The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.
The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.
Big Molecules with Small Building Blocks
The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.
We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.
You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.
When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.
Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.
The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.
Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.
On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.
The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!
If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.
The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?
If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.
In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.
Sugar and Fuel
A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.
Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.
Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.
Polysaccharides: Fuel and Form
Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.
Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.
Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.
Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.
The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.
Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.
The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.
That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.
These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.
Lipids: The Fatty Trifecta
Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.
Fats: the Good, the Bad, the Neutral
Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?
Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows. Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.
Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.
Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.
Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.
The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.
You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.
In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.
A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.
Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.
Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.
Phospholipids: An Abundant Fat
You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.
Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.
There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.
Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.
The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.
Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.
Steroids: Here to Pump You Up?
Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.
But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.
Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.
Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.
As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.
Levels of Structure
Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.
For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.
This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.
Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.
The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.
In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.
A Plethora of Purposes
What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.
As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.
How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.
Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.
DNA vs. RNA: A Matter of Structure
DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.
So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.
RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.
DNA vs. RNA: Function Wars
An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.
These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.
RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.
Have you seen the headlines? Skip them You’ve probably seen a lot of headlines lately about autism and various behaviors, ways of being, or “toxins” that, the headlines tell you, are “linked” to it. Maybe you’re considering having a child and are mentally tallying up the various risk factors you have as a parent. Perhaps you have a child with autism and are now looking back, loaded with guilt that you ate high-fructose corn syrup or were overweight or too old or too near a freeway or not something enough that led to your child’s autism. Maybe you’re an autistic adult who’s getting a little tired of reading in these stories about how you don’t exist or how using these “risk factors” might help the world reduce the number of people who are like you. Here’s the bottom line: No one knows precisely what causes the extremely diverse developmental difference we call autism. Research from around the world suggests a strong genetic component[PDF]. What headlines in the United States call an “epidemic” is, in all likelihood, largely attributable to expanded diagnostic inclusion, better identification, and, ironically, greater awareness of autism. In countries that have been able to assess overall population prevalence, such as the UK, rates seem to have held steady at about 1% for decades, which is about the current levels now identified among 8-year-olds in the United States. What anyone needs when it comes to headlines honking about a “link” to a specific condition is a mental checklist of what the article–and whatever research underlies it–is really saying. Previously, we brought you Real vs Fake Science: How to tell them apart. Now we bring you our Double X Double-Take checklist. Use it when you read any story about scientific research and human health, medicine, biology, or genetics. The Double X Double-Take: What to do when reading science in the news 1. Skip the headline. Headlines are often misleading, at best, and can be wildly inaccurate. Forget about the headline. Pretend you never even saw the headline. 2. What is the basis of the article? Science news originates from several places. Often it’s a scientific paper. These papers come in several varieties. The ones that report a real study–lots of people or mice or flies, lots of data, lots of analysis, a hypothesis tested, statistics done–is considered “original research.” Those papers are the only ones that are genuinely original scientific studies. Words to watch for–terms that suggest no original research at all–are “review,” “editorial,” “perspective,” “commentary,” “case study” (these typically involve one or only a handful of cases, so no statistical analysis), and “meta-analysis.” None of these represents original findings from a scientific study. All but the last two are opinion. Also watch for “scientific meeting” and “conference.” That means that this information was presented without peer review at a scientific meeting. It hasn’t been vetted in any way. 3. Look at the words in the article. If what you’re reading contains words like “link,” “association,” “correlation,” or “risk,” then what the article is describing is a mathematical association between one thing (e.g., autism) and another (e.g., eating ice cream). It is likely not describing a biological connection between the two. In fact, popular articles seem to very rarely even cover scientific research that homes in on the biological connections. Why? Because these findings usually come in little bits and pieces that over time–often quite a bit of time–build into a larger picture showing a biological pathway by which Variable 1 leads to Outcome A. That’s not generally a process that’s particularly newsworthy, and the pathways can be both too specific and extremely confusing. 4. Look at the original source of the information. Google is your friend. Is the original source a scientific journal? At the very least, especially for original research, the abstract will be freely available. A news story based on a journal paper should provide a link to that abstract, but many, many news outlets do not do this–a huge disservice to the interested, engaged reader. At any rate, the article probably includes the name of a paper author and the journal of publication, and a quick Google search on both terms along with the subject (e.g., autism) will often find you the paper. If all you find is a news release about the paper–at outlets like ScienceDaily or PhysOrg–you are reading marketing materials. Period. And if there is no mention of publication in a journal, be very, very cautious in your interpretation of what’s being reported. 5. Remember that every single person involved in what you’re reading has a dog in the hunt. The news outlet wants clicks. For that reason, the reporter needs clicks. The researchers probably want attention to their research. The institutions where the researchers do their research want attention, prestige, and money. A Website may be trying to scare you into buying what they’re selling. Some people are not above using “sexy” science topics to achieve all of the above. Caveat lector. 6. Ask a scientist. Twitter abounds with scientists and sciencey types who may be able to evaluate an article for you. I receive daily requests via email, Facebook, and Twitter for exactly that assistance, and I’m glad to provide it. Seriously, ask a scientist. You’ll find it hard to get us to shut up. We do science because we really, really like it. It sure ain’t for the money. [Edited to add: But see also an important caveat and an important suggestion from Maggie Koerth-Baker over at Boing Boing and, as David Bradley has noted over at ScienceBase, always remember #5 on this list when applying #6.] —————————————————————————– Case Study Lately, everyone seems to be using “autism” as a way to draw eyeballs to their work. Below, I’m giving my own case study of exactly that phenomenon as an example of how to apply this checklist. 1. Headline: “Ten chemicals most likely to cause autism and learning disabilities” and “Could autism be caused by one of these 10 chemicals?” Double X Double-Take 1: Skip the headline. Check. Especially advisable as there is not one iota of information about “cause” involved here. 2. What is the basis of the article? Editorial. Conference. In other words, those 10 chemicals aren’t something researchers identified in careful studies as having a link to autism but instead are a list of suspects the editorial writers derived, a list that they’d developed two years ago at the mentioned conference. 3. Look at the words in the articles. Suspected. Suggesting a link. In other words, what you’re reading below those headlines does not involve studies linking anything to autism. Instead, it’s based on an editorial listing 10 compounds [PDF] that the editorial authors suspect might have something to do with autism (NB: Both linked stories completely gloss over the fact that most experts attribute the rise in autism diagnoses to changing and expanded diagnostic criteria, a shift in diagnosis from other categories to autism, and greater recognition and awareness–i.e., not to genetic changes or environmental factors. The editorial does the same). The authors do not provide citations for studies that link each chemical cited to autism itself, and the editorial itself is not focused on autism, per se, but on “neurodevelopmental” derailments in general. 4. Look at the original source of information. The source of the articles is an editorial, as noted. But one of these articles also provides a link to an actual research paper. The paper doesn’t even address any of the “top 10″ chemicals listed but instead is about cigarette smoking. News stories about this study describe it as linking smoking during pregnancy and autism. Yet the study abstract states that they did not identify a link, saying “We found a null association between maternal smoking and pregnancy in ASDs and the possibility of an association with a higher-functioning ASD subgroup was suggested.” In other words: No link between smoking and autism. But the headlines and how the articles are written would lead you to believe otherwise. 5. Remember that every single person involved has a dog in this hunt. Read with a critical eye. Ask yourself, what are people saying vs what real support exists for their assertions? Who stands to gain and in what way from having this information publicized? Think about the current culture–does the article or the research drag in “hot” topics (autism, obesity, fats, high-fructose corn syrup, “toxins,” Kim Kardashian) without any real basis for doing so? 6. Ask a scientist. Why, yes, I am a scientist, so I’ll respond. My field of research for 10 years happens to have been endocrine-disrupting compounds. I’ve seen literally one drop of a compound dissolved in a trillion drops of solvent shift development of a turtle from male to female. I’ve seen the negative embryonic effects of pesticides and an over-the-counter antihistamine on penile development in mice. I know well the literature that runs to the thousands of pages indicating that we’ve got a lot of chemicals around us and in us that can have profound influences during sensitive periods of development, depending on timing, dose, species, and what other compounds may be involved. Endocrine disruptors or “toxins” are a complex group with complex interactions and effects and can’t be treated as a monolith any more than autism should be. What I also know is that synthetic endocrine-disruptors have been around for more than a century and that natural ones for far, far longer. Do I think that the “top 10″ chemicals require closer investigation and regulation? Yes. But not because I think they’re causative in some autism “epidemic.” We’ve got sufficiently compelling evidence of their harm already without trying to use “autism” as a marketing tool to draw attention to them. Just as a couple of examples: If coal-burning pollution (i.e., mercury) were causative in autism, I’d expect some evidence of high rates in, say, Victorian London, where the average household burned 11 tons of coal a year. If modern lead exposures were causative, I’d be expecting records from notoriously lead-burdened ancient Rome containing descriptions of the autism epidemic that surely took it over. Bottom line: We’ve got plenty of reasons for concern about the developmental effects of the compounds on this list. But we’ve got very limited reasons to make autism a focal point for testing them. Using the Double X Double-Take checklist helps demonstrate that. By Emily Willingham, DXS managing editor
But today, I’m writing about those of us who have at least two X chromosomes. You may know that usually, carrying around a complete extra chromosome can lead to developmental differences, health problems, or even fetal or infant death. How is it that women can walk around with two X chromosomes in each body cell–and the X is a huge chromosome–yet men get by just fine with only one? What are we dealing with here: a half a dose of X (for men) or a double dose of X (for women)?
The answer? Women are typically the ones engaging in what’s known as “dosage compensation.” To manage our double dose of X, each of our cells shuts down one of the two X chromosomes it carries. The result is that we express the genes on only one of our X chromosomes in a given cell. This random expression of one X chromosome in each cell makes each woman a lovely mosaic of genetic expression (although not true genetic mosaicism), varying from cell to cell in whether we use genes from X chromosome 1 or from X chromosome 2.
Because these gene forms can differ between the two X chromosomes, we are simply less uniform in what our X chromosome genes do than are men. An exception is men who are XXY, who also shut down one of those X chromosomes in each body cell; women who are XXXshut down two X chromosomes in each cell. The body is deadly serious about this dosage compensation thing and will tolerate no Xtra dissent.
If we kept the entire X chromosome active, that would be a lot of Xtra gene dosage. The X chromosome contains about 1100 genes, and in humans, about 300 diseases and disorders are linked to genes on this chromosome, including hemophilia and Duchenne muscular dystrophy. Because males get only one chromosome, these X-linked diseases are more frequent among males–if the X chromosome they get has a gene form that confers disease, males have no backup X chromosome to make up for the deficit. Women do and far more rarely have X-linked diseases like hemophilia or X-linked differences like color blindness, although they may be subtly symptomatic depending on how frequently a “bad” version of the gene is silenced relative to the “good” version.
The most common example of the results of the random-ish gene silencing XX mammals do is the calico or tortoiseshell cat. You may have heard that if a cat’s calico, it’s female. That’s because the cat owes its splotchy coloring to having two X chromosome genes for coat color, which come in a couple of versions. One version of the gene results in brown coloring while the other produces orange. If a cat carries both forms, one on each X, wherever the cells shut down the brown X, the cat is orange. Wherever cells shut down the orange X, the cat is brown. The result? The cat can haz calico.
Cells “shut down” the X by slathering it with a kind of chemical tag that makes its gene sequences inaccessible. This version of genetic Liquid Paper means that the cellular machinery responsible for using the gene sequences can’t detect them. The inactivated chromosome even has a special name: It’s called a Barr body. The XXer who developed a hypothesis to explain how XX/XY mammals compensate for gene dosage is Mary Lyon, and the process of silencing an X by condensing it is fittingly called lyonization. Her hypothesis, based on observations of coat color in mice, became a law–the Lyon Law–in 2011.
Yet the silencing of that single chromosome in each XX cell isn’t total. As it turns out, women don’t shut down the second X chromosome entirely. The molecular Liquid Paper leaves clusters of sequences available, as many as 300 genes in some women. That means that women are walking around with full double doses of some X chromosome genes. In addition, no two women silence or express precisely the same sequences on the “silenced” X chromosome.
What’s equally fascinating is that many of the genes that go unsilenced on a Barr body are very like some genes on the Y chromosome, and the X and Y chromosomes share a common chromosomal ancestor. Thus, the availability of these genes on an otherwise silenced X chromosome may ensure that men and women have the same Y chromosome-related gene dosage, with men getting theirs from an X and a Y and women from having two X chromosomes with Y-like genes.
Not all genes expressed on the (mostly) silenced X are Y chromosome cross-dressers, however. The fact is, women are more complex than men, genomically speaking. Every individual woman may express a suite of X-related genes that differs from that of the woman next to her and that differs even more from that of the man across the room. Just one more thing to add to that sense of mystery and complexity that makes us so very, very double X-ey.
[ETA: Some phrases in this post may have appeared previously in similar form in Biology Digest, but copyright for all material belongs to EJW.]
After decades of searching and many promising results that didn’t pan out, scientists working at the Large Hadron Collider in Europe announced Wednesday they had found a new particle. People got really excited, and for good reason! This discovery is significant no matter how you look at it: If the new particle is the Higgs boson (which it probably is), it provides the missing piece to complete the highly successful Standard Model of particles and interactions. If the new particle isn’t the Higgs boson, well…that’s interesting too.
So what’s the big deal? What is the Higgs boson? What does Wednesday’s announcement really mean? What’s the meaning of life? Without getting too far over my head, let me try to answer at least some of the common questions people have about the Higgs boson, and what the researchers in Europe found. If you’d rather have everything in video form, here’s a great animation by cartoonist Jorge Cham and an elegant explanation by Ian Sample. Ethan Siegel also wrote a picture-laden joyride through Higgs boson physics; you can find a roundup of even more posts and information at Wired and at Boing-Boing. (Disclaimer: my own article about the Higgs is linked both places, so I may be slightly biased.)
Q: What is the Higgs boson?
A: The Higgs boson is a particle predicted by the Standard Model. It’s a manifestation of the “Higgs field”, which explains why some particles have mass and other particles don’t.
Q: Whoa, too fast! What’s a boson?
A: A boson is a large mammal indigenous to North America. No wait, that’s bison. [Ed note: Ha. Ha. Ha.] On the tiniest level, there are two basic types of particles: fermions and bosons. You’re made of fermions: the protons, neutrons, and electrons that are the constituents of atoms are all fermions. On a deeper level, protons and neutrons are built of quarks, which are also fermions. Bosons carry the forces of nature; the most familiar are photons–particles of light–which are manifestations of the electromagnetic force. There are other differences between fermions and bosons, but we don’t need to worry about them for now; if you want more information, I wrote a far longer and more detailed explanationat my personal blog.
Q: What does it mean to be a “manifestation” of a force?
A: The ocean is a huge body of water (duh), but it’s always in motion. You can think of waves as manifestations of the ocean’s motion. The electromagnetic field (which includes stuff like magnets, electric currents, and light) manifests itself in waves, too, but those waves only come in distinct indivisible chunks, which we call photons. The Higgs boson is also a manifestation of a special kind of interaction.
Q: How many kinds of forces are there?
A: There are four fundamental forces of nature: gravity, electromagnetism, and the two nuclear forces, creatively named the weak and strong forces. Gravity and electromagnetism are the forces of our daily lives: Gravity holds us to Earth, and electromagnetism does nearly everything else. If you drop a pencil, gravity makes it fall, but your holding the pencil is electromagnetic, based on how the atoms in your hand interact with the atoms in the pencil. The nuclear forces, on the other hand, are very short-range forces and are involved in (wow!) holding the nuclei of atoms together.
Q: OK, so what does the Higgs boson have to do with the fundamental forces?
A: All the forces of nature have certain things in common, so physicists from Einstein on have tried to describe them all as aspects of a single force. This is called unification, and to this day, nobody has successfully accomplished it. (Sounds like a metaphor for something or other.) However, unification of electromagnetism with the weak force was accomplished, yielding the electroweak theory. Nevertheless, there was a problem in the first version: It simply didn’t work if electrons, quarks, and the like had mass. Because particles obviously do have mass, something was wrong. That’s where the Higgs field and Higgs boson come in. Scottish physicist Peter Higgs and his colleagues figured out that if there was a new kind of field, it could explain both why the electromagnetic force and weak force behave differently and provide mass to the particles.
Q: Wait, I thought mass is fundamental?
A: One of the insights of modern physics is that particles aren’t just single objects: They are defined by interactions. Properties of particles emerge out of their interactions with fields, and mass is one of those properties. (That makes unifying gravity with the other forces challenging, which is a story for another day!) Some particles are more susceptible to interacting with the Higgs. An analogy I read (and apologies for not remembering where I read it) says it’s like different shoes in the snow. A snowshoe corresponds to a low-mass particle: very little snow mass sticks to it. A high-mass particle interacts strongly with the Higgs field, so that’s like hiking boots with big treads: lots of places for the snow to stick. Electrons are snowshoes, but the heaviest quarks are big ol’ hiking boots.
Q: Are there Higgs bosons running around all over the place, just like there are photons everywhere?
A: No, and it’s for the same reason we don’t see the bosons that carry the weak force. Unlike photons, the Higgs boson and the weak force bosons (known as the W and Z bosons — our particle physics friends run out of creative names sometime) are relatively massive. Many massive particles decay quickly into less massive particles, so the Higgs boson is short lived.
Q: So how do you make a Higgs boson?
A: The Higgs field is everywhere (like The Force in Star Wars), but to make a Higgs boson, you have to provide enough energy to make its mass. Einstein’s famous formula E = mc^2 tells us that mass and energy are interchangeable: If you have enough energy (in the right environment), you can make new particles. The Large Hadron Collider (LHC) at CERN in Europe and the Tevatron at Fermilab in the United States are two such environments: Both accelerate particles to close to the speed of light and smash them together. If the collisions are right, they can make a Higgs boson.
Q: Is this new particle actually the Higgs boson then?
A: That’s somewhat tricky. While the Standard Model predicts the existence of a Higgs boson, it doesn’t tell us exactly what the mass should be, which means the energy to make one isn’t certain. However, we have nice limits on the mass the Higgs could have, based on the way it interacts with other particles like the other bosons and quarks. This new particle falls in that range and has other characteristics that say “Higgs.” This is why a lot of physics writers, including me, will say the new particle is probably the Higgs boson, but we’ll hedge our bets until more data come in. The particle is real, though: four different detectors (ATLAS and CMS at CERN, and DZero and CDF at Fermilab) all saw the same particle with the same mass.
Q: But I’m asking you as a friend: Is this the Higgs boson?
A: I admit: a perverse part of me hopes it’s something different. If it isn’t the Higgs boson, it’s something unexpected and may not correspond to anything predicted in any theory! That’s an exciting and intriguing result. However, my bet is that this is the Higgs boson, and many (if not most) of my colleagues would agree.
Q: What’s all this talk about the “God particle”?
A: Physicists HATE it when the Higgs boson is called “the God particle.” Yes, the particle is important, but it’s not godlike. The term came from the title of a book by physicist Leon Lederman; he originally wanted to call it “The Goddamn Particle”, since the Higgs boson was so frustrating to find, but his editor forced a change.
Q: Why should I, as a non-physicist, care about this stuff?
A: While it’s unlikely that the discovery of the Higgs boson will affect you directly, particle colliders like the LHC and Tevatron have spurred development of new technologies. However, that’s not the primary reason to study this. By learning how particles work, we learn about the Universe, including how we fit into it. The search for new particles meshes with cosmology (my own area): It reveals the nature of the Universe we inhabit. I find a profound romance in exploring our Universe, learning about our origins, and discovering things that are far from everyday. If we limit the scope of exploration only to things that have immediate practical use, then we might as well give up on literature, poetry, movies, religion, and the like right now.
Q: If this is the Higgs boson, is that the final piece of the puzzle? Is particle physics done?
A: No, and in fact bigger mysteries remain. The Higgs boson is predicted by the Standard Model, but we know 80% of the mass of the Universe is in the form of dark matter, stuff that doesn’t emit or absorb light. We don’t know exactly what dark matter is, but it’s probably a particle — which means particle colliders may be able to figure it out. Hunting for an unknown particle is harder than looking for one we are pretty sure exists. Finding the Higgs (if I may quote myself) is like The Hobbit: It’s a necessary tale, but the bigger epic of The Lord of the Rings is still to come.
Tonight—August 31, 2012— is the second full Moon of August. The last time two full Moons occurred in the same month was in 2010, and the next will be in 2015, so while the events are rare, they aren’t terribly uncommon either. In fact, you’ve probably heard the second full Moon given a name: “blue moon”. (The Moon will not appear to be a blue color, though, cool as that would be. More on that in a bit.) What you may not know is that this term dates back only to 1946, and is actually a mistake.
According to Sky and Telescope, a premiere astronomy magazine (check your local library!), the writer James Hugh Pruett made an incorrect assumption about the use of the term “blue moon” in his March 1946 article. His source was the Maine Farmers’ Almanac, but he misinterpreted it. The almanac used “blue moon” to refer to the rare occasion when four full Moons happen in one season, when there are usually only three. By the almanac’s standards, tonight’s full moon is not a blue moon (though there will be one on August 21, 2013).
However, even that definition of “blue moon” apparently only dates to the early 19th century. In its colloquial, non-astronomical sense, a “blue moon” is something that rarely or never happens: like the Moon appearing blue. The Moon is white and gray when it’s high in the sky, and can appear very red, orange, or yellow near the horizon for the same reason the Sun does. As far as I can tell, the only time the Moon appears blue is when there’s a lot of volcanic ash in the air, also a rare event (thankfully) for most of the world. The popular song “Blue Moon” (written by everyone’s favorite gay misanthrope, Lorenz Hart) uses “blue” to mean sad, rather than rare.
I’m perfectly happy to keep the common mistaken usage of “blue moon” around, though, since it’s not really a big deal to me. Call tonight’s full Moon a blue moon, and I’ll back you up. However, because it’s me, let’s talk about the Moon and the Sun and why this stuff is kind of arbitrary.
The Moon and the Sun Don’t Get Along
The calendar used in much of the world is the Gregorian calendar, named for Pope Gregory XIII, who instituted it in 1582. The Gregorian calendar, in turn, was based on the older Roman calendar (known as the Julian calendar, for famous pinup girl Julie Callender Julius Caesar). The Romans’ calendar was based on the Sun: a year is the length of time for the Sun to return to the same spot in the sky. This length of time is approximate 365.25 days, which is why there’s a leap year every four years. (Experts know I’m simplifying; if you want more information, see this post at Galileo’s Pendulum.)
A problem arises when you try to break the year into smaller pieces. Traditionally, this has been done through reference to the Moon’s phases. The time to cycle through all the phases of the Moon is called a lunation, which is about 29 days, 12 hours, 44 minutes, and 3 seconds long. You don’t need to pull out a calculator to realize that a lunation doesn’t divide into a year evenly, but it’s still a reasonable way to mark the passage of time within a year, so it’s the foundation of the month (or moonth).
Many calendars—the traditional Chinese calendar, the Jewish calendar, and others—define the month based on a lunation, but don’t fix the number of months in a year. That means some years have 12 months, and others have 13: a leap month. It also means that holidays in these calendars move relative to the Gregorian calendar, such that Yom Kippur or the Chinese New Year don’t fall on the same date in 2012 that they did in 2011. (The Christian religious calendar combines aspects of the Jewish and the Gregorian calendars: Christmas is always December 25, but Easter and associated holidays are tied to Passover—which is coupled to the first full Moon after the spring equinox, and so can occur in a variety of dates in March and April.)
Another resolution to the problem of lunations vs. Sun is to ignore the Sun; this is what the Islamic calendar does. Months are defined by lunations, and the year is precisely 12 months, meaning the year in this calendar is 354 or 355 days long. This is why the holy month of Ramadan moves throughout the Gregorian year, happening sometimes in summer, and sometimes in winter.
The Gregorian calendar does things oppositely to the Islamic calendar: while months are defined, they are not based on a lunation at all. Months may be 30 days long (roughly one lunation), 31 days, or 28 days; the latter two options make no astronomical sense at all. Solar-only calendars have some advantages: since seasons are defined relative to the Sun, the equinoxes and solstices happen roughly on the same date every year, which doesn’t happen in lunation-based calendars. It’s all a matter of taste, culture, and convenience, however, since the cycles of Sun and the Moon don’t cooperate with the length of the day on Earth, or with each other.
Blue moons in the common post-1946 usage never happen in lunation-based calendar systems because by definition each phase of the Moon only occurs once in a month. On the other hand, the version from the Maine Farmers’ Almanac is relevant to any calendar system, because it’s defined by the seasons. As I wrote in my earlier DXS post, seasons are defined by the orbit of Earth around the Sun, and the relative orientation of Earth’s axis. Thus, summer is the same number of days whatever calendar system you use, even though it may not always be the same number of months. In a typical season, there will be three full Moons, but because of the mismatch between lunations and the time between equinoxes and solstices, some rare seasons may have four full Moons.
The Moon and Sun have provided patterns for human life and culture, metaphors for poetry and drama, and of course lots of superstition and pseudoscience. However, one thing most people can agree upon: the full Moon, blue or not, is a thing of beauty. If you can, go out tonight and have a look at it—and give it a wink in honor of the first human to set foot on it, Neil Armstrong.
We started with a welcome and gratitude to the organizers and attendees and our tagline “Science, I am Just That Into You.” We were selected to appear with a lot of fantastic programming over the weekend.
We introduced our 3 panelists:
Adrienne Roehrich, your panel moderator and the chemistry editor at Double X Science
All 3 have PhDs in their respective fields – Emily is a developmental biologist, Ray is an analytical chemist, and Adrienne is a physical chemist. Emily and Ray are prolific writers. You can find their articles all over the internet and in print. Ray is a staff member for GeekGirlCon and Adrienne is a Special Agent volunteer. All 3 are active on social media and welcome live-tweeting and suggest the #DXS hashtag along with the #GGC12. And you can use the @DoubleXSci for the panel.
Then a poll of the room to see who had heard of the site. Only a few attendees were already familiar with the site, so we told them that DoubleXScience covers a lot of current science. For example on (the previous) Monday, Emily posted about the Mars Curiosity Rover touchdown. In July, the physics editor covered the Higgs particle announcement. We also cover timeless, yet updated science, such as pregnancy and other health issues that we editors perceive to be of interest to ourselves and our readers.
It’s hard to discuss what Double X Science is without discussing who it is.
After a review of who all the people on that particular slide are and what they have to do with Double X Science, three questions were asked by the moderator:
In November of 2011, Emily founded Double X Science, Emily what was your motivation in founding the site and what was then and is now your vision for it?
As mentioned, we have content from editors, other sites and contributors. Ray was the first contributor to the site – what attracted you to Double X Science?
What do the attendees want to know?
And then our discussion really got started. Thankfully, we had 3 great tweeters attending, so I can just point you along their tweets:
[&amp;amp;amp;amp;amp;amp;lt;a href="http://storify.com/fiainros/double-x-science-panel-at-geekgirlcon-2012" target="_blank"&amp;amp;amp;amp;amp;amp;gt;View the story "Double X Science panel at GeekGirlCon 2012" on Storify&amp;amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;amp;gt;]
Photo by Adrienne Roehrich and used with permission.
A case of ulcerative colitis, a form of inflammatory bowel disease. Photo via Wikimedia Commons. Credit: Samir.
A two-hit punch in the gut might explain why some people find themselves alone among their closest relatives in having inflammatory bowel disease (IBD). The double gut punches come in the form of a compromised intestinal wall coupled with a poorly behaved immune system, say Emory researchers, whose work using mice was published in the journal Immunity. IBDs include ulcerative colitis and Crohn’s disease, the latter of which is slightly more common in women.
An inflamed gut is the key feature of IBD, which affects about 600,000 people in the United States each year. Typical symptoms include bloody diarrhea, fever, and cramps, which can come and go with bouts of severe inflammation punctuating relatively calm periods. The going explanation for these disorders is a wonky immune system, but some breach of the barrier that keeps your gut contents in their place is also implicated. Researchers also have identified a link between bouts of gastroenteritis–known around my house as “throw-up” illnesses–and development of IBD. What’s remained unclear is how people who have these so-called “leaky guts” don’t develop a disease like Crohn’s when a close family member with a leaky gut does.
These hints in humans led the Emory investigators to examine the interaction of a compromised gut and the immune system in mice. The mice in the study had ‘leaky’ gut walls because they lacked a protein that usually ties cells together into water-tight sheets. Without these proteins sealing up the intestinal lining, bacteria and other components can make their way their deeper into the intestinal wall, triggering chronic inflammation.
The thing is, these mice with their leaky guts don’t develop colitis spontaneously, a situation, the investigators hypothesized, that reflects families full of people with leaky guts but rarely IBD. Permeable intestines alone aren’t enough. Some other dysfunction related to the immune system, they figured, must pile onto that leakiness and bring on the inflammatory disorder.
If you’re an immunologist–which I am not–an obvious choice for investigation is a class of immune cells called T cells. These cells come in a dizzying array of types, but one way to narrow them down relies on a protein that some but not all of them make. Pulling out the T cells that make this protein, says Timothy Denning, PhD, a mucosal immunologist at Emory and study author, is “the simplest way” to start examining the immune system involvement because these cells play a ton of roles in balancing different immune responses. So, they first collected the T cells carrying this protein from the mouse intestines.
“There are good and bad” versions of T cells carrying these identifier molecules, though, says Denning, so the next step was to find the “good” ones that might be protecting mice in spite of their sieve-like intestinal linings. To achieve that goal required some fancier lab moves. “We stimulated the cells and looked at the cytokines (immune signaling molecules) they make,” explains Charles Parkos, MD, PhD, an experimental pathologist and mucosal immunologist at Emory and also a paper author. “We found that the cells in the mice that were better protected predominantly secreted TGF-beta, a prototypic marker for ‘good’ cells.”
One of the things T cells do with TGF-beta is to talk to B cells, another class of immune cell. B cells take responsibility for remembering what’s attacked you in the past and marshaling forces if it attacks again. Also, when B cells are stimulated, explains Parkos, one way they respond is to release proteins–antibodies–that target the offending invaders. In the gut, the kind of antibody the B cells make in response to the TGF-beta message is immunoglobulin A, or IgA. This antibody “keeps bacteria in check,” says Denning, and also probably “broadly neutralizes lots of different microorganisms” in the intestines, adds Parkos.
The Emory-based team found that when the leaky-gut mice also had an IgA deficiency, they became more open to the types of immune cells that cause gut inflammation. The animals also were far more susceptible to colitis triggered by a chemical treatment in the lab and had much worse disease. Without the IgA, the mice couldn’t dampen inflammation triggered by bacteria slipping through the intestinal breaches. The results of this two-step physiological fail, in mice, at least: severe inflammatory gut disease.
Denning cautions that these results in mice don’t suggest a rush to TGF-beta or IgA treatment for inflammatory diseases. “TGF-beta has many effects and on many different cell types, and too much is not a good thing because it’s known to play a role in fibrosis and cancer,” says Denning. “If your child had IBD, the last thing you’d want to do is to give TGF-beta.” Much more work has to be done, he adds, for a better understanding of the implications of these results before anyone starts talking about therapies. Parkos agrees. “To our knowledge, administration of TGF-beta is not a viable therapy.”
The same applies for IgA, Denning says. “We couldn’t just take any old B cells and get them to make IgA and put it in and hope that it would do something,” he says. The reason, he explains, is because B cells make many different types of IgA molecules specific to foreign invaders they encounter, a process that happens on the spot, not in a lab dish. “We need to understand much more about the basic mechanisms, but we do believe that these pathways would be critical to induce in people who are more susceptible to IBD, such as first-degree relatives.”
Some research groups are conducting trials to treat IBDs with helminth worms–intestinal parasites–on the hypothesis that their presence would induce a balance in the immune system and tamp down an overactive inflammatory response. The balance in this case is supposed to be between two competing aspects of the immune system, called Th1 and Th2. But one issue in these intestinal inflammatory disorders, says Denning, is that Crohn’s is linked to Th1 hyperactivity while ulcerative colitis is associated with Th2.
Yet the worms appear to show some beneficial effects in both disorders, in spite of the different involvement of Th1 and Th2. The TGF-beta signaling effect on IgA that the Emory group identified operates by a third component, tentatively identified as Th3. Both Denning and Parkos are intrigued by the possibility that the presence of helminths might trigger this pathway, rather than influencing Th1 or Th2, explaining why worm treatment has sometimes proved useful for both Crohn’s and ulcerative colitis.
As for why IBD arises, the researchers hope their findings answer some questions. “There are different camps in the IBD community,” says Parkos. “Some say immune system, some say barrier, others say genetics or environment.” What they have with their results, he says, is evidence showing that a leak alone is not enough and that a wonky immune system alone is not enough. But the double-whammy of a leaky gut and an absence of immune protection “dramatically increase susceptibility to disease, and that helps explain why diseases are so complicated,” he says.
The use of parasitic worms for these inflammatory diseases arose from the concept of the hygiene hypothesis, the idea that we’re too clean in the modern developed world, leading to an immune imbalance that can include chronic inflammation and autoimmune disorders. Asked about any links between the hygiene hypothesis and this pathway to IBD they identified in mice, Denning says, “It’s not obviously all about the parasites. That’s just one key thing–it’s probably an exposure to a lot of different types of things in your gut and airways.” He describes the immune system as being a thermostat that registers a specific set-point early on based on these exposures. This set-point, he says, is lower in people who grow up in developed countries like the United States and leads to a “trigger-happy immune system that is ready to fire much more easily.”
That doesn’t mean that a worm infection or just being dirty will prevent your developing IBD. That said, these immunologists both have the same general advice for parents regarding their children. “Being too clean is not a good thing,” they agree. As immunologists, he adds, “We feel exactly the opposite. Go play in the dirt.”
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!
I Love Science T-shirt, Amazon, $19.99 Let your loved ones tell the world around them that they are into science with this cool take on a T-shirt. I doubt that any of the Kardashians will be wearing this one.
The way we work by David Macaulay, Amazon, $23.10Recommended for ages 5 and above, this book elegantly demonstrates how and why our bodies function the way they do, from digestion, to respiration, to reproduction, all from the perspective of an engineer and illustrator.
Here Comes Science by They Might Be Giants, Amazon, $8.99 This is a seriously wonderful music/DVD combo that uses catchy tunes and big voices to turn science into singable fun! My personal favorite is “Electric Car.” Here is a video form this collection about why the sun shines (my kids know every word):
Hometown Puzzle, National Geographic, $39.95Forget 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.
DNA Gel Travel Mug, Cafe Press, $24.50What’s in your cup is not nearly as cool as what’s on your cup! I’ve always said that DNA is beautiful, and with this mug, everyone will be able to see it. I’d venture to say that it would be a great conversation piece as well.
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.]
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!
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Recommended reading about the importance of women in science and women into science