Biology Explainer: The big 4 building blocks of life–carbohydrates, fats, proteins, and nucleic acids

The short version
  • The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
  • Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
  • Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
  • Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.                                                                                                      
  • The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.

                                                  

Big Molecules with Small Building Blocks

The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.

We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.
Carbohydrates

You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.

When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.

Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.

The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.

Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.

On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.

The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!

If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.

The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?

If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.

In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.

Sugar and Fuel

A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.

Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.

Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.

Polysaccharides: Fuel and Form

Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.

Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.

Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.

Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.

The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.

Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.

The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.

That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.

These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.

Lipids: The Fatty Trifecta

Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.

Fats: the Good, the Bad, the Neutral

Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?

Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows.  Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.

Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.

Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.

Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.

The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.

You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.

In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.

A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.

Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.

Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.

Phospholipids: An Abundant Fat

You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.

Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.

There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.

Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.

The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.

Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.

Steroids: Here to Pump You Up?

Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.

But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.

Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.

Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.

Proteins

As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.

Levels of Structure

Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.

For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.

This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.

Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.

The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.

In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.

A Plethora of Purposes

What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.

As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.

Nucleic Acids

How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.

Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.

DNA vs. RNA: A Matter of Structure

DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.

So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.

RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.

DNA vs. RNA: Function Wars

An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.

These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.

RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.


 By Emily Willingham, DXS managing editor 
This material originally appeared in similar form in Emily Willingham’s Complete Idiot’s Guide to College Biology

Happy belated birthday, Mary Anning!

Mary Anning and a small, non-fossilized dog. (Source)

[Today, we're featuring a post by Mike Rendell, author and keeper of Georgian Gentleman, a blog chronicling aspects of 18th century life. Mike spent 30 years as a lawyer--poor fellow--before he retired to time travel in his mind back to the 18th century, where he has set up mental shop permanently. By what he calls a "curious stroke of luck," he has all of the 18th century papers of his great-great-great-great (that's four) grandfather, including diaries, accounts, letters, and even shopping lists. In 2011, he published the story of this ancestor's life as a social history, "The Life of a Georgian Gentleman,' and thus, a blog was also born. We thank Mike for having graciously given us permission to publish his post here because we are huge fans of Mary Anning, who, as was typical, did not receive recognition from or entree into male scientific society of her day. We have added in a few explanatory links, too.]
Today the spotlight is turned not on a well-educated man, or a wealthy daughter with aristocratic connections, but on a girl who was amongst the poorest of the poor; who in many ways led a miserably hard and short life; who could barely read and write, and yet was someone who amazed the scientific world in the first half of the nineteenth century.
Her name was Mary Anning, born in Lyme Regis in Dorset on 21st May 1799. She cannot be said to have had an auspicious start in life. She was one of ten children – but eight died in childhood. An elder sister had already been called Mary but she had perished in a fire when her clothes were ignited from some burning wood shavings. Our heroine was born five months after this tragic death, and was named Mary in memory of her dead sibling.
Mary had luck, of a sort, on her side. When she was eighteen months old she was being held in the arms of a neighbour called Elizabeth Haskings who was in a group of women watching a travelling show. A storm sprang up and the group took shelter beneath an elm tree, but a bolt of lightning struck the tree, killing three of the women including Elizabeth. Yet Mary was apparently unscathed. Fate had something quite remarkable in store for the young girl…
Mary’s parents were Dissenters, meaning that education opportunities were limited and the family were subject to legal discrimination. A member of the Congregationalist Church, she attended Sunday School and here learned the rudiments of reading and writing. The Congregational Church, unlike the Anglican Church, attached great importance to education, particularly for young girls, and she was encouraged in her development by the pastor Revd James Wheaton. Her prized possession was apparently a copy of theDissenters’ Theological Magazine and Review Continue reading

A Once-in-a-Lifetime Truly Double X Event: Venus in Transit

By DXS Physics Editor Matthew Francis, who usually brings you Everyday Science. As you will see, this is science of the Not-So-Everyday sort.

Perhaps the most important question to ask in science is “how do we know?” While it’s appropriate to ask this every day, today it feels even more so, as we prepare to witness a very rare astronomical event. This time, it’s happening on June 5, 2012; when this event occurred during the 18th century, it allowed astronomers to make the first precision measurements of the size of our Solar System. Captain James Cook, best known for his exploration of the Pacific (for Europe, that is—the natives already knew what was there), took a set of scientific instruments aboard his ship to Tahiti; other teams of researchers took measurements at those locations.

The rare event they observed was the transit of Venus: when Venus travels directly between Earth and the Sun, blocking a tiny amount of light. Astronomers in different locations timed the crossing of Venus across the Sun’s disc, and by comparing their numbers, were able to determine the distance between Earth and the Sun. With that distance in hand, they were able to calibrate the size of the entire Solar System. The 1769 observation was an international scientific effort (to use modern language), and while the results weren’t as good as the astronomers of the day had hoped, they still agreed with modern measurements.

Today we use a variety of techniques to measure distances, including radar ranging (bouncing radio waves off planets and timing the round trip), so we don’t have to wait for Venus transits anymore—which is good, since they aren’t common! The last Venus transit was in 2004, but the previous one before that was in 1882, and the next one will be in 2117. I got up very early in the morning on June 8, 2004, joining some fellow astronomy enthusiasts at the Rutgers observatory, where we took the photo you see at the top of the post.

The seemingly odd intervals between transits are because Earth’s and Venus’ orbits around the Sun don’t lie in the same plane. If you draw Earth’s orbit as an ellipse on a sheet of cardboard, and Venus’ orbit on another sheet of cardboard, they need to overlap in a small X pattern, as shown in the picture. The only times Venus will transit is when both Earth and Venus are on the same side of the Sun, and only when they are in the region where the cardboard pieces overlap. The angle (3.5°) in the picture is correct, but I’ve exaggerated the size of the Sun and the sizes of the “transit zones”; in truth, even though the Sun is huge compared to Earth, it’s not that big on the sky. If you do the real calculation, you find that Venus transits happen roughly twice per century, and those two events are separated by 8 years. It’s a rare and wonderful event!

Viewing the Transit

If you want to view the Venus transit, the first thing you should do is see if it will be visible where you live. (Hopefully the weather will cooperate too! Such is the life of an astronomer.) In Richmond, Virginia (where I live), the transit begins around 6 PM. If you’re in the area, the Science Museum of Virginia is hosting a free viewing on the lawn; many other cities and towns have similar events.

A common sense warning: please don’t look directly at the Sun! However, you don’t need fancy equipment or a big observatory to witness the transit. Two weeks ago, I observed the solar eclipse using nothing but a microwave macaroni-and-cheese container. By piercing a hole in the bottom of the tub, I created a simple pinhole camera. A small and kind of fuzzy image of the eclipse appeared on a piece of paper, which I photographed. (Obviously you can do better if you have better equipment—I happened to be far from home during the eclipse and used what I had on hand.) A piece of cardboard covered in aluminum foil with a small hole works better, and you can project the image right onto the sidewalk, the side of a building, or another screen.

If you have a pair of binoculars that use glass lenses (since plastic will melt), point the larger lens toward the Sun and the smaller lens onto a flat surface. (Again, don’t look through the binoculars if you value your eyeballs!) If you have a telescope with a mirror or glass lenses, you can also project the image onto a flat surface, or create a sun funnel. There are a lot of ways to view the Sun if the ones I mention don’t appeal to you.

As a word of caution: the Venus transit won’t look as impressive as a solar eclipse, since Venus is a lot farther away than the Moon. It will appear to be a small round shadow on the Sun’s disc. The thrill (for me at least) lies in the knowledge: you are viewing a planet not much smaller than Earth as it crosses between us and our home star! If it isn’t enough these events are rare, think of how significant it is to catch a glimpse of the sheer size of our Solar System, in a way we don’t usually get to see. And always, always remember to ask the question: “how do we know?”

Further Reading

If you want to know more about transits and why they are still scientifically important today, try these links:

Happy Venus-watching!

Double Xpression: Meghan Groome

Meghan Groome, PhD, Director of K12 Education and Science & the City, New York Academy of Sciences
[Ed. note: Double X Science has started a new series: Double Xpression: Profiles of Women into Science. The focus of these profiles is how women in science express themselves in ways that aren’t necessarily scientific, how their ways of expression inform their scientific activities and vice-versa, and the reactions they encounter.]
Today’s profile is an interview with Meghan Groome, PhD, New York Academy of SciencesDirector of K12 Education and Science & The City, who answered our questions via email with DXS Biology Editor Jeanne Garbarino.

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

MG: I was a bio major since age two. Growing up (and still today) I had a deep love of all things gross, icky, creepy, and crawly and a deep dislike of anything math related. My parents didn’t really know what to do with me, so a theme to my scientific background is that although I was a straight-A student in my bio classes, no one had any idea that I should be doing enrichment programs or making an effort to learn math. I figured that by being a great bio major, I would become a great scientist. So I was an excellent consumer of scientific knowledge but only realized late in life that I needed to be a producer to actually become a scientist.

Being a straight-A student doesn’t actually get you a job when you graduate from a small liberal arts college with a degree in biology and theater, and out of desperation, I took a job teaching. While I wasn’t a good scientist, I turned out to be an excellent teacher and loved the creativity, energy, and never-ending questions that go along with being a science teacher. If you teach from the perspective that science is an endless quest for knowledge, you’ll never get bored taking kids on that journey.

While my background is in biology, my graduate degree is in science education, and I study gender dynamics and student questioning the middle-school classrooms. I currently work for the New York Academy of Sciences as the Director of K12 Education and public programs and spend most of my day convincing scientists that education outreach is not only part of their jobs but a lot of fun.

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

MG: I’m also a photographer and spend a lot of time wandering around neighborhoods in Brooklyn with a special love of decaying buildings and empty lots. I love how nature conquers things that we humans consider to be permanent – like how we have to constantly beat back the invading hordes of plants and animals even in one of the most man-made environments in the world.

I was also a theater major, so (I) have a strong background in costume design and stage directing. I hate acting but love dance. If I had any talent I would have become a musical theater star but unfortunately enthusiasm and determination can only get you so far.

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

MG: I find great joy in seeing how nature conquers human engineering. When I learned about Lynn Margulis’ Gaia hypothesis, I began seeing it everywhere and I think I love photography because I’m documenting the Earth fighting back.

Most of my creative energy comes from working with kids and listening to the wonderful way in which they think about the natural world. Adults can be so rigid in their thinking and are often afraid to say ideas that are out of the mainstream thinking. The older a kid gets, the more we expect them to conform to the adult way of thinking. Middle-school kids are old enough to express their wacky ideas, and young enough to not recognize that their ideas are considered “wrong.”

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?

MG: People tell me all the time “You’re not what we expected” and I’m not really sure how to respond.

In the science education world, my research is informed by my experiences teaching in a very poor district and from a social justice perspective. It’s a rather controversial theoretical framework because it says, “I have an agenda to use my research to bring about equity in an unequal world.” From a research perspective, it means you need to be explicit in your point of view and your biases and have much greater validity and reliability to show that your research is solid. My work is very passion driven so I’ve had to learn when it’s appropriate to pull out my soap box and go full-out social justice to them.

This is changing, but for a long time I kept my personality under wraps in a professional setting. It’s only now — with 10 years professional experience, great organizations on my resume, and a PhD — that I can be clever, confront those I disagree with, and even smile. Anyone who’s ever had a beer with me knows that I’m a goofball and will do just about anything to make someone laugh. I’m a science person, a theater person, a teacher, researcher, policy maker, consultant, and have seen a lot of exquisitely bad and good stuff in my life and so I am frequently the voice of an outsider even though I look and sound like a total insider. That can really freak people out especially if they’ve only read my bio or seen me in my most professional mode.
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?

MG: I approach teaching science from a fairly theatrical perspective. In my class we dance, sing, laugh, talk about the real world. I’ve never used the textbook, and I’m very insistent that everything be in the first person when writing or speaking about science. I much prefer teaching regular classes — not honors or AP — and can’t stand kids who remind me of myself in high school.

I approach scientists in the same way and try to make them comfortable admitting that their more than a brain on a stick. I’ve found one of the biggest fears of young scientists is that their PI will find out that they’re interested in something more than life in the lab so I always try to work within the existing power structure and make sure the PIs and Deans indicate to them that working with the (New York) Academy (of Sciences) is okay.

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?

MG: This question confounds the heck out of me. I am still such a tomboy and have always chosen to present myself as a somewhat genderless individual. I’ve always considered myself “smart not pretty” because I can control how smart I am but not how pretty. A few years ago, my sisters pulled me aside and told me I needed to stop dressing like such a slob. They started buying me pretty, fashionable clothes and insisting that I wear skirts above the knee and get a real hair cut.

Since I started working at the Academy, I have a very public facing role and have grown to accept that I should look nice. This goes along with slowly feeling comfortable letting my personality out in professional settings but I still consider myself a tomboy and consider my outward appearance to be a costume designed to do a job.

So I guess the answer is, femininity, what femininity?

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?

MG: I think very few people are brains on a stick but that being a scientist often requires us to pretend we have no life outside the lab. I’ve now worked with hundreds of young scientists who spend time working with kids and I’m so pleased to see how quickly they shift from lab geek to real person when talking with a 4th grader. I want scientists to be evangelicals for science, and I want that to include the fact that scientists are real, fallible, wacky, wonderful people too.

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?

MG: I was always encouraged to be an individual and be myself. I credit my parents with allowing me to pursue my passion and not try to box me in to one identity. It’s never been easy to forge my own path, and I dedicate a lot of myself to my work.

My advice to my younger self would be to slow down a bit, know that you don’t have to get 100% on everything, and know that the problems of the world don’t have to be solved right now.

And perhaps to learn how to be a bit more like a girl. It’s incredibly powerful to see yourself as smart and pretty.


———————————————————————
Meghan Groome is the Director of K12 Education and Science & the City at the New York Academy of Sciences, an organization with the mission to advance scientific research and knowledge, support scientific literacy, and promote the resolution of society’s global challenges through science-based solutions. After graduating from Colorado College in Biology and Theatre, she desperately needed a job and took one as a substitute teacher at a middle school in Ridgewood, NJ. She discovered that she had a knack for making science interesting and enjoyable, mostly through bringing in gross things, lighting things on fire (but always in a safe manner), and having a large library of the world’s best science writing and science fiction. After teaching in both Ridgewood and Paterson, NJ, she completed her PhD at Teachers College (TC) Columbia University with a focus on student question-asking in the classroom. While at TC, she was a founding member of an international education consulting firm and worked on projects from Kenya to Jordan with a focus on designing new schools and school systems in the developing world. 

After graduating, Dr. Groome became a Senior Policy Analyst at the National Governors Association on Governor Janet Napolitano’s Innovation America Initiative. Prior to her work at the Academy, Dr. Groome worked at the American Museum of Natural History and authored the policy roadmap for the Empire State STEM Education Network and taught urban biodiversity in the Education Department. At the Academy, she is responsible for the Afterschool STEM Mentoring program, which places graduate students and postdocs in the City’s afterschool programs, and the Science Teacher program, where she designs field trips and content talks to the City’s STEM teachers. Connect with her on Twitter, and read her NYAS blog!

Double Xpression: Karyn Traphagen, co-founder of ScienceOnline

Hanging out with Al.

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

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

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

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



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

Karyn enjoys creating art with…LEGOS!

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Karyn collecting water samples in Molokai, Hawaii

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

From alchemist to chemist: What kind of chemistry is that?


Figure 1: The Alchemist Discovering Phosphorus

What does the word chemistry  mean to you? For many, it was a class in high school or college to get through. In these introductory courses, called general chemistry, one gets a mix of all the flavors of chemistry – but the flavors are very different. To those who hear the calling of chemistry, it isn’t just any chemistry that will do. Some courses are more interesting to them than others. 

Many instructors start their general chemistry course with a history, introducing alchemy. Alchemy is considered to be the process by which to turn [name item of your choice] into gold. Alchemists were chemists by accident in that they performed many chemical reactions in their quests, discovering a number of elements in the process - embodied by Hennig Brandt’s discovery of phosphorus from the refinement of urine.
Alchemy relates to all the fields of chemistry. In perhaps the most famous of alchemy pictures, that by Joseph Wright of Derby entitled “The Alchemist Discovering Phosphorus,” the alchemist is kneeling by a very large round bottom flask. For many in modern chemistry, the round bottom flask signifies hours in the organic chemistrylaboratory mixing chemicals together to create something new.


Organic chemistry is the “branch of chemistry that deals with the structure, properties, and reactions of compounds that contain carbon” according to the American Chemical Association (ACS). Organic chemistry is the largest of chemistry fields in terms of number of people working in it. Organic chemists strive to make new compounds, usually to improve upon an existing one for a purpose and the field is often thought of in terms of synthesis applications.


The actual process of converting urine to phosphorus generally falls along the lines of inorganic chemical reactions. The form of phosphorus in urine is in the chemical sodium phosphate (Na3PO43-). Heating phosphates along with the organic products also in urine will form carbon monoxide (CO) and elemental phosphorus (P). The sodium phosphate, carbon monoxide, and elemental phosphate are all inorganic chemicals, falling under the field of inorganic chemistry.


Inorganic chemistry is “concerned with the properties and reactivity of all chemical elements,” according to UC-Davis chemwiki. While organic chemistry requires the presence of carbon in a specific type of bond, inorganic chemistry involves all the elements present in the periodic table. Inorganic chemistry delves into theories surrounding the bonding of metals to molecules and the shapes of molecules themselves.


Figure 2: Components of Urine
While the process of collecting phosphorus from urine requires organic and inorganic chemical reactions, the process of making the products in urine is biochemistry. Note in figure 2 that the primary product in urine is urea.


For students of biochemistry, images of the urea cycle (aka the Krebs cycle) are well known. According to the ACS, biochemistry is “the study of the structure, composition, and chemical reactions of substances in living systems.” Besides the chemical cycles to produce and use up necessary chemicals in biology, biochemistry encompasses protein structure and function (including enzymes), nucleic acids such as DNA, and biosynthesis.


As the alchemist turned urine to phosphorus, he added heat. The addition of heat to a reaction involves thermodynamics, a subsection of physical chemistry. If heat hadn’t been added, the reaction products would have been kinetic, which is another subsection of physical chemistry.


In a suite of physical chemistry courses, a student would also take quantum mechanics, rounding out the aim of physical chemists, which is to “develop a fundamental understanding at the molecular and atomic level of how materials behave and how chemical reactions occur,” according to the ACS. Physical chemists work by applying physics and math to the problems that chemists, biologists, and engineers study.


The alchemists who took exact measurements of their reactants and products, using quantitative methods, employed analytical chemistry. Presumably, the alchemists did this because every ounce of gold was precious, and they wanted to know how much substance they started with to produce the coveted metal.


Analytical chemistry focuses on obtaining and processing information about the composition and structure of matter. There are so-called wet lab ways to determine these quantities that often been employed. However, most analytical labs consist of the precision instrumentation that you may have seen on forensic crime shows, such as a mass spec, short for mass spectrometer, a frequent player on CSI.


While the alchemists were only trying to produce a substance to enrich pockets, they ultimately led to a rich science with several subfields, each with a trail leading from the practice of alchemy.

Adrienne M Roehrich, Double X Science Chemistry Editor
References:

(1734-1797), Joseph Wright of Derby. “English: The Alchemist Discovering Phosphorus or the Alchemist in Search of the Philosophers Stone.” Derby Museum and Art Gallery, Derby, U.K., 1771.

Lawton, Graham. “Pee-Cycling.” New Scientist, 20 December 2006 2006.

Weeks, Mary Elvira. “The Discovery of the Elements. Xxi. Supplementary Note on the Discovery of Phosphorus.” Journal of Chemical Education 10, no. 5 (1933/05/01 1933): 302.

Geektastic gift-giving ideas from Double X Science!



Shirt available via Zazzle


With the holidays fast approaching, the Double X Science team has come up with a great list of science-themed gifts to help you in your quest for the perfect present.  Not only are these gifts thoughtful, they are full of thought.  So go forth and spread some nerd love this year!

Apparel

Art

Books


DVDs and Music

Games

  • Hometown Puzzle, National Geographic, $39.95 Forget those generic puzzles found on the shelves of cookie-cutter toy stores, this highly personalized jigsaw will tickle the fancy of puzzle-lovers anywhere.  I’m probably going to get this for my mom.  NOTE: You need to order this by 12/13 if you want it by 12/25.
Hands-on

Household

Jewelry

Toys

Other links

We are not the only blog containing geektastic gift suggestions. You can find some other great geeky gift-giving ideas here:


Compiled by Double X Science Editor and MotherGeek Jeanne Garbarino