendel (who also was a monk), our understanding of reproductive cell division, and modern genetics–exactly how it all works. Our traits–whether winners or losers in the fitness Olympics–have genes that determine them. These genes exist in us in pairs, and these pairs separate during division of our reproductive cells so that our offspring receive one member or the other of the pair. When this gene meets its coding partner from the other parent’s cell at fertilization, a new gene pair arises. This pairing may produce a similar outcome to one of the parents or be a novel combination that yields some new version of a trait. But this separating and pairing is how nature keeps things mixed up, setting up choices for selection.

Ernst Mayr, via PLoS.
With a growing understanding in the twentieth century of genetics and its role in evolution by means of natural selection, a great evolutionary biologist named Ernst Mayr (1904–2005) guided a meshing of genetics and evolution (along with other brilliant scientists including Theodosius Dobzhansky, George Simpson, and R.A. Fisher) into what is called The Modern Synthesis. This work encapsulates (dare I say, “synthesizes?”) concisely and beautifully the tenets of natural selection in the context of basic genetic inheritance. As part of his work, Mayr distilled Darwin’s ideas into a series of facts and inferences.

Facts and Inferences

Mayr’s distillation consists of five facts and three inferences, or conclusions, to draw from those facts.
  1. The first fact is that populations have the potential to increase exponentially. A quick look at any graph of human population growth illustrates that we, as a species, appear to be recognizing that potential. For a less successful example, consider the sea turtle. You may have seen the videos of the little turtle hatchlings valiantly flippering their way across the sand to the sea, cheered on by the conservation-minded humans who tended their nests. What the cameras usually don’t show is that the vast majority of these turtle offspring will not live to reproduce. The potential for exponential growth is there, based on number of offspring produced, but…it doesn’t happen.
  2. The second fact is that not all offspring reproduce, and many populations are stable in size. See “sea turtles,” above.
  3. The third fact is that resources are limited. And that leads us to our first conclusion, or inference: there is a struggle among organisms for nutrition, water, habitat, mates, parental attention…the various necessities of survival, depending on the species. The large number of offspring, most of which ultimately don’t survive to reproduce, must compete, or struggle, for the limited resources.
  4. Fact four is that individuals differ from one another. Look around. Even bacteria of the same strain have their differences, with some more able than others to with stand an antibiotic onslaught. Look at a crowd of people. They’re all different in hundreds of ways.
  5. Fact five is that much about us that is different lies in our genes–it is inheritable. Heredity undeniably exists and underlies a lot of our variation.
So we have five facts. Now for the three inferences:

  1. First, there is that struggle for survival, thanks to so many offspring and limited resources. See “sea turtle,” again.
  2. Second, different traits will be passed on differentially. Put another way: Winner traits are more likely to be passed on.
  3. And that takes us to our final conclusion: if enough of these “winner” traits are passed to enough individuals in a population, they will accumulate in that population and change its makeup. In other words, the population will change over time. It will be adapted to its environment. It will evolve.
Other mechanisms of evolution

A pigeon depicted in Charles Darwin’s
Variation of Animals and Plants
Under Domestication
, 1868. U.S.
public domain image, via Wikimedia.
When Darwin presented his idea of natural selection, he knew he had an audience to win over. He pointed out that people select features of organisms all the time and breed them to have those features. Darwin himself was fond of breeding pigeons with a great deal of pigeony variety. He noted that unless the pigeons already possessed traits for us to choose, we not would have that choice to make. But we do have choices. We make super-woolly sheep, dachshunds, and heirloom tomatoes simply by selecting from the variation nature provides and breeding those organisms to make more with those traits. We change the population over time.

Darwin called this process of human-directed evolution artificial selection. It made great sense for Darwinbecause it helped his reader get on board. If people could make these kinds of choices and wreak these kinds of changes, why not nature? In the process, Darwin also described this second way evolution can happen: human-directed evolution. We’re awash in it today, from our accidental development of antibiotic-resistant bacteria to wheat that resists devastating rust.

Genetic drift: fixed or lost

What about traits that have no effect either way, that are just there? One possible example in us might be attached earlobes. Good? Bad? Ugly? Well…they don’t appear to have much to do with whether or not we reproduce. They’re just there.

When a trait leaves nature so apparently disinterested, the alleles underlying it don’t experience selection. Instead, they drift in one direction or another, to extinction or 100 percent frequency. When an allele drifts to disappearance, we say that it is lost from the population. When it drifts to 100 percent presence, we say that it has become fixed. This process of evolution by genetic drift reduces variation in a population. Eventually, everyone will have it, or no one will.

Gene flow: genes in, genes out

Another way for a population to change over time is for it to experience a new infusion of genes or to lose a lot of them. This process of gene flow into or out of the population occurs because of migration in or out. Either of these events can change the allele frequency in a population, and that means that gene flow is another was that evolution can happen.

If gene flow happens between two different species, as can occur more with plants, then not only has the population changed significantly, but the new hybrid that results could be a whole new species. How do you think we get those tangelos?

Horizontal gene transfer

One interesting mechanism of evolution is horizontal gene transfer. When we think of passing along genes, we usually envision a vertical transfer through generations, from parent to offspring. But what if you could just walk up to a person and hand over some of your genes to them, genes that they incorporate into their own genome in each of their cells?

Of course, we don’t really do that–at least, not much, not yet–but microbes do this kind of thing all the time. Viruses that hijack a cell’s genome to reproduce can accidentally leave behind a bit of gene and voila! It’s a gene change. Bacteria can reach out to other living bacteria and transfer genetic material to them, possibly altering the traits of the population.

Evolutionary events

Sometimes, events happen at a large scale that have huge and rapid effects on the overall makeup of a population. These big changes mark some of the turning points in the evolutionary history of many species.

Cheetahs underwent a bottleneck that
has left them with little genetic variation.
Photo credit: Malene Thyssen, via
Bottlenecks: losing variation

The word bottleneck pretty much says it all. Something happens over time to reduce the population so much that only a relatively few individuals survive. A bottleneck of this sort reduces the variability of a population. These events can be natural–such as those resulting from natural disasters–or they can be human induced, such as species bottlenecks we’ve induced through overhunting or habitat reduction.

Founder effect: starting small

Sometimes, the genes flow out of a population. This flow occurs when individuals leave and migrate elsewhere. They take their genes with them (obviously), and the populations they found will initially carry only those genes. Whatever they had with them genetically when they founded the population can affect that population. If there’s a gene that gives everyone a deadly reaction to barbiturates, that population will have a higher-than-usual frequency of people with that response, thanks to this founder effect.

Gene flow leads to two key points to make about evolution: First, a population carries only the genes it inherits and generally acquires new versions through mutation or gene flow. Second, that gene for lethal susceptibility to a drug would be meaningless in a natural selection context as long as the environment didn’t include exposure to that drug. The take-home message is this: What’s OK for one environment may or may not be fit for another environment. The nature of Nature is change, and Nature offers no guarantees.

Hardy-Weinberg: when evolution is absent

With all of these possible mechanisms for evolution under their belts, scientists needed a way to measure whether or not the frequency of specific alleles was changing over time in a given population or staying in equilibrium. Not an easy job. They found–“they” being G. H. Hardy and Wilhelm Weinberg–that the best way to measure this was to predict what the outcome would be if there were no change in allele frequencies. In other words, to predict that from generation to generation, allele frequencies would simply stay in equilibrium. If measurements over time yielded changing frequencies, then the implication would be that evolution has happened.

Defining “Not Evolving”

So what does it mean to not evolve? There are some basic scenarios that must exist for a population not to be experiencing a change in allele frequency, i.e., no evolution. If there is a change, then one of the items in the list below must be false:

·       Very large population (genetic drift can be a strong evolutionary mechanism in small populations)

·       No migrations (in other words, no gene flow)

·       No net mutations (no new variation introduced)

·       Random mating (directed mating is one way nature selects organisms)

·       No natural selection

In other words, a population that is not evolving is experiencing a complete absence of evolutionary processes. If any one of these is absent from a given population, then evolution is occurring and allele frequencies from generation to generation won’t be in equilibrium.

Convergent Evolution

Arguably the most famous of the
egg-laying monotremes, the improbable-
seeming platypus. License.
One of the best examples of the influences of environmental pressures is what happens in similar environments a world apart. Before the modern-day groupings of mammals arose, the continent of Australiaseparated from the rest of the world’s land masses, taking the proto-mammals that lived there with it. Over the ensuing millennia, these proto-mammals in Australiaevolved into the native species we see today on that continent, all marsupialsor monotremes.

Among mammals, there’s a division among those that lay eggs (monotremes), those that do most gestating in a pouch rather than a uterus (marsupials), and eutherians, which use a uterus for gestation (placental mammals).

Elsewhere in the world, most mammals developed from a common eutherian ancestor and, where marsupials still persisted, probably outcompeted them. In spite of this lengthy separation and different ancestry, however, for many of the examples of placental mammals, Australiahas a similar marsupial match. There’s the marsupial rodent that is like the rat. The marsupial wolf that is like the placental wolf. There’s even a marsupial anteater to match the placental one.

How did that happen an ocean apart with no gene flow? The answer is natural selection. The environment that made an organism with anteater characteristics best fit in South America was similar to the environment that made those characteristics a good fit in Australia. Ditto the rats, ditto the wolf.

When similar environments result in unrelated organisms having similar characteristics, we call that process convergent evolution. It’s natural selection in relatively unrelated species in parallel. In both regions, nature uses the same set of environmental features to mold organisms into the best fit.

By Emily Willingham, DXS managing editor

Note: This explanation of evolution and how it happens is not intended to be comprehensive or detailed or to include all possible mechanisms of evolution. It is simply an overview. In addition, it does not address epigenetics, which will be the subject of a different explainer.

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.

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.

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

Giving girls…and science…their due

Respecting both is key to bringing girls into the sciences.

By Susan E. Matthews

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

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

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

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

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.

Why blueberries won’t turn you blue and other blueberry facts

Blueberries. Credit.

by Adrienne Roehrich, Chemistry Editor

Blueberries in the Northwestern semisphere are the fruit of several shrubs in the genus Vaccinium L.  They grow in all provinces in Canada and all but two of the United States (Nebraska and North Dakota). In the Northwestern semisphere, one can find 43 species of blueberries, depending on the region. Blueberries are found and produced in all hemispheres of the world. However, the species can vary by region.

Kingdom: Plantae (Plants)
Subkingdom: Tracheobionta (Vascular plants)
Subdivision: Spermatophyta (Seed plants)
Division: Magnoliophyta (Flowering plants)
Class: Magnoliopsida (Dictyledons)
Subclass: Dilleniidae
Order: Ericales
Family: Ericaceae
Genus: Vaccinium

There are 43 species and 46 accepted taxa overall. Some of the species include fruits we do not necessarily recognize as blueberry, including farkleberry, bilberry, ohelo, cranberry, huckleberry, whortleberry, deer berry, and lingonberry.  (Source

Blueberries are a very popular fruit in the U.S., and is consumed in fresh, frozen, and canned forms. While blueberries are a great fruit to eat to meet your suggested fruit intake, it also is one of the foods that are purported to have properties that it just does not have. This undeserved reputation results from the high levels of anti-oxidants, leading those predisposed to looking for “super foods” to classify blueberries into the anti-oxidant super food category. While eating more healthy foods is always a good idea, no food has curative effects all on its own.

Other aspects of blueberry nutrition includes it as a source of sugar. One cup (148 g) of blueberries contains about 15 g of sugar and 4 g of fiber, a single gram of protein, and half a gram of fat. If you are counting carbs, this cup has 21 g of them. That one cup of blueberries averages about 85 calories, which is approximately the same as a medium apple or orange. While almost all the vitamins and minerals nutrition gurus like to report on are present to some amount, for the 2000-calorie diet, that one cup of blueberries will provide the recommended daily value of 24% of Vitamin C, 36% of Vitamin K, and 25% of manganese. The remaining values range from 0-4%. (Values obtained from and verified through multiple sources.)

The Wikipedia entry is quite good and well researched (as of August 18, 2012). 

The photo above shows all of the life stages of a blueberry. Berries go from the little red nub at the end of the branch to round and juicy blueberries through fertilization of the ovary, which swells rapidly for about a month, then its growth ceases. The green berry develops with no change in size. The chemicals responsible for the blue color, anthocyanins, begin to turn the berry from green to blue as it develops over about 6 days. The volume of the berry increases during the change in color phase.

Will blueberries turn you blue? In short, no. You can achieve blue skin through the ill-advised practice of drinking silver or you can achieve orangish-yellow skin by eating a large number of carrots. This is because the chemicals causing the skin color are fat soluble and are present in a large quantity in the fat just under the skin, giving the skin those colors. Anthocyanin, the primary chemical causing the blue color in blueberries, is not fat soluble and will not reside in the fat under your skin.

Anthocyanins is a class of over 30 compounds. The chemical structure is generally as shown below. They are polyphenolic, which indicates the 3 ring structures. The “R” indicates different functional groups that change depending on which anthocyanin the structure represents. 

Interestingly, anthocyanins are also pH indicators because their color ranges from yellow to red to blue depending on the local pH. The blue color indicates a neutral pH. The wikipedia page on anthocyanins is also informative (as of August 18, 2012). 

As mentioned before, blueberries are a popular fruit. Recipes abound, but here is one from my own Recipe Codex for Surprise Muffins with blueberries:

  • 6 Tbsp. butter
  • 3/4 cup sugar
  • 2 eggs
  • 1/2 cup milk
  • 1/2 – 1 pint blueberries, fresh or frozen (defrosted)
  • Food coloring, optional
  • 2 cups all-purpose flour
  • 1/4 tsp. salt
  • 1 Tbsp. baking powder
  • Your favorite mini-treat (Hershey’s Kisses, Hugs, Reese’s Mini Cups, strawberry jam, etc.)
  1. Preheat the oven to 350º. In a large bowl, cream the butter and sugar. You can use a wooden spoon, a potato masher or handheld electric mixer. Mix in the eggs, one at a time, and add the milk.
  2. Rinse the strawberries and cut off the green stem. Mash the berries with a potato masher or puree in a blender. Then stir the berries into the butter and milk mixture. TIP: For muffins with a more blue color, add a few drops of blue food coloring.
  3. In a separate bowl, sift the flour, salt and baking powder. Stir well. Add the flour mixture to the berry mixture. Use a wooden spoon to stir until all the white disappears.
  4. Line the muffin tin with paper liners. Drop the batter from a tablespoon to fill the cups halfway.
  5. Add a surprise: an unwrapped mini treat or 1/2 teaspoon of jam. Then spoon more batter to fill almost to the top.
  6. Bake until the muffins begin to brown and a toothpick inserted near the center (but not in the mini-treat) comes out clean, about 20-25 minutes.
  7. Remove the muffins from the tin and cool.
Or perhaps you are in less of a cooking scientist mood and more in a home lab mood. Try this at-home lab with blueberries about dyes. Adapted from the Journal of Chemical Education.

Items You Need
  • 4 microwavable/stove top staff glasses, pots, or containers at least 1/2 cup in volume
  • tablespoons or 1/4 cup measuring cup
  • water
  • spatula
  • alum (available in the grocery store spice aisle)
  • cream of tartar (available in the grocery store spice aisle)
  • hot pads and tongs
  • at least four small (1-2 in.) squares of white cotton cloth
  • yellow onion skins
  • blueberries
  • spoon
  • paper towels
  • vinegar
  • baking soda
  • a dropper
  • notebook for experimental observations
In each step, you will want to record your observations, paying special attention to colors.
  1. Pour 4 tablespoons (1/4 cup) into container 1. Add a pea-sized scoop of alum and about half that amount of cream of tartar and stir. Bring the solution to a boil on the stove top or by microwaving for about 60 seconds. (Your microwave may vary.) Add two small squares of white cotton cloth and boil for two minutes. Set the container aside. The squares will be used in steps 4 and 6.
  2. Tear the outer, papery skin from a yellow onion into pieces no more than 1 inch square. Place enough pieces in a second container to cover its bottom with  2 or 3 layers of onion skin. Add about 4 tablespoons of water to the container. Bring the solution to a boil on the stove top, continuing to boil for 5  minutes.
  3. Wet a new square of cloth with water. Place it in container 2 so it is completely submerged and boil for 1 minute. Using tongs, remove the cloth and rinse it with water. Place the cloth square in the appropriate area on a labeled paper towel.
  4. Use tongs to remove one of the cloth squares from beaker 1. Repeat step 3 using this square. Compare to the dyed cloth square from step 3.
  5. Pour 4 tablespoons of water in a third container. Add 4-5 blueberries to the container and mash them with a spoon. Bring the solution to a boil on the stove, and continue to boil for 5 minutes.
  6. Repeat steps 3 and 4 substituting the blueberry mixture in container 3 for the onion skin mixture in container 2.
  7. Mix a small scoop of baking soda with a tsp of water in a clean container. With a dropper, place 1-2 drops of the baking soda solution in one corner of each cloth square. What happens? Rinse the dropper thoroughly, then place 1-2 drops of vinegar on the opposite corner of each square. What happens? Rinse the fabric squares under cool running water. Is there a change? Allow the squares to dry overnight. Is there any change of the cloth dries?
Optional: Try variations in the procedure such as changing the amount of dye source, the length of time the cloth spends in the dye solution, and the temperature of the dye solution.

Questions to consider
The solution in step 1 is called a mordant. Based on your observations, what is the purpose of a mordant?
Is the dye produced by blueberries really blue? Why might some people not want to wear clothes dyed with blueberries?

All in all, enjoy your blueberries. As a shrub, it is quite pretty. As a fruit, it is quite yummy. And as the tool in an experiment, it is quite fun.

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

Excerpts from Sophie’s Diary: A Mathematical Novel

Today we enjoy a bit of math, as told in Sophie’s Diary: A Mathematical Novel. Written by Dr. Dora Musilek, this novel was inspired by the French mathematician Sophie Germain, an important contributor to number theory and mathematical physics. Her correspondence with some of history’s great mathematicians such as Lagrange, Legendre, and Gauss are known while her life prior to that is shrouded in the unknown. Dr. Musilek explored Germain’s early life and uses the concept of an adolescent’s diary to discuss how Germain may have taught herself math while dealing with the social upheaval of the French Revolution, which occurred at this time in her life. Read on for an engaging lesson in math.

Monday | January 2, 1792

I begin the new year with more determination and a renewed resolve to study prime numbers. One of my goals is to acquire the necessary mathematical background to prove theorems.

Prime numbers are exquisite. They are whole pure numbers, and I can manipulate them in myriad ways, as pieces on the chessboard. Not all moves are correct but the right ones make you win. Take, for example, the process to uncover primes from whole numbers. Starting with the realization that any whole number n belongs to one of four different categories:

The number is an exact multiple of 4 : n = 4k

The number is one more than a multiple of 4 : n = 4k + 1

The number is two more than a multiple of 4 : n = 4k + 2

The number is three more than a multiple of 4 : n = 4k + 3

It is easy to verify that the first and third categories yield only even numbers greater than 4. For example for any number such as k = 3, 5, 6, and 7, I write: n = 4(3) = 12, and n = 4(6) = 24; or n = 4(5) + 2 = 22, and n = 4(7) + 2 = 30. The resulting numbers clearly are not primes. Thus, I can categorically say that prime numbers cannot be written as n = 4k, or n = 4k + 2. That leaves the other two categories.

So, a prime number greater than 2 can be written as either n = 4k+ 1, or n = 4k + 3. For example, for k= 1 it yields n = 4(1) + 1 = 5, and n = 4(1) + 3 = 7, both are indeed primes. Does this apply for any k? Can I find primes by using this relation? Take another value such as k = 11, so n = 4(11) + 1 = 45, and n= 4(11) + 3 = 47. Are 45 and 47 prime numbers? Well, I know 47 is a prime number, but 45 is not because it is a whole number that can be written as the product of 9 and 5. So, the relation n = 4k + 1 will not produce prime numbers all the time.

Over a hundred years ago Pierre de Fermat concluded that “odd numbers of the form n = 4k + 3 cannot be written as a sum of two perfect squares.” He asserted simply that n= 4+ 3 a2 + b2. For example, for k = 6, n = 4(6) + 3 = 27, and clearly 27 cannot be written as the sum of two perfect squares. I can verify this with any other value of k. But that would not be necessary.

And now we skip ahead to another excerpt where differential calculus is described.

Wednesday | February 27, 1793

I feel strong enough to resume my studies. My mind is clear again to meet the challenges of a new topic that at first seemed insurmountable. I resumed my studies of differential calculus.

There is something magical about Infiniment petits. I went back to the basic definition: “a derivative of a function represents an infinitesimal change in the function with respect to whatever parameters it may have.” The simple derivative of a function f with respect to x is denoted by f’(x), which is the same as df/dx. Newton used fluxions notation dz/dt = ż, but it means the same, so I will use f’ or df/dx from now on. Well, I can now take the derivative of certain classes of functions because I just follow certain rules.

If my function is of the type xn, I use the fact that d/dx(xn) = nxn−1.So, if I have f(x) = x5, its derivative should be 5x4. This is easy. If Ianalyze trigonometric functions such as sin x and cos x, then I use thederivatives d/dx(sinx) = cos x, and d/dx(cosx) = − sin x.

Taking derivatives is so easy! I could spend hours deriving more complicated functions. However, I wish to learn also how to see the world through mathematics. I must find the connection between differential equations and physics. I am eager to explore this applied aspect of mathematics.

Let’s start with a differential equation, an equation involving an unknown function and its derivatives. It can be relatively easy such as

or a bit more complicated such as the linear differential equation:

or even a nonlinear equation such as this: 

A differential equation is linear if the unknown function and its derivatives appear to the power 1 (products of these are not allowed) and nonlinear otherwise. The variables and their derivatives must always appear as a simple first power. Nonlinear equations are difficult to solve and some are impossible.

First I need to master linear equations. Some mathematicians use the notation y’ for the dy/dx derivative, or y’’ for d2y/dx2, and so forth. Thus,the previous linear equation would be written as (x2 + 1)y’ + 3xy = 6x. I need to keep these differences of notation in mind, since I am studying from five different books.

I studied the properties of differential equations and learned to solve them. Now, I must learn how to apply differential equations. But how do I translate a physical phenomenon into a set of equations to describe it? It is impossible to depict nature in its totality, so one usually strives for a set of equations that describes the physical system approximately and adequately.

Say that I want to predict the growth of population in Paris. To do it, I can use an exponential model, that is, an equation that represents the rate of change of the population that is proportional to the existing population. If P(t) represents the population change in time (t), I write

where the rate k is constant. I observe that if k > 0, the equation describes growth, and if k < 0, it models decay. The exponential equation is linear with a solution P(t) = P0ekt, where P0is the initial population, i.e., P(t = 0) = P0.

Mathematically, if k> 0, then the population grows and continues to expand to infinity. On the other hand, if k < 0, then the population will shrink and tend to 0. Clearly, the first case, k > 0, is not realistic. Population growth is eventually limited by some factor, like war or disease. When a population is far from its limits of expansion, it can grow exponentially. However, when nearing its limits, the population size can fluctuate. Well, I think that the equation I use to predict the rate of change of population can be modified to include these factors to obtain a result closer to reality.

Aristotle thought that nature could not be expected to follow precise mathematical rules. But Galileo argued against this point of view. He envisioned the experimental mathematical analysis of nature to be used to understand it. Newton was inspired by Galileo and later developed the laws of motion and universal gravitation. Newton, Leibniz, Euler, and other great people then created the mathematics that help us converse with the universe.

Oh, how glorious it is to speak such a language and understand the whispers from the heavens and the world around me.

Dr. Dora Musilek is a research scientist and also lectures on the role and contributions of women scientists and mathematicians. She holds a Ph.D. in aerospace engineering. You can learn more about Dr. Musilek and her novel at You can learn more about Dr. Musilek’s writing process at MAAA Books Blog.

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