Monday, June 1, 2009

The tiny world around us

In the wake of the Influena A-H1N1 chaos, you must have known I’d get around to writing about germs eventually. Hopefully most of us have calmed down now, and been able to put the H1N1 threat into the proper context and realized that, like seasonal flu, it tends not to affect healthy individuals all that severely, and it is best prevented with the same old remedies Mom taught you of good hand-washing and covering your mouth when you cough or sneeze. And, if you are sick, with any ailment, stay home and don’t spread it. But, it gets me around to the concept of germs, or more specifically, viruses, bacteria, and other tiny micro-organisms (oh my!).

Viruses, like H1N1, are just tiny packages of genetic material wrapped in a cozy protein coat. They reproduce inside host cells (i.e., you) using the hosts’ genetic machinery (i.e., yours). They make thousands of copies of themselves and then spread, implementing their little genetic programmes. Viruses do not always cause disease, but they usually cause an immune response, and once your body has produced that response you often have lifetime immunity to the virus (notable exceptions would be the herpes virus, hepatitis B, etc which elicit an incomplete immune response and remain with the host for life). Vaccines typically contain killed virus in order to cause the body to produce the desired immune response, when then protects the host from future invasions by this particular viral agent. Viruses are not killed by antibiotics, specifically because they are not “biotic.” Viruses lack the components of living cells that make them susceptible to antibiotics. Viruses, however, are the most abundant “life” form on the planet.

Bacteria are living cells. They live everywhere on earth, and we are able to culture only a tiny fraction of them. The vast majority are completely harmless, many are quite helpful, and a special few can be devastating. Most are easily dispatched by our immune system, and those that aren’t can sometimes be killed by antibiotics (but, not every harmful bacteria has a known antibiotic, and many are evolving resistance to known antibiotics). There are perhaps ten times more bacterial cells in your body than human cells. You are your own walking bacterial ecosystem.

A recent study [Science, 23 May 2008, p. 1001] looked to quantify the numbers of different types of bacteria living on the human body, and where. They swabbed all the places you might normally think of as well as some you probably don’t want to think of (mostly external), and the big winner? Not what you might think…it was our forearms; 500 to 1000 species of bacteria live on our skin.

Other tiny biological structures include prions, which are proteins that re-fold themselves to adopt a shape that causes them to interfere with normal protein function. And, fungi, which come in many forms, ranging from microscopic to the size just right for veggie pizza and portobello burgers. Mold is in this group, which is good for cheese, bad for heating and ventilation ducts, and pretty useful as a class of antibiotics.

When it comes to these tiny organisms, we humans are greatly outnumbered. Just a little humbling, isn’t it?

Wednesday, April 22, 2009

This is a test

This is a test of my ability to post from my iPhone. This is only a test. Had this been a real post, you would have been directed to think critically about something in your life. This is only a test.

Thursday, April 2, 2009

Spitballs, Splitballs, Dry Spitters, and Physics

In 1920 the spitball was outlawed in baseball. Arguably this was in response to the death of Ray Chapman of the then Cleveland Indians, who was hit with a ball and killed while at the plate. Witnesses state that he never attempted to avoid the ball, which led to speculation that he never saw it coming. This was the end of the era known as the dead-ball era in baseball, which I wrote about previously in “Into the Swing of Things”.

The dead-ball era was characterized by the use of balls that literally wore out and died during the game, because they were practically never replaced. Knowing this, every pitcher considered it his responsibility to hurry along the death of the ball with the application of any and every substance possible: spit, tobacco juice, grease, licorice, sand paper, nail files, nails, blades, spikes, you name it. Dead balls were hard to see clearly. It is unknown if the ball that hit Chapman was simply dead from over use, or if the pitch was a spitball, as many speculate. According to the Society of American Baseball Research, pitcher Carl Mays was famous for his spit ball (then legal), and the sound of the ball hitting Chapman’s skull was so loud that Mays thought the ball had been hit by the bat, fielded it, and threw it to first. Chapman died twelve hours later. His team went on to win the World Series.

Spitballs were banned that year. Batting helmets were not made mandatory until 1971.

Since 1920 we have been in the ‘live-ball’ era. Balls are replaced routinely. Spitballs, shine balls, mud balls, emery balls, and cut balls are illegal. The reason for this is that dead or manipulated balls are no longer smooth or truly round; therefore, they fly through the air with an unpredictable trajectory.

When a ball is thrown, it rotates while in the air. So long as the ball is essentially the same everywhere on its surface, with the center of mass being at the center of the ball, the rotation is symmetrical and the ball flies straight and true. As soon as you change the surface, you change two aspects of the ball. First, you change the airflow over the ball, or friction. Second, if you change the outside enough, the ball is no longer round, and the center of mass is shifted away from the center.

Lets deal first with friction. Friction induces drag, or resistance to flow. If there is more drag on one part of the ball, caused by say, roughing up the surface, then it is not going to slide through the air as easily at that point. Air slides easily past all the other points, and the rough bit actually starts to be slowed down relative to the rest of the ball. The result is that a rotation is going to be caused at that point. Hence, the trajectory of the ball will eventually begin to curve.

Shifting the center of mass causes a similar problem. If you have ever tried to spin a top, you know that if you keep the handle or center bit straight and true, and in the center of the top, the top spins cleanly. As soon as you move the handle to one side, you’ve got wobble. Out-of-round baseballs with a shifted center of mass will wobble during the pitch in much the same way.

Of course, really good pitchers can pitch the dry spitter; legal because nothing is being added to the surface of the ball, so- named because they behave like spitballs. Knuckleballs and split-balls fall into this category. By controlling the release of the ball, the pitcher can control the spin of the ball and therefore the flow of air over the ball. Knuckleballs don’t spin as much, or at all, compared with fastballs. This makes them slow. Without spin and, importantly, without speed, the differences in airflow over the smooth parts of the ball compared with over the stitches are more pronounced. The points on the ball with stitches experience increased drag, and the ball’s trajectory eventually will tend to curve around those points. Faster pitches like the split-ball rely on basically this same principle –controlling the release of the ball so that you can impart a predictable rotation or drop onto the ball’s trajectory.

Wednesday, April 1, 2009

Into the Swing of Things

A baseball is a 3-inch diameter sphere traveling at upwards of 100 miles an hour, at least in the pro leagues. It is 9 inches in circumference, and 5 ounces in weight. And, it is darn hard to make contact with it. It is in fact so hard to hit this ball that hitting it 3 out of 10 times is considered really quite good. If you were in one of my courses and got 30% correct on an exam I gave, I would ask you to seriously reconsider your career choices.

It is so hard to hit that little white ball that batting in baseball is a metaphor for life. If you push yourself to take on something really challenging you ‘step up to the plate’, if you are working really hard and aren’t giving up you ‘keep on swinging’, if you failed entirely you ‘struck out’, and if you pulled it off beautifully you ‘hit a home run’.

According to the Baseball Almanac, the best batting average in a single season, ever, is by Tip O’Neil. A 0.485. He earned this in 1887 playing for the St. Louis Browns. Of course, in 1887, they counted walks towards your batting average. But, that is not the case for several other 400 hitters on the list. In the first part of the 1900’s Ty Cobb made the list 10 times, and he is Number One on the list of all time leaders, with a lifetime average of 0.366. It is getting harder and harder to make the list, and those 400 hitters are a thing of the past. On the list of the top 100 batting averages in a single season, there are only three who played the game during years when I was alive. Ranked number 53 is George Brett of the KC Royals with a 0.390 earned in 1980. Rod Carew of the Twins batted a 0.388 in 1977, giving him the 61st spot. And Larry Walker of the Rockies batted a 0.379 in 1999, earning him the 94th spot. If you look at any of these sorts of lists, you’ll see the batting averages steadily trending downwards over time.

What is interesting, from a physics standpoint, is that those 400 scores were achieved during what was known as the dead-ball era. This is an era in baseball where the balls themselves were rarely replaced during the game, and thus they literally wore out and died over the course of the game. The dead-ball behaved unpredictably – it was not firm or smooth anymore, and therefore its trajectory was atypical. And, of course, this was hastened along during the game by the pitcher’s liberal application of spit, grease, sand-paper, and emery boards, all of which are now illegal. It seems odd that the batting averages should be higher during a time when hitting the ball was arguably harder.

It has been suggested that the live-ball baseball (where the balls are replaced at the first sign of wear) favors the hitter. Therefore, many a baseball analyst has tried to explain why batting averages have not increased over time. Enter the science of statistics and the laws of probability, another love of the science-y types. Explanations range from new pitching styles that don’t favor putting runners on the bases, to hitters that favor hitting home runs and new parks that don’t favor homeruns by design. More night games make it harder to see and hit the ball, and more relief players give batters less familiarity with individual pitching styles and reduce the chance of a hit. There has also, arguably, been an overall increase in the skill of all baseball players over time. This means that a great batter is far more likely to encounter a great pitcher, and therefore success at bat is likely to be lower than for great batter in the past. In the past great batters were rare, but great pitchers were even rarer. These all seem to contribute to a trend of increasing strike-outs or walks, and less hits relative to at-bats.

And so, they keep on swinging.

Thursday, March 5, 2009

The Science of Baseball

Ah, it is nearly Spring, and springtime means baseball! The pros are at their spring training camps in the warmer parts of the United States like Florida and Arizona. And, 300+ youths in our fair city are at Los Arboles and Preston parks swinging away with at least as much enthusiasm if not more.

Scientists love baseball. I cannot explain exactly why this is. But, this is a sport that unites geeks and jocks from coast to coast. And, in fact, the President of our city's Pony Baseball and Softball league is a geek-jock himself, scientist by day, baseball empresario by night, weekend, and most school holidays from December to July (that’d be Mr. Dr. SwimsWithFishes again).

Perhaps this is because baseball, unlike life, conforms so well to the laws of physics, where things are predictable, orderly, and behave utterly sensibly. Now, this does not mean baseball players and umpires behave so sensibly. But, ball, interacting with bat, behaves quite predictably. You can calculate, quite reliably, exactly how to hit a ball so that you will get a home run every time at bat. You can draw it on paper; determine forces, angles, and trajectories; form and solve the equations.

The sport comes in figuring out how to get a pitcher to pitch that ball to you, and how to get your body to hit that ball, just like on paper. It is the interaction between the players, and trying to figure out how to achieve a known outcome, that drives our passion for the sport. This interaction is like a dance. Even as spectators, we watch the dance with the same anxiety and emotion, fear and adrenaline as we felt back in the age of innocence at our first school dance and the boy/girl of our dreams was watching us from across the room (and all we hoped for then was that we might get to ‘first base’ with Dream Boy/Girl).

The science of a baseball home run is all in the angles. Line drives, that travel with no arc, no change in height off the ground as they leave the bat, are darn fast, but they don’t travel far. This is because of our old constant friend, gravity. The ball leaves the bat with some inertia, or some force, imparted by the swing of the bat. The magnitude of that inertial force depends on how hard the bat hits the ball. Harder hits impart greater velocities and therefore greater inertia. But, the ball is experiencing friction as it travels through the air. As it slows, eventually the force of gravity, pulling the ball down, will be larger than the inertial force and the ball will begin to fall.

Now imagine the ball is hit with the same speed but with a slight upward arc. At the time when inertial forces begin to weaken, and gravitational forces start to take over, the ball will be higher in the sky. The increased distance to the ground, and the trajectory of the arc, ensure that the ball travels farther before actually contacting the ground. Intuitively, we know this. Line drives rarely hit the home run fence. Home runs are big arcing hits that soar into the grandstands.

It is actually more difficult to hit a ball fast with an upward trajectory than with a straight one. Line drives are fast and pitchers hit with these balls get hurt, badly. However, even if the force imparted onto the ball is lower, a sufficient arc will take the ball farther. A little arc goes a long way, and you can get too much of a good thing. Obviously, a ball hit straight up goes nowhere at all except up. The science is in finding the just right arc. In baseball, as in life.

Which Way the Wind Blows

With the Wind Festival right around the corner, I thought it was a fine time to talk about the science behind how and why the fair city in which I live is so darn windy. Most of the cities in our region have a token produce item that they celebrate annually. But, what makes our city unique? It is the wind, no doubt. I love that we have a festival dedicated to that oceanographic feature that so defines our fair city.

That’s right, I called the wind an oceanographic feature, and it is not just that I am a marine scientist that makes me view the wind in this way.

Wind is formed by a pretty basic principle - hot air rises. When hot air rises, the cooler air rushes in to take its place, and viola, you’ve got wind. That basic principle explains global wind patterns, as the air is warmer at the equator than at the poles, and local wind patterns, such as the off-shore winds that surfers use to predict how good the surf will be. The ocean is a strong factor in determining which way the wind blows, as ocean temperatures drive the giant conveyor belt of air that winds its way around the globe, interrupted by the land masses that form a mere 30% of the earth’s surface.

Spring, Wind Festival time, is probably the consistently windiest time of year here. This is because the ocean off our coast is at its coolest temperature, thanks to spring upwelling. Upwelling is the movement of cool deep waters up to the ocean surface. They are brought to the surface because of global winds, winds blowing towards the equator. Air at the equator is hot and rising, cooler polar air masses are moving in to replace it. As these winds blow down past our coast, the rotation of the earth causes the surface water to be pulled by the winds the to west, or out to sea. As the surface water is pulled away from our coast, the cool deeper water rises up to take its place. Thusly, as any surfer knows, the water off our coast is the coldest in the spring.

Cooler ocean temperatures mean cooler air temperatures sitting on top of that water. As the inland air gets warmer and rises, the cool coastal air is sucked inland to replace it. This temperature differential is probably the greatest in the spring, and particularly in the afternoon in the spring. That means lots of wind.

Land heats and cools faster than the ocean. The ocean actually changes temperature by only a few degrees. This means we typically get offshore winds when the inland areas are cool, like in winter (off shore winds are good for surf, along with big swells brought by winter storms generated far away). We get on-shore winds when the inland areas are warm, such as during the upwelling periods described above. We might get on-shore and offshore winds in the same day depending on the temperature change inland. In our city, we know this well, as we spend our summers watching the fog “burn off” in the late morning and get pushed out to sea (as the heat reduces the moisture content in the air), only to get sucked back on land in the late afternoon.

Sunday, February 1, 2009

New Year’s Resolutions, A Little Belated: Five Ways to Get A Little Greener

Dr. Think Science (aka me) is a biologist. As such, you might think I am the model for living an earth-friendly life. I am not, nor are most of my colleagues. I mean, we all try to do our best, but I am no environmentalist. For 2009, I took the opportunity to look around me and came up with five really simple ways to green my, and maybe your, lifestyle.

1. Recycle more. Most of us recycle pretty well at home, but do we go to the effort of taking the water bottle home to recycle it since there is not a recycling bin handy wherever we are at right at that moment?

2. Use a re-fillable water bottle/coffee-mug. I highly recommend aluminum (they’re a bit of an investment, but consider your investment into bottled water over the past year to put it into perspective). Plastic bottles release a number of nasty compounds as they age.

3. Bring re-usable bags to the store, at least some of the time. I admit I am only halfway successful at this. I have the bags in the back of my car, and constantly forget to lug them into the actual store. Plastic grocery bags are an environmental success story in that they are one of the most reused items in the house, according to National Geographic. If you use your plastic grocery bags, like me, for trash bags instead of purchasing more plastic bags at the store, at least they’re used twice. But, even I still end up with far too many bags to re-use. Consider taking them with you to the store to be recycled (most stores have bins), and consider using reusable bags when at those stores who don’t provide bags suitable for your re-use needs. You can also check out http://www.reusablebags.com/.

4. Use less, or less of, toxic cleaners. I try to use earth-friendly cleaning products as much as possible, like vinegar or baking soda for mold and mildew. But, there are those times when you need the extra power of one of the not-so-earth-friendly ones. Mildew is my personal nemesis. In those cases, I started trying to use a really small amount. For example, you can apply the products to target areas with small brushes or Q-tips instead of spraying everywhere. You can also place the products in glass jars (placed in kid-safe storage) so that you can soak items, like your detached shower head that has really bad lime scale, instead of spraying and spraying and spraying. And, you can then reuse, reuse, reuse.

5. Unplug it. The credit for this idea goes to a friend, but she is saving loads on her energy bill just by unplugging the appliances when they are not in use. The energy it takes to keep those little clocks on our toasters and coffee-makers going really adds up.

Now, I expect I’ll have about a thousand pairs of eyes out there helping me to keep these new resolutions! I don’t mind if you give me a little poke to remember. Do you have ideas too that you can share?