The 2013 Flame Challenge Question: What is time?

By Biology Editor Jeanne Garbarino

Last year, Alan Alda presented scientists all over the globe with a challenge: explain what a flame is to an 11 year old. This was born out of his personal experience when, at age 11, he asked his teacher what a flame was and was given a one word, and completely incomprehensible answer, “oxidation.”

As a founding member of Stony Brook University’s Center for Communicating Science, Alda is committed to promoting better science communication from scientists. In an effort to enhance the dialogue between scientists and the general public in a fun and meaningful way, Alda initiated the first ever The Flame Challenge competition. Much to everyone’s surprise, this creative competition was a big hit, and over 800 entries were submitted (including mine!). Each entry was vetted for accuracy and then judged by entire classrooms of 11-year-olds located all over the world. The winner of the first Flame Challenge was a graduate student and father, Ben Ames, who presented the public with an incredible story and original music that thoroughly explained the concept of a flame.

Because of the success of last year’s Flame Challenge, Alda has set out to do it again.  However, instead of asking the question himself, he crowdsourced the question from — you guessed it — actual 11-year-olds. “Last year’s contest question came from a real 11-year-old: me,” Alda said. “But when I asked what a flame was at the age of 11, I was probably younger in some ways than most 11-year-olds are now. They’re asking a very deep question this year. It’s going to be fun to see how scientists around the world answer that one in everyday language.” 

According to the press release, the Center for Communicating Science collected about 300 questions from children, ranging from “Does the universe have a known end?” and “How does the brain store all that information?” to “Why are Shetland ponies so small?” But, once the votes were counted, there was one question that reigned supreme: What is time?











Scientists will have until March 1, 2013, to submit their answer, and this year, there will be winners selected from two categories: written and video/graphics. Once submitted, the explanations of time will be scrutinized by over 5,000 11-year-olds worldwide. The winning scientists will be rewarded with a trip to New York City and honored at a World Science Festival event on June 1, 2013. 

For more information on entering or judging the contest, or to see last year’s top entries, please visit www.FlameChallenge.org


If you are planning to enter, best of luck! I can’t say that this is an easy question, and I look forward to seeing all the wonderful answers come spring. Happy sciencing!

Ben Ames award winning explanation of a flame:

 

Life and science challenges: flames, Hawkeye, the needle and the damage done

(source)

Of Heroin, Honorable Mentions, and Hawkeye: A day I will never forget

By Double X Science Biology Editor Jeanne Garbarino


“I look forward to seeing you in 3 months when you will be a whole person again.”

Those were my parting words to a special person in my life who was embarking on an undoubtedly difficult journey toward sobriety.  It was only 7:45am on Friday, June 1st, but already I had learned that the strings from a bikini top make a good tourniquet, and I actually held the syringe that, only moments before, contained a bolus of heroin.  I am still trying to believe that this really was the last time.  

As I attempted to wrap my head around what was happening, I remembered a description of a heroin high as told to me by a former addict.  According to this person, being on heroin feels like you’ve been swaddled in a warm blanket, and gently rocked by a loving mother, except the loving mother was actually the devil.  

Though I could never really understand what it feels like to be hooked on heroin, this helped me make some sense of it.  But, as much as I wanted to be sympathetic, I also wanted to grab my friend by the shoulders and scream.  “Why have you done this to yourself?  Why have you done this to us?”  It has truly been a difficult time, watching this person struggle.  And finding out that I can’t control any of it was probably the hardest lesson I’ve ever learned.

Still, life must go on.

I took a few deep breaths, which helped to quiet the tremble, and began to gather my thoughts.  What was it that I had to do today?  As if I flipped some switch, I began to plan out my day – renew my parking permit, finish that Western blot, read that thesis, and get that new post up on the site.  

Then, around 8:15am, I received an unexpected phone call.  It was Liz Bass from the Center of Communicating Science at Stony Brook University.  She was calling to see if I could make Alan Alda’s World Science Festival discussion about the Flame Challenge, which was to occur at 4pm that afternoon.  Not really knowing what was in store, I quickly accepted (um, hello, Alan Alda).  A second phone call about 20 minutes later informed me that I would be joining Alan on stage.  Was this really happening?  In about 30 minutes time, I went from despair to elation.  I also went to the store to buy a skirt since I was already in transit to my lab (and was dressed like a “scientist”).

As I sat on the train, I began to reflect.  Much of my free time during the month of March was dedicated to producing an entry to Alan Alda’s Flame Challenge contest, which, in an effort to raise science communication awareness, asked scientists from all over the world to define a flame to an 11 year old.  Because I enjoy working on a team, I asked my fellow scicommies, Deborah Berebichez and Perrin Ireland, to join me on this endeavor (three times the brain power!).  For several weeks, we worked on the script, and regularly discussed our progress during late night Google hangouts (which is a fantastic way to collaborate).  This was mostly due to the fact that we all have day jobs and obligations outside of work.  Luckily for me, Debbie and Perrin were willing to meet at a time that coincided after my children’s bedtime routine.

This experience was truly fun and rewarding.  Each of us has a certain set of strengths, which when combined, seemed to just synergize.  We literally examined every word in the script to make sure that it was clear, concise, and hopefully captivating.  Furthermore, we wanted to make sure that it was something an 11-year-old would both learn from and enjoy.

But, we did labor over one particular issue, and that was our use of the Bohr Model to represent an atom.  While this model might be commonplace in many classroom textbooks, scientists now know that electrons exist in orbitals, also known as electron clouds, and the calculations to determine the exact location(s) of an electron are based on probability.  Clearly, this was something very different than stating that electrons simply orbit around a nucleus.  

The analogy that electrons travel around the nucleus in the same way that planets travel around the sun is downright inaccurate.  However, this is an analogy that is still commonly used and is, in my opinion, a great example of how we sacrifice accuracy for simplicity.  I believe that this is the greatest challenge for a science communicator.  

As we talked through this issue, we tried to not lose site of the actual mission, which was to explain a flame to an 11 year old.  Would it help our story to break down the currently accepted atomic theory or would it detract from it?  In the end, we decided to keep our atomic structure simple, but noted that it was a simplified version of an atom.  We figured that by having this little disclaimer, it would inform our audience that there is more to it that what we showed, and maybe it would lead them down a road of scientific inquiry.  

Perhaps it was this attention to detail that landed our Flame Challenge video a spot in the top 15 entries (FYI there were close to 900 entries).   Or perhaps it was because our entry was cute and artistic.  Whatever the reason, we proudly accepted our honorable mention, and I was looking forward to discussing our video with the man himself.

Getting back to Friday, June 1st.   I arrived at the Paley Center for Media around 3:30pm (in a new skirt) and was immediately brought up to the 11th floor and into the green room of Alan Alda.  There, I met my fellow awardees (a combination of finalists and honorable mentions), and of course Alan Alda, who was fantastically charming and funny.  We all sat, around an old table, on which was a lovely array of cheese, nuts, banana chips, and get this, Swedish fish!  I don’t know what it was about the Swedish fish, but seeing this candy helped calm my nerves.

Alan helped us all to break the ice, and discussed his plans for the event.  Apparently we would be leading a panel discussion, and I would be on that panel.  On a stage.  In front of a very large audience.  And it was to be webcasted.  So I popped a few of those Swedish fish and told myself to not be nervous.

As my jaw worked to chew those sticky sweet candies, I couldn’t help but think about when I was a kid and how I used to sit with my dad and watch M*A*S*H.  I never would have believed you if you told me that I was going to be hanging out with Hawkeye when I was older.  But, there he was, telling us about the birth of the Flame Challenge.  I was tempted to ask him where Corporal Klinger is these days, but decided that my time would be better spent getting the plan for the panel firmed up in my brain.

After some quick chitchat, we were asked to make our way to the auditorium.  Seating was charted and mics were checked and around 4pm, it all began.  About an hour into it, we were asked to come on stage.  Each of our entries were highlighted, followed by a chance speak our piece.  Add in some Q&A from the audience and the panel discussion was complete.  A hearty round of applause later, I found myself getting whisked away for pictures.  

When the dust began to settle, I grabbed a beer and started to decompress.  I just couldn’t believe how this day turned out, especially given its start.  The stresses my family and I have been dealing with have certainly taken its toll on all of us, and I am grateful for that little dose of Hawkeye to help lighten things up.  I’m not sure if I will ever experience a day like that again, but that’s ok with me.  

Explosions, Just a Bit More Than Fireworks

Image by Nux. (Source)

By Adrienne M Roehrich, Chemistry Editor


It’s that time of the year in the U.S. – when we blow up pretty bombs in celebration of the approval of the Declaration of Independence, declaring the independence from the Kingdom of Great Britain. Around this time of year, there is no dearth of articles about the chemistry of fireworks, but the chemistry editor here could not let her secret love of this topic pass by.


What is an explosive? An explosive is a combination of materials that when reacted produce an abundance of light, sound, heat, and pressure. A firework encompasses all 4 of those: we are familiar with the light – the whole reason we view fireworks, we are familiar with the sound – the boom that follows especially large displays, we are familiar with the pressure if we are close enough – that’s the force that pushes into you and the “shock wave” pictured in movies after large explosions; and we are familiar with the heat – ever held a sparkler?


There are three main types of explosives: chemical, nuclear, and mechanical. The bulk of this post will focus on chemical explosives with a short bit about nuclear and mechanical.


If we start at the beginning – well, we’ll skip to the “accepted” first explosive – black powder. Black powder, also called gun powder and the precursor to fireworks, is coined a chemical explosive. Chemical explosions generally fall into a specific classification of chemical reactions called oxidation.


The earliest definition of oxidation was the addition of the element oxygen to a compound, also called combustion. Due to limits of this definition, it was later changed to be the loss of electrons from an element (within a compound.) The original definition can easily be shown in terms of explosives. The simple mixing of hydrogen and oxygen with the addition of just a bit of heat, will form water in an explosive display:


2H2 + O2 –> 2H2O



The little flame used to catalyze the reaction in the video is actually much more energy than is necessary to cause this reaction to occur, but it’s difficult to get an even littler source of heat and safely demonstrate this reaction. You might also note a lot more energy comes out of that reaction once started in terms of light and heat and sound. I’ve been the one lighting that reaction in a demo without both ears plugged and I couldn’t hear out of one ear for the rest of the lecture.


If we focus on the loss of electrons version of oxidation, we get specific colors. This is what the flame video by The Fabulab focused on in their entry for Alan Alda’s Flame Challenge. I direct your attention to 1:08 and the discussion of electrons.


Metals are the simplest example (and most used) example of oxidation as the loss of electrons and the color change associated. Because some electrons are lost, we now have a different set of electrons changing energy and a different color appears.



From here, it is easy to see how fireworks fall into this category of explosives. Fireworks are always being further refined to produce a specific set of light and sound. For a bit more information, this video gets fairly specific.

The vast majority of explosives in use today are considered chemical explosives. This covers a range of materials, including the aforementioned black powder and fireworks, nitroglycerin, dynamite, plastic explosives (C4 for Mythbusters and sci-fi television show fans), and the ones with water now restricting the amount of water one is allowed to bring onto an airplane in the U.S.


Another type of explosive is a nuclear explosive. The energy in these explosives come from a nuclear reaction. Wikipedia differentiates types of nuclear explosions into stellar and man-made. Another way to differentiate nuclear reactions is by fission and fusion. The explosions at the heart of stars fall under nuclear fusion and are called stellar nucleosynthesis.


Nuclear fusion is the process of forcing 2 atoms into 1 new, larger atom.  The CNO cycle, diagrammed here, is one of the nuclear fusion reactions occurring in stellar nucleosynthesis.


Source

Nuclear fission is the process involved in nuclear weapons. 


Nuclear fission is the process of dividing an atom into 2 or more smaller atoms. In both nuclear fusion and nuclear fission processes, specific types of radiation are emitted because the new atoms produced do not have the same energy as the starting material. The radiation emitted in these reactions is not just from a change of electrons but from a change from the nucleus of the atom. This emission of radiation is part of the light and heat from the sun and the light and heat of a nuclear bomb.


The third and last type of explosive I will cover is a mechanical explosive. These explosions occur as a purely physical process, but can then incite a chemical explosion. Mechanical explosions occur due to a sudden release of a build up of pressure. A specific kind of these explosions are under conditions where a liquid is pressurized in a vessel and a rupture brings it above its boiling point, called a boiling liquid expanding vapor explosion, BLEVE. Steam powered trains were sometimes damaged by these type of explosions. An explosion of a water heater falls into this category. Mechanical explosions are the rarest and perhaps least covered types of explosives.


Water heater explosion by the Mythbusters. 



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

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

Book Review: Science Myths Unmasked: Exposing the misconceptions and counterfeits forged by bad science books


 

By DXS Biology Editor Jeanne Garbarino

Do you remember that old candle experiment involving a lit candle in a jar? You know, the one where you place a lit candle in a bowl of water, then place a jar over the candle, and rather quickly, the candle extinguishes? If you were like me, you probably learned that the candle goes out because all of the oxygen gets used up (oxygen is a requirement for combustion).  However, according to David Isaac Rudel in his multi-volume series Science Myths Unmasked, this is one of the many science demonstrations that are wholly misinterpreted.

Unfortunately, the science textbooks used by thousands of schools across the US are chock-full of what Rudel calls “pseudo-explanations” for many complicated scientific phenomena. Instead of presenting clear explanations, including the establishment of a basic scientific foundation, many science textbooks present certain concepts using shortcuts, with the assumption that these so-called shortcuts make it easier for kids to understand science. 

Rudel argues that these shortcuts, which are often associated with an “abuse of [scientific] language,” only confuse students. In fact, included on the back cover of Science Myths Unmasked, Volume 2: Physical Sciences is a quote from Richard Feynman regarding science textbooks: “They said things that were useless, mixed-up, ambiguous, confusing, and partially incorrect. How anybody can learn science from these books, I do not know, because it’s not science.”

My husband, a public high school chemistry and biology teacher, is wholeheartedly aligned with this particular opinion of Feynman and Rudel and for many years, has not used a textbook to teach science. When I asked why, he simply stated, “They just confuse the kids.” 

As an example to what is wrong with science textbooks, let’s get back to the candle-in-a-jar experiment. In Science Myths Unmasked Volume 2: Physical Science, this very common scientific demonstration is thoroughly dissected, explaining why “the candle goes out when the oxygen content of the air is no longer high enough to support combustion” is an incorrect conclusion found in many textbooks, especially since it overlooks how the products of combustion affect the candle flame. After elaborating on the precise conditions point by point, and providing an outline for easy demonstrations to “expose the myth,” the following is stated:

Candles in closed containers do not go out because they use up all the oxygen.  Rather, the hot carbon dioxide (and to a lesser extent water vapor) given off in combustion accumulates at the top, pushing down other gases (most importantly, oxygen), and eventually stifles the flame. 

If the jar’s rim is submerged in water, the liquid rises not because water is replacing the oxygen used up in combustion.  Rather, the air inside the jar cools as the flame dies down and hot gases offload heat to the glass container.  As the air cools, it applies less pressure to the water than it did when the jar was first put over the candle.  The water rises as a result of the decreasing pressure from the air against it.           

In the Science Myths Unmasked series, a great number scientific factoids and processes that are often misrepresented in the classroom are correctly explained, and in great detail.  In addition to the candle experiment described above, Rudel tackles simple machines, circuits, phase change, and waves, just to name a few. However, this book is not for those without at least some background in science, as it does get technical. I would, though, recommend that these books find a way onto the shelves of science educators, as it seems they would benefit the most from the lessons and demonstrations covered. It is also good for people who, like me, have a scientific background and wish to properly explain scientific concepts to their kids, as I am sure those questions are bound to come up.  

For more on the Science Myths Unmasked series, go here.    

Two Science Online 2012 sessions for your consideration


Tomorrow, I head for North Carolina to attend Science Online 2012. I attended last year as an an information sponge and observer who knew no one and experienced some highlights and lowlights. This year, I’m attending as a participant and as a moderator of two sessions. The first session, on Thursday afternoon, is with Deborah Blum, and we’ll be leading a discussion about how and when to include basic science in health and medical writing without distracting the reader. The second session I’m moderating is with Maia Szalavitz, and we’ll be talking about whether or not it’s possible to write in health and medicine as an advocate and still be even-handed. Session descriptions are below, as are the topics that we’ll be tossing around for discussion.


Thursday, 2:45 p.m.: The basic science behind the medical research: Where to find it, how and when to use it. 

Sometimes, a medical story makes no sense without the context of the basic science–the molecules, cells, and processes that led to the medical results. At other times, inclusion of the basic science can simply enhance the story. How can science writers, especially without specific training in science, find, understand, and explain that context? As important, when should they use it? The answers to the second question can depend on publishing context, intent, and word count. This session will involve moderators with experience incorporating basic science information into medically based pieces with their insights into the whens and whys of using it. The session will also include specific examples of what the moderators and audience have found works and doesn’t work from their own writing.

Deborah and I have been talking about some issues we’d like to raise for discussion. The possibilities are expansive. Some highlights:

  • Scientific explanation (and understanding) is the foundation for the best science writing. In fact, if the writer doesn’t understand the science, he or she may miss the most important part of the story. But we worry that pausing to explain can slow a story down or disrupt the flow. In print, writers deal with this by condensing and simplifying explanations and also by trying to make them lively and vivid, such as by use of analogy. But online, we use hotlinks as often if not more often for the same purpose. 
  • Reaching a balance between links and prose can be a difficult task. Another possible pitfall is writing an explanation that’s more about teaching ourselves than it is about informing a reader sufficiently for story comprehension. How many writers run into that problem?
  • On-line the temptation is to do the barest explanation and the link to the fuller account, but that approach has pros and cons. More information is available to the reader and the sourcing is transparent. But how often do readers follow those links – and how often do they return? Issues with links include that they are not necessarily evergreen or can lose reader (can be exit portal), or that the reader may not use them at all, thus losing some of the story’s relevant information.
  • A reader may actually learn more from a print story where there are no built-in escape clauses. So how does the on-line science writer best construct a story that illuminates the subject? Are readers learning as much for our work as they do from a print version? (And there’s that age-old question of, Are we here to teach or to inform?)
  • Are we diminishing our own craft if we use links to let others tell the story for us? If we simply link out rather than working to supply an accessible explanation, negatives could include not pushing ourselves as writers and not expanding our own knowledge base, both essential to our craft.
  • How much do we actually owe our readers here? How much work should we expect them to do?
  • What are some ways to address issues of flow, balance, clarity? One possibility is, of course, expert quotes. Twitter is buzzing with scientists, many of whom likely would be pleased to explain a concept or brainstorm about it. (I’ve helped people who have “crowdsourced” in this way for a story, just providing an understandable, basic explanation for something complex).
  • Deborah and I are considering a challenge for the audience with a couple of basic science descriptives, to define them for a non-expert audience without using typical hackneyed phrases. Ideas for this challenge are welcome.
  • We also will feature some examples from our own work in which we think we bollixed up something in trying to explain it (overexplained or did it more for our own understanding than the reader’s) and examples from our own or others’ work of good accessible writing explaining a basic concept. We particularly want to show some explanations of quite complicated concepts–some that worked, some that didn’t. Suggestions for these are welcome!
  • Finally, when we do use links in our online writing– what consitutes a quality link?
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Saturday, 10:45 a.m.: Advocacy in medical blogging/communication. Can you be an advocate and still be fair?
There is already a session on how reporting facts on controversial topics can lead to accusations of advocacy. But what if you *are* an avowed advocate in a medical context, either as a person with a specific condition (autism, multiple sclerosis, cancer, heart disease) or an ally? How can you, as a self-advocate or ally of an advocate, still retain credibility–and for what audience?

The genesis of this session was my experience in the autism community. I’m an advocate of neurodiversity, the basic premise of which is that people of all neurologies have potential that should be sought, emphasized, and nurtured over their disabilities. Maia, the co-moderator of our session, has her own story of advocacy to tell as a writer about pain, pain medication, mental health, and addiction. 


Either of these topics is controversial, and when you’ve put yourself forward as an advocate, how can you also present as a trustworthy voice on the subject? Maia and I will lead a discussion that will hit, among other things, on the following topics that we hope will lead to a vigorous exchange and input from people whose advocacy is in other arenas:

  • Can stating facts or scientific findings themselves lead to a perception of advocacy? Maia’s experience is, for example, about observing that heroin doesn’t addict everyone who tries it. My example is about noting the facts from research studies that have identified no autism-vaccine link.
  • Any time either of us talks about vaccines or medications for mental health, we’ve run into accusations of being a “Big Pharma tool” or with worse terminology. What response do such accusations require, and what constitutes a conflict of interest here? What is the level of corruption of data that’s linked to pharma involvement? If they are the only possible source of funding for particular studies…do we ignore their data completely?
  • We both agree that having an advocacy bias seems to strengthen our skeptical thinking skills, that it leads us to dig into data with an attitude of looking for facts and going beyond the conventional wisdom in a way that someone less invested might not do. Would audience members agree?
  • In keeping with that, are advocates in fact in some ways more willing to acknowledge complexities and grey areas rather than reducing every situation to black and white?
  • We also want to talk about how the passion of advocacy can lead to a level of expertise that may not be as easily obtained without some bias.
  • That said, another issue that then arises is, How do you grapple with confirmation bias? We argue that you have to consciously be ready to shift angle and conclusions when new information drives you that way–just as a scientist should.
  • One issue that has come to the forefront lately is the idea of false equivalence in reporting. Does being an advocate lead to less introduction of false equivalence?
  • We argue that you may not be objective but that you can still be fair–and welcome discussion about that assertion.
  • And as Deborah and I are doing, we’re planning a couple of challenge questions for discussants to get things moving and to produce some examples of our own when we let our bias interfere too much and when we felt that we remained fair.

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The entire conference agenda looks so delicious, so full of moderators and session leaders whom I admire, people I know will have insights and new viewpoints for me. The sheer expanse of choice has left me as-yet unable to select for myself which sessions I will attend. If you’re in the planning stages and see something you like for either of these sessions, please join us and…bring your discussion ideas! 


See you in NC.