Ice Ice Baby

                Ice floats in water.  Ice is less dense than water.  Ice has a more open structure than water.

                What in the world does all that mean aside from making my summer beverage more refreshing?

                I’m going to tell you.  No!  Wait.  I’m going to show you.

                Let’s start at Figure 24.4 from my Play Ball! post (GO PHILLIES!).  It shows how atoms/molecules/ions (blue circles in the figure) line up in the solid, liquid and gas phases.  You’ll notice that the atoms/molecules/ions are very close together in the solid phase, move further apart in the liquid phase and are further apart still in the gaseous phase.  This is generally how close atoms in each phase can be described.  Key word: generally.

Now let’s discuss density.  Sure, we all learned the equation in third grade – mass divided my volume – but what does that mean in real words?  Mass is directly related to the number of atoms/molecules/ions (also called particles) present.  So, if you look at the same volume of a solid, liquid or a gas, how many particles can you find there?  Figure 69.1 shows that for a particular volume (orange square) the solid has 9 particles; the liquid has 4 and the gas has 1.  The solid’s density is greatest (most amount of atoms/molecules/ions in the volume), the gas’s density is least and liquid is in the middle.  This means that if we had a cube of solid nitrogen and a glass of liquid nitrogen (brr!) and we dropped the cube in the liquid, the cube would sink to the bottom.  Why?  Because the cube is MORE dense than the liquid.  Again, this is generally true for most substances.

When particles come together to form a solid, many things need to be considered such as the size and charge of the particles.  The atoms/molecules/ions need to align themselves as close together as possible in the solid form, but without ticking each other off.  For example, two positive charges close together would be repulsive and unfavorable.  How do particles deal with this balancing act?

                To explain this, I’m going to show you two examples: solid NaCl (table salt) and solid water (ice).

NaCl: Solid NaCl is ions of sodium and chloride all packed very closely together.  A sodium ion is positively charged while a chloride ion is negative charged.  Obviously two chlorides aren’t packing directly next to each other because they both have the same charge.  Instead, the ions arrange themselves such that a chloride ion is surrounded by sodium ions in a very ordered array.  This way, the negatively charged chlorides are pacified by the positively charged sodiums enough such that the ions can pack close together (Figure 69.2).

Water:  I’ve discussed water and its fun properties a few times on this blog: Soap! and What Does Water Look Like? come to mind so you should be familiar with what a molecule of water looks like and how parts of it are positively and negative charged (Figure 69.3).  Similar to NaCl, water must not place two positive or negative charges too close together in the solid form.  Water’s shape, however, is quite different than ions of Na⁺ and Cl^- so its shape comes into play when ordering itself in the solid phase.  Figure 69.4 shows how water molecules line up when forming ice.  Compare it to solid NaCl (Figure 69.2) and the generic example of solids I showed in Figure 24.4.  Do you notice the differences?

Water molecules adopt a very open conformation.  Yes, the water molecules are close together, but there’s a lot of room between the molecules, which is not true in NaCl.  This kind of arrangement minimizes the steric and charge clashing of water molecules the most so it is the most favorable way that water molecules can pack together.  It is not air between those water molecules, it is empty space (I discussed air and its properties in my Play Ball! Post).

                If we now return the idea of Figure 69.2, but redraw the solid phase so it more accurately represents water, we can see that liquid water, not solid water, has the most molecules per volume.  

                As the ice is warmed to form water, the lovely ordered structure falls apart.  Instead of being held in an array, the molecules fall into a disordered jumble which results in more water molecules being present in a particular volume than would be true for ice.  More water molecules in the same volume of space means a higher density (Figure 69.5).  Solid water is LESS dense than liquid water and therefore floats in it.     

                Exceptions exist for every rule and, in the case of decreasing density from solid to liquid to gas, water is the exception.

Ions: Atoms that have either more or less electrons than the number of protons in their nuclei.

Density: the measure of how much mass is present per unit volume.  Less dense items float in more dense items.

Particles: an alternative name for atoms, molecules, or ions

REFERENCES

Zumdahl, Steven S. “Chemical Principles, 4^th Edition” (2002) Houghton Mifflin Company, Boston, MA.

Migraines

                 “I’ve had a strange day.”

                “Oh?”

                “I spilled formaldehyde on my desk today and now I smell it everywhere.  I can’t wash my hands enough.  It’s not like I spilled it on myself, just on the bench top, but the smell!  I feel like it’s on everything!”

                “Weird.”

                “Oh, that’s not all.  My salad tasted like everything was coated in sugar.  And those crackers at Happy Hour?  Peanut butter-flavored.”

                “Okay.  The crackers were not made with peanuts and I’m assuming you didn’t dip your lettuce in sugar.  What’s wrong with you?”

                Soon after, I came down with a terrible headache associated with sensitivity to light and smells.  The pain was originally diffuse but then localized to a throbbing area over my right eye.  It took a few doses of Excedrin coupled with a dark room, sleep and lots of positive thinking from myself before the pain receded.  Unfortunately, the nausea took a few more days to go away.  The residual pain roamed to the left side of my head and back to my right side before throbbing again twenty fours later.  One last dose of Excedrin extinguished it.

                Migraine is a complex brain disorder – it is not simply “a bad headache.”  The International Headache Society has criteria that define migraines with and without aura, cluster headaches and tension headaches.  You can read the definitions here, but the most common characteristics of a migraine headache are pain on one side of the head that pulsates or throbs, inhibition of daily activities, sensitivity to light or sound and nausea or vomiting.  

                What is even more interesting is that migraine headaches are not the only kind: abdominal migraines are experienced by nearly 2% of all children.  The severe pain typically occurs in the abdomen near the belly button and is associated with nausea, cramping and vomiting.  Interestingly, many of these patients go on to suffer from migraine headaches as an adult.  

                The underlying molecular mechanisms that lead to a migraine are not well understood.  In my research for this post, I found many migraine research papers in journals that focus on neuroscience and several ideas that neurons (brain cells) hold the keys to understanding what triggers migraines.  Some recent studies have made use of functional magnetic resonance imaging (fMRI, or as my favorite podcasters call it: the wonder machine).  These types of studies can identify areas of the brain that become activated prior to or during migraine headaches.  Since the symptoms combine pain, light, sound, and smell stimuli, the overwhelming conclusions must be that patients suffer from occasional disturbances of their central nervous system’s ability to process sensory information.  fMRI results have highlighted the brain stem, as well as other brain structures, as potential key players.

                Anyone who suffers from migraines will talk about their triggers, which are environmental situations that commonly lead to a migraine attack.  For me, triggers are dehydration and alcohol; for others, it might be caffeine or strong smells.  They are variable and personal.  In addition, migraines tend run in families.  This fact implies that something in our genes also plays a role.  To this end, researchers are hunting through the genomes of migraine sufferers and comparing their results with non-migraine patients to identify any common differences.

                How is this accomplished?  I will give you an example!

                A paper was published recently that was a combined effort between scientists in Australia, Tasmania, Germany and the United States that focused on identifying SNPs or single nucleotide polymorphisms on the X chromosome of migraine sufferers in an isolated population.  Let’s break down what that means.

SNPs: As was covered in the Central Dogma post, DNA leads to RNA, which leads to protein.  Our DNA is actually a blueprint for building all the proteins our cells need to survive.  The As, Gs, Ts and Cs encode for the amino acids necessary to build a functional protein.  The proteins then carry out all sorts of biological processes.  

Genes are more than that, though.  When an RNA molecule is transcribed from DNA gene, it has the information necessary to make a particular protein but it also has extra bases added to the end (called the 5’ untranslated region or 5’-UTR).  In addition, the RNA molecule has regions that must be cut out and spliced back together before the ribosome can properly read it.  The sequence of bases within the gene is important not only for making a functional protein, but also for ensuring proper processing of a new RNA molecule.

Sometimes, for whatever reason, a base in the DNA becomes something else.  For example, perhaps at one particular point, where most people have a G, you have a T.  It might affect what amino acid is placed in the protein or it might affect processing of the RNA molecule.  It also might affect nothing; considering you are alive and well, the change must not lead to catastrophic consequences on cellular behavior.  These changes at one particular base within a DNA molecule are called single (just one) nucleotide (base) polymorphisms (differences).

X chromosome: Human cells have 23 chromosomes with two of them being the sex chromosomes, X and Y.  A male has an X and an Y while a female has two Xs.  Females are more likely to suffer from migraines as opposed to men so when looking for SNPs these scientists chose to focus on the X chromosome.

Isolated Population: As described above, migraine is a combination of environmental factors (triggers) and genetics (since migraines run in families).  Teasing out the relative contribution of each on a person’s likelihood of developing migraines is difficult.  Part of what keeps a population healthy is genetic variability.  Scientists might be able to identify SNPs in migraine patients across the world, but those people probably each have their own very diverse set of SNPs that might counteract, exacerbate or have no effect on migraines.  The best way to identify DNA base changes that might play a role in migraines is to look at a population where most people have exactly the same genes.  

While difficult to achieve in this day and age, populations like this still exist!  The scientists in this paper went to Norfolk Island, an off shoot of Pitcairn Island, in the Pacific Ocean.  The inhabitants are all descendants of the Bounty mutineers and their Tahitian women (I love the story of the Bounty’s mutiny!!  READ IT!).  The population has also been incredibly isolated since that time and those living there share a significant proportion of their genes.

                And so, the scientists sequenced the X chromosome of many migraine and non-migraine patients on the island to identify nucleotide differences between the two groups.  A particular area of the X chromosome was identified as having a few SNPs.  One protein at this locus in particular, hephaestin, is known to be expressed in several areas of the brain and has been shown in mice to be necessary for iron homeostasis in the central nervous system.  Ah – we come full circle!

REFERENCES             

Abdominal Migraines: http://www.webmd.com/migraines-headaches/abdominal-migraines-children-adults

IHS Headache Standards: http://www.medicine.ox.ac.uk/bandolier/booth/migraine/IHScrit.html

Migraine Info: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001728/

 

Russo et al. “The pain in migraine beyond the pain of migraine.” (2012) Neurol. Sci. 33 (Suppl 1), pgs S103 – 106.

Maher et al. “X Chromosome Associated Scan of the Norfolk Island Genetic Isolate Provides Evidence for a Novel Migraine Susceptibility Locus at Xq12.” (2012) PLos One, 7(5), e37903

The Lost City of Z: A Review

            I love to read.  I’ll read just about any non-fiction book that is put in front of me as long I’m interested in the topic (and I’m interested in most topics).  My mother often tells me that I have strange tastes in books because I’ll happily jump from The Goblet of Fire (fiction, Harry Potter) to The Secret Life of Lobsters (non-fiction, an in depth study of a lobster’s habitat and mating techniques).  My library has “In the Heart of The Sea” (the real-life inspiration for Moby Dick), several books about The Bounty (I have a thing for old sea stories!), and “The Boy who came back from Heaven” (a father’s narrative about his young son’s near death experience).  Seriously – I’ll read anything.  When I happened upon “The Lost City of Z” by David Grann, I assumed it was right up my alley: non-fiction, exploration, science-bent.  What’s not to love?  Apparently, a lot.  While I admit that some fascinating details exist in this story, the overall arc of the book did not work for me.

The Basics:

Percy Harrison Fawcett disappeared on his (obviously) final expedition into the Amazon rainforest.  In his later years, he had become obsessed with finding the fabled El Dorado, or as he referred to it, Z.  Fawcett was an early protégé of Britian’s Royal Geographical Society and was sent to map parts of Brazil and Argentina at age 39.  He then continued to return to the Amazon on several expeditions and was one of few experts on this region in the world.  Over the years, he developed a reputation for ceaseless penetration of the unknown forest, friendly relations with native inhabitants, robust health in harsh conditions, and a love for exploration.  

Unfortunately, this devotion pushed his family to the brink of destitution.  He truly believed that El Dorado existed and if he could just find it, the subsequent windfall would support his wife and children.  Gambling on this discovery, Fawcett had lost much of his savings and some of his reputation.  It took him years to raise the necessary money for his final trek into the unknown with his eldest son Jack and his close friend Raleigh.  His wife Nina staunchly supported these efforts and served as Fawcett’s voice and spokesperson while he was away.

But Fawcett never came back.  What happened to his party of three in South America?  The moral of this book is that we’ll never know.

The Good:

This time period is notable for its ballooning of scientific knowledge.  I’ve often wanted to research the different scientific societies of this age and the public’s reaction to them.  Fawcett was contemporaries with Thomas Edison, Nikola Tesla and Edward Shackleton; he came in the wake of Charles Darwin.  This was a time when regular people would attend scientific lectures to learn what they knew.  Some were so inspired by these talks that they wrote novels involving the theories (such as, Sir Arthur Conan Doyle with “TheLost World,” who later inspired Michael Crichton).  David Grann did an excellent job describing the times and the inertia that placed Fawcett and his competitor Dr. Alexander Rice deep in the Amazon rainforest. 

The Bad:

Many people went searching for Fawcett over the years.  Spurred by the success of H.M. Stanley finding David Livingstone, new explorers plunged into the rainforest in search of Percy Fawcett.  Sadly, many of those adventurers never returned either.  These tales are all cliff-hangers and excellent hooks to begin a story.  Unfortunately, Grann poorly executes and confuses the reader (ie - me).  Fawcett goes missing in Chapter 1.  James Lynch is kidnapped by natives while trying to find Fawcett in Chapter 2.  Chapter 3 features the author himself and he suspensefully tells us that he, too, is lost in the Amazon looking for Fawcett.  What the what?  I can’t keep track of these people and the time periods.  It was at this point that I nearly gave up on this crazy book, but I did persevere.  

Sadly, the pay off for Lynch’s tale comes a few chapters later in the form of Grann saying “And then I met James Lynch.”  If you’re going to set up the mystery, follow it through logically.  We never did learn why Grann was “lost in the Amazon,” but a full 250 pages will pass before we are reunited with Fawcett’s story and his obsession for Z.  Two hundred and fifty pages.  The book is called “The Lost City of Z” and it’s only the final few chapters that discuss it and even then, it’s tangential to Fawcett’s disappearance.  I wanted to know so much more about Z.  Maybe there isn’t much to know, but then name the book “Fawcett’s Obsession” and don’t set me up to be angry when I never hear much about the namesake of the book. 

The Ugly:

A key character in this book is the Amazon.  Grann does provide some background about the river itself and explains in vivid detail the bugs, plants, and animal-life inside the rainforest.  There are times when you can truly feel the hunger, bug bites or desperation of those who are trekking under the canopy.  One part about maggots moving inside a man’s elbow joint haunted and disgusted me for several days.    

However, in contrast to the flora and fauna explanations, very little substantial information is offered up about the Indians living there.  Grann mentions often how westerners were convinced that civilizations could not survive there, yet the many appearances by Indian tribes suggested otherwise.  Clearly some things are known about these people or we wouldn’t have Grann chatting it up with them (and being offered tales about Fawcett’s bones at the end, a truly eye-rolling event), but the author never shares.  He hides half of the main character’s development from us and I was left highly disappointed.  

                In all, the book was informative and interesting, but a bit difficult to slog through since I was mostly interested in Z.  If you love adventure stories, I’d recommend this book, but please go in with your eyes open.  This isn’t a story about El Dorado or the Amazon, it’s simply a narrative about a man and the times in which he lived.  

                Other books about adventures that I, in comparison, highly recommend:

Into Thin Air by Jon Kraukauer (anything by this man, actually)

The trio of books: Mutiny on the Bounty, Men Against the Sea, and Pitcarin Island.  These might be my absolute favorites ever.  They are not non-fiction, but give depth to an incredible true story.  They will inspire you to research Captain William Bligh and First Mate Fletcher Christian.  Do read them.