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.

A Cry from a Scientist

                 This post is going to be a lot of venting so I apologize in advance.  However, part of science is anger – full-fledged, I want to throw something against the wall (or kick a trashcan across the room) seething rage.  Mine has been building up for close to two years and there are days when I feel like I can’t take it much longer.  Lucky you gets to read it, but at least you can read it knowing that I am not the only scientist with these thoughts or rages.  At one point or another, all professionals reach a point where life has handed them too much.

                I read a lot of message boards about various life topics.  I enjoy being able to escape science every now and then because, let’s be honest, when your experiments aren’t working, you are about two inches away from jumping off a cliff.  Recently, I’ve been reading my fair share of pregnancy and marriage boards because that’s the state of life I’m currently living.  It’s interesting to hear from real people about what happens next.  Unfortunately for me, I’ve read too many vaccine debate threads recently.  They make me want to tear my hair out.  It’s no one’s fault, of course – the internet is littered with horrible websites expounding ideas that are entirely false.  And then, in this celebrity-obsessed culture, we have Jenny McCarthy spewing some of the most inaccurate theories ever that some people are more than willing to lap up, so I want to throttle her.  Plus, we have the media who finds a story and holds onto it obsessively like a dog that has gotten his very first treat.  One paper linked vaccines to autism; tens of papers have since refuted it and all but one of the authors on the original paper has recanted.  Yet, the “debate” rages on. 

Today, an article appeared on CNN.com entitled “Science journal could provide recipe for bioterrorism.”  I cursed too many times to repeat my exact reaction here when I read it.  The best part?  It’s at least a week too late; Nature published one of the two articles in question last week.  I posted about it on both this blog and Dr. Amedeo.  So, if the recipe for bioterrorism is out there (which it really isn’t) then it was leaked seven days ago.  But, you know what really gets me about the article?  It’s inflammatory journalism about a topic that not too many people have the background to understand.  I am in no way saying they are ill educated - I am saying that they need the proper setting to understand why these papers are linked to bioterrorism and to see that they aren't.  CNN.com doesn't provide such context. They just spew out words like “avian flu,” “pandemic,” and “d-e-a-t-h” so people will read it and think that scientists are irresponsible.  The fact that a moratorium was placed on this research months ago and that many major scientific institutions discussed the research before publishing it is inconsequential.  Scientists are out to make a super-duper avian flu, they are unethically publishing this work, bioterrorists are going to read it to kill us all, and we’re definitely covering up that vaccines cause autism.  Oh, and we’re responsible for all the “chemicals” in the world.  What else?

Let me just be one scientist to say: holy god, we are NOT doing any of the above.  Also, don’t get your scientific information from your local news, CNN, FoxNews, a freaking celebrity or anyone other than a real live, honest-to-goodness scientist with a Ph.D. who has done real research that has been published in a peer-reviewed journal.

Let’s also talk about these statements: “All this money given to scientific research and they still don’t have a cure for cancer!” or “How has science not come up with a medication for that yet?”  Believe me – if it’s a subject worthy of research, someone out there is working on it.  Do you know how many labs are working on cancer research?  “Cancer” is also such an all-inclusive word.  Each cancer is different and has its own set of problems.  This isn’t going to be a one-medicine-fits-all cure.  Scientific research is also expensive.  Supplies, ideas, and troubleshooting experiments take time and money.  And don’t think that the scientists doing the research are making money hand over fist here, either.  I could tell you what I made as a graduate student (which is a position in lab just as hard-working as a post doctoral associate or staff scientist), but I don’t want to scare off anyone who might be interested in science.  What I make as a post doc is a matter of public knowledge and can be found on the NIH’swebsite.  Yes, the government determines the worth of my Ph.D. and, let me tell you, they don’t think highly of it.  The scientists who are doing the cutting edge research are not fairly compensated for their time, efforts, and thoughts.  And then, as a thank you for all the work we do, we are slandered in the media, discussed incorrectly by the general public, and generally on the receiving end of all sorts of fear-mongering.

All of this goes back to why I write this blog.  I want people to understand.  I want more people to get it.  I wish everyone understood that we’re in the trenches here, getting little recognition or payment and doing it out of our love for science.  I’m sure every profession has a part of the experience ladder like this.  I am not special or different, but I at least have a platform to vent my frustrations.  I know that my husband could sit down and write an equally impassioned post about how lawyers are thought to be something they aren’t, as well.  He has taught me quite a bit about how the law profession works and removed a lot of my knee-jerk reactions to lawyers.  He should get a blog, too.

Read Science (www.sciencemag.org) or Nature (www.nature.com) for excellent information pertaining to scientific topics.

Order in Nature

                It’s spring!  Not that this winter on the East Coast was bad, but I am always happy to leave those cold months behind.  I like being able to roll out of bed, put on some flip flops and walk to the bagel store at 8am on Saturday without being cold.  In fact, I like walking anywhere without being cold.  I’m not a big fan of cold.  Or wind.  Or the word “blustery.”  

                The upturn in temperatures means more greenery, more life outside and more flowers.  One of my most (er, only) favorite parts of living in Boston was the Public Garden in springtime.  The flowers and trees were always so gorgeous.  Now I have cherry blossoms to look at and petals flying all over Rittenhouse Square in Philadelphia.  I still love it.

                Here are some beautiful photographs of flowers that I found on NationalGeographic.  

                So pretty.  So ordered.  Life is very ordered, is not?  These flowers have very specific patterns.  The body of a human being is a well-engineered machine.  People build homes, cities, and roadways to create order out of the world.  Our computers have files that are logically organized and our homes have places for just about everything.

                But then… things aren’t ordered, are they?  I’ve neglected my apartment for the past two months due to illness (damn kidneys!) and it swiftly became a war zone.  Bring one baby into a home and blankets, toys, bottles, and diapers are quickly strewn about.  It takes a lot of energy to keep things organized and almost none to mess it up.  

                In science, we talk about entropy (also referred to as S) and often times equate it to the degree of disorder in a system.  Higher entropy means more disorder and lower entropy means less disorder.   Just as a ball will roll down a hill or heat will flow from a warm place to a cold place, systems tend towards states of more disorder.  By sheer probability, this has to be the case.  Think about a deck of cards.  There is only one way that deck of 52 cards is ordered (in a stack on the table), but there are literally millions of other ways the cards could be thrown around the room.  The probability of your deck of cards being a mess is nearly 100%.

                The second law of thermodynamics states that the entropy of the universe is always increasing.  This means that the universe is always moving towards more and more disorder.  If that is true, how do we explain those beautifully, ordered flowers?  Or living organisms with organized bodies?  Or any kind of order in our world?

                Let’s use the example of the deck of cards.  

   We are going to call the deck of cards our system and everything else the surroundings.

System:

Imagine that all 52 cards are randomly spread across the floor.  That deck of cards has a large amount of entropy. 

Now, you pick up the cards, organize them and stack them neatly on the table.  The deck of cards now has a small amount of entropy.

Scientists like to talk about the change in the system.  A natural question for a scientist to ask about our system now is “What was the change in entropy?” 

Change in entropy can also be written as ΔS and means this:

(Entropy of the final state of our cards) minus (the entropy of the initial state of our cards)

For our purposes, the actual number is not important.  We are more interested to know if that number is positive or negative.

What was the entropy of our final state of cards?  A small number.

What was the entropy of our initial state of cards? A large number.

A small number minus a large number equals a negative number.  

If you told a scientist that the ΔS of your system was negative, he would know immediately that your system went from more disorder to less disorder.

Surroundings:

Systems don’t live in vaccuums.  Depending on what the system does, the system will absolutely affect its surroundings.  If the system heats up, that heat will dissipate into the surroundings.  If the system cools down, it might draw heat from the surroundings into it.  These two parts are intertwined.

So, by picking up the deck and organizing the cards, what have we done to the surroundings?

A person came in, moved around haphazardly scattering air molecules all over the place.  The deck was placed together and probably tapped around a lot to make cards match in height, which probably increased the heat and movement of the air molecules.  Before that person came in, the air was calm.  

Think about what the ΔS of the surroundings would be.

What was the entropy of our initial state? Low.  Lots of order.

What was the entropy of our final state?  Higher.  More disorder.

A large number minus a smaller number equals a positive number.

If you told a scientist that the ΔS of your surroundings was positive, he would know immediately that your surroundings went from less disorder to more disorder.

Second Law of Thermodynamics

This law says that the entropy of the universe is always increasing.  It is always going from less disorder to more disorder.  ΔS universe is always positive.  

So, why did we spend so much time talking about a system and surroundings?

Because this is how the three are related:

ΔS universe = ΔS system + ΔS surroundings

The second law states that ΔS universe must be a positive number.

ΔS system + ΔS surroundings must equal a positive number. 

For our case:

ΔS universe = negative number + positive number

As long as the surroundings become very disordered (a large positive number), then the ΔS universe will be a positive number. 

If you look at any system and surrounding situation in nature, carefully measure its entropy changes and add them together, you’ll always get a positive number.  If they don’t add up to a positive number, then it does not occur in nature.

So, the flowers and people and organized life exist in this world.  If you think of them as systems, then their entropy is definitely decreasing.  However, they must disorder their surroundings quite greatly to compensate.  This is also true.  People are constantly moving, breathing and changing their surroundings.  Plants are no different.  Living organisms are constantly uptaking some nutrients and giving off others.  Their surroundings are always changing.  As the organism gets more ordered, the surroundings become more disordered and so the universe becomes more disordered and we’re all here.

Okay - if I've totally confused you, then here are more pretty flower pictures to relax your brain.

REFERENCES

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

My Pyelonephritis

              It started Wednesday night with a painful bladder and frequent pee breaks.  I pretended that the racking chills and shaking I experienced on my way to work on Thursday was just stress.  Being cooped up in a train for forty five minutes with the above symptoms was enough to worry anyone.  I decided the mild pain and pressure in the middle of my back was due to leaning over my computer.  I happily assured myself that, after sitting at my desk for 1.5 hours without a bathroom break, there wasn’t anything seriously wrong.  Unfortunately, at 2am on Friday morning, the intense shivering gained a new symptom: vomiting.  Off the emergency room – I was not okay.

                This is why I love the city.  At any time of day, there is a place where everyone is awake and waiting to help you, get you some place or give you food.  Cabs were plentiful at 3am, cheery doctors and nurses were waiting for me, and some people-watching helped pass the time.  Please don’t think I was in a good mood (quite the opposite), but I appreciated the beacon of civilization in the middle of a miserable evening.  I didn’t feel so alone.

                A quick urine test sealed my fate – pyelonephritis, also known as a kidney infection.  Great.  May I have some antibiotics, please, sir?

How does this happen?  Urinary tract infections (UTIs) happen when bacteria get in the urethra/bladder.  They find it very cozy there and begin to multiply.  Early symptoms include bladder pain, frequent need to pee, and pain during urination.  If left untreated, the bacteria can spread up to your kidneys.  The symptoms then progress to back pain, fever, shaking chills and vomiting.  Women are more likely to get UTIs than men due to shorter urethras and proximity to a haven of E. coli.  

How does the test work? I had wanted a urine analysis on Thursday afternoon but was unable to get one (because of my own inability to procure a primary care doctor when switching insurance.  Seriously, this whole debacle was a series of failures on my part).  What would a urine analysis have shown?

                Human urine contains nitrate, shown in Figure 51.1.  Some bacteria are able to uptake nitrate and turn it into nitrite (Figure 51.1).  Presence of nitrite in your urine suggests bacteria are present!

               I got my urine analysis in the emergency room.  After telling my story to the doctor, she asked the nurse if my analysis showed blood because my symptoms were more in tune with kidney stones than an infection.  

               "No," he happily replied.  "No blood, but she had nitrites!"

How do the antibiotics work? In order to clear the infection, the bacteria must be killed so antibiotics are necessary.  The word antibiotic is quite simple: “anti” means against in Greek, while “bios” means “life.”  Many different kinds of antibiotics exist, but they all do the same general thing: disrupt bacterial cells without disrupting human cells.  How does one achieve this?

                In broad strokes, bacteria do the same functions as human cells: replicate their DNA, transcribe DNA into RNA, translate RNA into protein (Central Dogmapost), but the proteins they use to do it are a bit different than human proteins.  For example, a protein known as DNA Polymerase is responsible for replicating DNA in cells.  Human DNA polymerase looks very different than bacterial DNA polymerase.  If you can identify a drug that will – say – bind to bacterial DNA polymerase and make it unable to function, then the bacteria will die.  Since human DNA polymerase looks different, that same molecule can’t inactive human DNA polymerase.  Win.  You kill bacteria cells without killing human cells!

                Antibiotics target different things.  Some keep bacteria from making their cell walls, some inhibit different enzymes necessary for bacterial life.  My drug of choice is levofloxacin, which specifically blocks bacterial topoisomerase IV and DNA gyrase.  Both of these are involved in unwinding DNA for replication.  If the bacteria can’t unwind their DNA, they can’t replicate it or continue to grow.  

                After three doses of antibiotics, I feel almost human.  I have three more to go.  Bouncing back from this hasn’t been quite as fast as I’d hoped (today is the first day I can sit at my computer and focus on work), but the shivering chills have stopped and I’m slowly regaining my appetite.  I have weird cravings when I’m sick – tonight, all I want for dinner is fried chicken.

                Much more info is available on UTIs, kidney infections, and antibiotics.  Read more if you are interested!  Also, if you get any of those symptoms, go to a freaking doctor!  Don’t be stupid like me.

                My apologies for being a little MIA in the past week.  Obviously, this is why.  I’m working to update all my blogs now and catch up on work that I’ve missed over the past week.  I have all the Sickle Cell posts outlined so they should be up soon!

REFERENCES

UTI Info from the Mayo Clinic: http://www.mayoclinic.com/health/urinary-tract-infection/DS00286

Some medical info on urine cultures, common UTI bacteria: http://www.medindia.net/education/familymedicine/utinfection-urineculture.htm

Generalized antibiotic information: http://www.medicalnewstoday.com/articles/10278.php

Levofloxacin information: http://bacteria.emedtv.com/levofloxacin/levofloxacin.html

Carbon Monoxide Poisoning

This post was requested several weeks ago.  My apologies in not pulling it together sooner.

Also?  The hemoglobin protein is directly involved in Sickle Cell Disease.  Check out a small blurb on this subject on Mini-Amedeo - LINKY. (http://miniamedeo-amedeo.blogspot.com/2012/01/sickle-cell-trait.html)

**        

                We’ve all heard of it.  We all think we understand what it does.  We’re all convinced it’s red.  Such is the general knowledge of hemoglobin.  Now, I’m going to take you now on a guided tour of this protein.  Come along.

                Figure 47.1 shows you one molecule of hemoglobin.  It’s a small protein (the α subunit for humans is only 142 amino acids, P69905).  You’ll notice, however, that hemoglobin isn’t solely comprised of amino acids!  There is a large, flat molecule associated with it called a heme group (colored red).  

Once the protein has been created by the ribosome (Central Dogma post…), a heme group nestles itself inside the hemoglobin protein molecule.  Heme groups are not protein.  They are not encoded by our DNA.  They are simply molecules that our cells make for the sole purpose of sticking them inside hemoglobin.  Think of lovely wrapped present.  The hemoglobin protein is the wrapped box and the heme group is the bow – tacked on the top, but totally completes the package.

Figure 47.2 shows you exactly what a heme group looks like.  Don’t worry, you only need to understand one thing about the heme group: it binds oxygen.  This means that a hemoglobin protein without a heme group cannot bind oxygen.  It is, in essence, useless.

Hemoglobin is an interesting protein.  

For one, it is a tetramer.  The picture in Figure 47.1 is not complete.  Some proteins are content to hang out on their own but others like to be in groups.  Hemoglobin is one of those proteins.  In fact, it likes to be in groups of four.   This means that the mature hemoglobin proteins in our blood look essentially like the above picture times four.  This is shown more easily in Figure 47.3.  Each individual molecule carries its own heme group so this means that a tetramer of hemoglobin can bind four oxygen molecules total.

Secondly, hemoglobin helps itself bind oxygen.  This property is called cooperativity.  When one heme group within the tetramer binds oxygen, it becomes more likely that the other heme groups in the tetramer will bind oxygen.  It may seem like an odd concept at first, but oxygen is crucial to our survival.  Hemoglobin’s job is to pick up oxygen at our lungs and then carry it to various places in our body.  Anything that will make the pick-up of oxygen more efficient, such as the cooperative nature of oxygen binding, is greatly desired.

The left of Figure 47.4 shows you what oxygen looks like.

The right of Figure 47.4 shows you what carbon monoxide, also called CO, looks like.

My, my.  They look really similar, don’t they?

They actually are really similar.  

Sadly, they have one huge difference.  Oxygen likes binding to the heme group in hemoglobin, but is perfectly content popping off when needed.  Obviously, hemoglobin is meant to drop oxygen off at cells so the oxygen must be able to get off the heme group when necessary.  Carbon monoxide, however, has no interest in getting off.  It loves the heme group and will stay there.  Forever.

This leads to a two-fold problem when a person continues to breathe in carbon monoxide.

One.  All the hemoglobin traveling to the lungs to pick up oxygen are picking up carbon monoxide instead - carbon monoxide that will never get off their heme groups.  The amount of oxygen available to your cells is going to drop rapidly.

Two. Oxygen is important to your cells.  Everyone knows that we breathe oxygen in and carbon dioxide out (plants do the opposite!), but what is its role once inside the body?  I touched on it briefly in the post Conferencesand Cancer Cells, Part 2.  I’ve placed Figure 21.1 below that reviews how the cell gets energy (which is called ATP).  Oxygen is crucial to the last step, called the Electron Transport Chain.  If oxygen is not around, that entire diagram stops running, which means that the cells are now starved ATP.  Without energy, many essential biological processes simply stop and cells begin to die.

                Carbon monoxide is ordorless, colorless, etc…  You can’t see it or smell it and there’s no way to know there’s a problem until it’s far too late.  Some people have carbon monoxide detectors in their homes.  Many know not to stand in a closed garage with a car running.  Be wise about carbon monoxide.

                This entire post reminds me a scene from the movie “The Client.”  Jerome “Romy” Clifford drives out to a deserted area, runs a hose from his exhaust pipe to the window of his car and tries to kill himself.  It would have worked nicely if it wasn’t for the two kids who happen upon him.  Good movie; better book (John Grisham).  Go read it!

Heme group: a special group of molecules that binds to hemoglobin and is responsible for binding oxygen.

Tetramer: Protein molecules sometimes come together to form higher order groupings.  A single, functional protein is called a monomer.  Two protein molecules that come together are called dimers.  Three = trimers.  Four = tetramers.  This goes on as high as you can imagine…

Cooperativity: The act one of process helping another (there’s more to this definition, but let’s leave it at that for now).

REFERENCES

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

Alberts et al. “Molecular Biology of the Cell, 4^th Edition.”  Garland Science, New York, New York. (2002).

Grisham, John.  “The Client” (1993) Bantam Dell, Random House.  New York, New York.

Hemoglobin PDB code: 1HHO, pictures were made in PyMOL

Extinct Species

                 I listened to a podcast the other day about the pros and cons of zoos.  As with just about everything nowadays, it’s a controversial topic.  Unfortunately, it’s hard to land in a place of knowing exactly what you’re talking about when you’re basing your opinions on feelings.  I feel like that on just about every controversial topic known to man.  So, I'm not going to put up opinions.  Instead, I’m going to offer you some of my experiences with zoos, some pros and cons, and talk about one success story that just warms my heart.

                The last time I visited a zoo was about two years ago.  I live ~ 3 miles from the Philadelphia Zoo.  With its giant Zoo Balloon floating over the river as a serious advertisement, I was drawn to go for the third time.  The zoo had recently opened their new Big Cat Falls exhibit (sponsored by some company – it changes and I’m not about to perpetuate the advertisement here).  Lions are my absolute favorite so I was pretty psyched.  

This new enclosure is supposed to mimic their natural habitat as best as possible.  The male lion, Merlin, and his three female companions, in addition to the jaguars, leopards, pumas and tigers, can frolic among large rocks, waterfalls, and fallen trees.  The lions are also miked in some way so that we can hear them roar (or grumble, as the case may be).  It was an impressive and overall happy experience.

Following the lions, we saw the lone polar bear.  This is where my heart broke.  It was 90 degrees and hovering at 90% humidity.  That bear looked sad, confused, and mostly especially, hot.  All the animals, which came from everywhere on the globe, were subjected to the climes of Philadelphia – meaning summer highs of 95 degrees F and winter lows of 20 degrees F.  The polar bear had to deal with the Philadelphia summer just as much as the African lions have to deal with the winter cold.  The zoo’s website claims the big cats are fine with it, but they do heat some of the rocks so they have a warm place to hang out during the cold days. 

Are zoos bad for animals?  In the case of elephants, zoos were ultimately deemed to be bad.  Elephants are quite social and like to walk long distances each day.  The small pens were not conducive to them and a movement was started several years ago to close all elephant exhibits.  I was able to see the Philadelphia elephants before they were re-homed in 2007.  Figure 41.1 is a picture of Petal, Callie (African elephants) and Dulary (Asian elephant) in their old pen.  Beautiful animals.  They are now in Tennessee and Baltimore and (according to reports) are happier.  Elephants are hardly the only animals to suffer in zoos, unfortunately.  Some develop weird, repetitive behavior that is only seen in captive animals.  So far, only elephants have received the push to be removed, however.

On the flip side, zoos do allow us to see animals we may not have an opportunity to view otherwise.  In this way, zoos offer an educational experience.  They also are highly involved in conservation projects around the world and have played a key role in re-introducting extinct species back in the wild.  Case in point: Père David’s Deer.

Have you heard of these animals?  I had not until yesterday.  You can see a picture of them in Figure 41.2.  Aren’t they amazing?

Elaphurus davidianus (Père David’s Deer) was originally found in East Asia, but was extinct in the wild before the close of the 19^th century.  Interestingly, from 1890 to 1900, the 11th Duke of Bedford collected the remaining deer from Berlin, Paris, and Antwerp and created his own herd at Woburn Abbey in England.  By 1945, this collection had grown from 18 deer to 250.  

These deer were then transferred to other reserves and zoos throughout the world with eventual reintroduction to the wild.  Beginning in 1985, three separate herds of deer were introduced into China at Beijing Père David’s Deer Park, Dafeng Père David’s Deer Nature Reserve, and Shishou (Tianezhou) Père David’s Deer Nature Reserve.  As of 2005, over 1500 deer are now living in these parks and maintaining their own populations.  Genetic diversity among the deer is still low, but scientists are working to develop ways to increase it among the current populations and any future reintroductions.

Accordingly to Soulé et al and Frankham et al, thousands of terrestrial vertebrates may require captive breeding programs with subsequent reintroduction in the next 200 years to stave off extinction.  

One of the issues I always consider when looking at animals in zoos is whether they accurately represent the animal in all ways.  Sure, we can look at a gorilla.  We can appreciate its size and its features, but does it actually act like a gorilla when in captivity?  Are we really looking at a fully functional gorilla or a nice replica of what the animal merely looks like?  How much of their natural disposition is removed and/or bred out by living in zoos?

Père David’s Deer were actually studied to this effect.  In a paper published by Li et al in August 2011, the deer were subjected to various pictures and sounds of common animals and natural predators.  The scientists wanted to know if, after years of captivity, the deer could still respond to their natural predators with fear and caution.  

Interestingly, they do.  Tiger roars especially led to strong reactions among the deer.  The last sentence of their abstract reads, “Our study implies that Père David’s deer still retain the memories of the acoustic and visual cues of their ancestral predators in spite of the long term isolation from their natural habitat.”  It seems that, at least for these deer, captivity didn’t completely dampen their senses to predators. 

 

This is an interesting function of zoos that I hadn’t considered before.  It seems that with most controversial topics, we get a healthy serving of good and bad points.  Obviously, we are all left to make our own opinions about zoos and I won’t offer my own (somewhat misinformed and emotional) opinion to cloud this topic until I have time to fully research it.  I merely wanted to convey the success story of Père David’s Deer.

Along the same lines, did you know that we have seed banks?  Started by the botanist Nikolai Vavilov in Russia, seeds have been collected from all over the Earth and stored with the idea to avoid extinction of plants.  Such dedication the men had who looked over the seed banks that one died instead of eating the edible seeds during a long famine.  Very interesting concept that deserves some study! 

REFERENCES

http://philadelphia.about.com/od/philadelphiazoo/a/zoo_elephants.htm

Zeng, Jiang and Li. “Genetic variability in relocated Père David’s deer (Elaphurus davidianus) populations – Implications to reintroduction program.” (2007) Conservation Genetics. 8 pgs 1051 – 1059.

Soule et al. “The millennium ark: How long a voyage, how many staterooms, how many passengers?” (1986) Zoo Biol. 5, pgs 101 – 113

Frankham, R. “Stress and adaptation in conservation genetics.” (2005) J. Evolution Biol. 18, pgs 750 – 755.

http://www.philadelphiazoo.org/

Li et al. “Do Pere David’s Deer Lose Memories of Their Ancestral Predators?” PLoS One. (2011) 6(8) pgs 1 – 6.

Figure 41.1 Images: http://www.virginmedia.com/digital/features/endangered.php?ssid=6 and http://www.independent.co.uk/environment/nature/a-quarter-of-the-worlds-mammals-risk-extinction-952989.html?action=Gallery&ino=2  

Batman Likes Equilibrium

               It’s getting on towards Halloween.  Lots of grim reapers, skeletons and one tied up Barbie doll line my trek from the train station to work.  The Barbie doll creeps me out actually – her hands are tied behind her back with duct tape.  That ain’t right.

                Keeping that spirit of death alive, I’m going use this post to explain the following phrase:

A cell at equilibrium is dead.

                What does that mean?  Why is it dead?  Did the Devil come and steal its life?

                In order to understand it, we’ll need to learn a few things.  I’ll try to make it painless.

Thing #1: Batman likes chemistry.

                I’m sure you’ve seen chemical reactions written out as in Figure 40.1.  I’m not going to use real chemicals.  We’re going to keep it simple with A and B.  A and B are related to each other in that they can turn into each other: think of A as Bruce Wayne and B as Batman.  

Pretend we have 100 Bruce Waynes in a room.  All those Bruce Waynes look around and decide there’s way too many of them so some become Batman.  For simplicity’s sake, let’s say 25 Bruce Waynes become Batman.  Now we have 75 Bruce Waynes and 25 Batmans in one room.

25 Batmans / 75 Bruce Waynes = 1 Batman / 3 Bruce Waynes.

            Everyone in the room is happy with this mix of Bruce Waynes and Batmans. 

Let me take a minute and describe this moment when everyone is happy with the ratio.  It is called equilibrium!   The room likes being 75% Bruce Wayne.  However, this does not mean that individuals in the room stop changing back and forth between Bruce Wayne and Batman.  If one guy really wants to become Batman – he’s welcome to! - as long as one Batman then agrees to become Bruce Wayne.  Equilibrium is about the overall numbers.  Individuals within the room are still changing back and forth, but the total number of Bruces Waynes and Batmans are no longer changing.

Oops. We wasted too much talking about equilibrium and now 20 Batmans have left the room. 

           Our room now has 75 Bruce Waynes and only 5 Batmans.  

We established above that the room likes 1 Batman for every 3 Bruce Waynes.  In this new situation, we don’t have enough Batmans.  How do we get more?  

Some more of the Bruce Waynes need to change.

            And so, 15 Bruce Waynes become Batman.

20 Batmans / 60 Bruce Waynes = 1 Batman / 3 Bruce Waynes.

We’re back at equilibrium!

I’m sure you can see that there are many ways we can adjust the above situation. 

Examples:

What if 20 Bruce Waynes left the room? (You’d need more Bruce Waynes!)
What if 200 Bruce Waynes entered the room? (You’d need more Batmans!)

What if you made the room bigger? (They don’t care about the room size, they care about how many Batmans and Bruce Waynes there are.  Duh.)

Whatever you do the room, the overall numbers of Bruce Waynes and Batmans must adjust themselves to fulfill the ratio.

Thing #2: Chemistry likes the Bruce Wayne and Batman Scenario.

                Chemical reactions work like the above example.  To bring it back a little to the real world, consider again the equation in Figure 40.1.

                A will turn into B (and B can turn into A!).  If you put a bunch of A in a test tube, it will start turning into B until enough of B builds up that A says “okay, we’re done.”  The reaction is now at equilibrium.  Remember, individual molecules of A and B will still flip back and forth, but the overall numbers of A and B will no longer change.  

What governs how much B needs to be made before the reaction says enough?  A lot of things.  Suffice it to say that each chemical reaction has its own equilibrium point.  

A reaction is always trying to get to its equilibrium point.  Science, our cells, and life exploit that one fundamental fact mercilessly.

Thing #3: Equilibrium is not for live cells.

                Let’s go back to our test tube example with A turning into B.  Instead of allowing B to build up so the reaction reaches equilibrium, we’re going to continually remove B from the test tube.  Each time A turns into B, we’re going to take out the B.  

                A chemical reaction is always trying to reach equilibrium.  If we keep removing B, A is going to keep turning into B.  It’s going to keep trying to get to equilibrium, but we are foiling its plans.  We are ensuring that A keeps turning into B.

                Why is that useful?  In the Diabetes mellitus post, I told you that glucose is a precious energy source for the body.  The way that energy is extracted is to break down the molecule through a series of steps.  The first step turns glucose into glucose-6-phosphate.  Glucose-6-phosphate is then quickly turned into something else.  

Think of glucose as A and glucose-6-phosphate as B.  B is continually being removed from the reaction because it goes on to be something else.  This means that A will keep turning into B.  A is trying so hard to reach equilibrium with B but it can’t because B keep disappearing.   As long as glucose keeps turning into glucose-6-phosphate and glucose-6-phosphate keeps turning into C, glucose keeps getting broken down and our cells keep getting energy.   

   

What if glucose reaches equilibrium with glucose-6-phosphate?  Overall numbers of glucose becoming glucose-6-phosphate won’t change, which means that glucose is not being broken down efficiently anymore and that our cells are no longer getting energy.  

This pulling of reactions towards B is used in every chemical reaction within our bodies and keeps the reactions happening that keep us alive.

A cell at equilibrium is dead.

REFERENCES

 

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

Alberts et al. “Molecular Biology of the Cell, 4^th Edition.”  Garland Science, New York, New York. (2002).

Me, myself, and I