Friday, November 30, 2012

Thoughts from my Dad: The Space Program

Left to right: Eisele, Schirra, Cunningham
I knew when I was in the first grade that I wanted to be an astronaut and that and I wanted to marry Julie Bentley. I never became an astronaut but that year, behind the school building during lunch recess, I married Julie. I remember many things from my first grade because of my teacher, Mrs. Jones - she was mean and this was surprising to me because her name was my name too. I remember getting out of music class and going down to the lunch room. Julie was not far away. This was my first experience with the space program - sitting on top of the lunch room tables watching Apollo 7, the first manned Apollo mission. That was October 11, 1968 - with Walter M. Schirra, Jr., Donn F. Eisele, and Walter Cunningham. It orbited the earth once.

The following December I was concerned about getting a GI Joe Astronaut. He had life-like blonde hair.  At school Mrs. Jones was teaching us about the Apollo 8 that was about to launch. I don’t remember seeing this in the lunchroom but throughout the 2nd and 3rd grades we had special assemblies highlighting the space program. It was broadcasted on television and we watched from the classroom or at home on our T.V.  (that only had 2 channels). While I don’t have a perfect memory of the space program, there are few important dates that I do remember.

January, 27 1967
I remember watching a program on Apollo-Saturn (AS) 204. On the launch pad at Kennedy Space Center. On this date, At 6:31 p.m., the capsule was engulfed in flames and the three astronauts aboard—Gus Grissom, Ed White, and Roger Chaffee—died of asphyxiation. In retrospect I see now why the Apollo 7 mission was such a big deal when I was in the first grade.

Major Matt Mason (A doll...)
July 20, 1969
Neil Armstrong and Edwin Aldrin Jr. make the first manned soft landing on the Moon and the first moonwalk. What I remember the most about that “One small step for mankind” was the following January for my birthday, I received the bendable astronaut named Major Matt Mason. I bent his arms until they fell off and the flag was worn. I miss that toy. GI-Joe and his accessories were called dolls back then, but I wish my siblings had called them action figures instead. My interest in science and space travel was one of ridicule and teasing, but the GI Joe Henshin Cyborg Base Station was worth the ridicule.

Now that I think of it, most of my memories from the space program from 1969-1977 come from my toys and food - the Pillsbury Space Food Sticks at my grandmas (Chewy Chocolate was my favorite). Space sticks with Tang was a meal fit for any astronaut.

April 11, 1970
Although many events, both tragic and celebratory, happened during this time period, I don’t remember any excitement in school that compared with the - Apollo 13 launch which suffered an explosion in its SM oxygen tanks. Its Moon landing was aborted, and the crew, James A. Lovell, Jr., John L. Swigert, Jr. and Fred W. Haise, Jr., return safely. I remember that some thought it was a ploy to get American's attention on the fading interest in the space program. I was only 9 years old so I remember some things just in passing.

July 30, 1971
Apollo 15 astronauts David Scott and James Irwin drive the first moon rover. The next year, Apollo 17 astronaut Harrison Schmitt drives a similar rover. I do remember this and not for the science or interest in space exploration but more so because I wanted the GI-Joe Commander Space Lunar Moon Rover for Christmas. When I was about 15 I was less interested in becoming an astronaut and more concerned about the girls in the playground (my first grade marriage did not last).

January 28, 1986
Challenger explosion.jpg
The Challenger Explosion
The Space Shuttle Challenger was destroyed and its crew of seven—Francis R. (Dick) Scobee, Michael J. Smith, Judith A. Resnik, Ronald E. McNair, Ellison S. Onizuka, Gregory B. Jarvis, and Christa McAuliffe—was killed during its launch from the Kennedy Space Center. The explosion occurred 73 seconds into the flight as a result of a leak in one of two Solid Rocket Boosters that ignited the main liquid fuel tank. For me it happened at 9:40 AM and I was watching the news and getting ready for my trigonometry class. I can still recall walking on campus to my class, looking up at the clouds and trying to imagine the shock those bystanders must have felt with the realization of what had happened. For some the realization of what had just happened did not come until several minutes later. During the following weeks I learned that the cause of the explosion was the result of faulty “O” rings. They were manufactured not far from where I lived.

By 1977 I was less interested in GI Joe, but I do remember that GI Joe goes interplanetary in the form of a new 8-inch space-exploring super Joe. These action figures are smaller, cheaper and just not like they use to be. At this time I was 15, and my interest in the Voyager program was the jokes I could make about Voyager traveling to Uranus. I knew about Skylab, and around this time there were many firsts including an untethered spacewalk, a women walking in space, and other experiments that were being performed in space. I remember Reagan being the first president that I voted for, and again near my birthday January 25, 1984, President Ronald Reagan made an Apollo-like announcement to build a Space Station within a decade as part of the "State of the Union Address" before Congress. Reagan's decision came after a long internal discussion as to the viability of the station in the national space program.

It wasn't until recently that my curiosity of space exploration was once again sparked. On August 6th the Curiosity landed on Mars. The rover has traveled hundreds of feet over the Martian surface. In the process, it has left its mark on the surface leaving behind a trial in the sandy red planet and a tiny piece of itself behind. Unlike the Apollo astronauts' footprints on the moon, Curiosity's trails will probably be wiped away by the planet's frequent wind and sand storms. Though the physical traces won't last- for others its impact lives on in the images the rover is sending back to Earth. For me, it’s not the images or the trail that will leave lasting memories but the comments like this from my grandchild and child that fuel my interest:
"Dad, someday I'm going to walk on Mars!" To this day he talks on and on about Mars. We watched the video of the Curiosity rover landing and now he's excited to see the rover in person someday.
My grandson (5 yrs old) has several girlfriends…and as of yet I have not received a wedding invitation. Maybe he won’t get married in the first grade like I did, but he may one day make it to Mars. Until then I will dream of space travel and all the excitement in store for future generations.

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Thursday, November 29, 2012

Time Reversal Asymmetry

Today's post is by David Zaslavsky, a physics graduate student who writes a blog called ellipsix informatics. It's a fairly advanced physics blog, but if you have the stomach for some math I highly recommend it.

About a week ago, a particle physics experiment called BaBar published a big discovery. Not as big as the Higgs boson, so it's probably not the kind of thing you would have heard of if you're not a physicist. But it's still pretty interesting, and it does have the exotic-sounding name of "time reversal asymmetry."

If you love science fiction as much as I do (and who doesn't?), you might think "Whoa, they figured out how to reverse time?" That would be awesome. But no, sadly, that's not what happened. Time reversal asymmetry just means that, if you could reverse time, certain particles would behave differently than you'd expect. Of course, the fact that you can't reverse time means that the scientists had to get pretty creative to figure out what would happen if you did. They were lucky enough to find two sequences of particle decays that are time-reversed versions of each other — that is, if you could reverse time, you'd turn each one into the other.

The special sequences start with an exotic particle called a "neutral B meson" and its antiparticle, linked together by quantum entanglement. Each one of the two particles can decay in one of two ways (that this experiment cares about): either "hadronically," into two lighter but still somewhat exotic particles, or "leptonically," into something like an electron and other stuff which we don't care about. Since the particles are entangled, if they were normal particles, both of them would always decay the same way, either both hadronically or both leptonically. So, for example, if you see the first B meson decay leptonically, then normally that tells you the other one will also decay leptonically.

However, B mesons (and their antiparticles) are not normal. They can oscillate, which means that they spontaneously flip back and forth between "wanting" to decay hadronically vs. leptonically. This oscillation is what the scientists at BaBar measured. They picked out the times when the first B meson in a pair decayed leptonically, thus forcing its partner into a leptonic decay state, but the partner oscillated back to decaying hadronically, and also the times when the first B meson in a pair decayed hadronically and the partner oscillated back to decaying leptonically, and they compared how many times each one happened. It turns out that the leptonic to hadronic oscillation occurs significantly more often than the hadronic to leptonic oscillation in the time before the B meson decays. Presto, time reversal asymmetry!
Time reversal symmetry violation in B meson oscillations
Although this didn't come as a surprise, not even a little, it's good to know that it works the way it does, because it helps confirm that the theory we use to understand how particles behave is correct, in a way that hasn't ever been directly tested before.

For a full-length explanation of this experiment and what it means for theoretical physics, check out the original post on my website!

Wednesday, November 28, 2012

Big Pharma doing well, but clinical trials still lacking transparency

Pharmaceutical companies are a constant target for conspiracy theorists who say that "Big Pharma" controls disease for profit. Some think that since these companies make money from people that are ill they must have some evil plot to keep people ill. In some cases this means that Big Pharma is responsible for creating diseases. In others it means they lie about the efficacy of things like homeopathy.

There are, of course,  flaws in the way we develop, test, and market prescription drugs,1 but the real issues have nothing to do with the conspiracy theories. A recently released report - The Access to Medicine Index (2012) - brings us some good news about the pharmaceutical industry.

Cover 2012 Access to Medicine Index The Access to Medicine Index is an independent review that ranks 20 pharmaceutical countries on how they help developing countries. Each company is ranked by their performance in:

  • General Access to Medicine Management
  • Public Policy and Marketing Influence
  • Research and Development
  • Pricing, Manufacturing, and Distribution
  • Patents and Licencing
  • Capability Advancement
  • Donations and Philanthropy

The highest ranked company in 2010 and 2012 was GlaxoSmithKline. Johnson & Johnson and the French company Sanofi, who ranked 9th and 5th in 2010, now rank at a very close second and third. Of course, these results are just comparative - they don't say anything about how "Big Pharma" as a whole is doing. What else can this report tell us?

Access to medicine in developing countries has improved and this is largely attributed to better organization. GlaxoSmithKline, for example, established a Developing Countries and Market Access department. Five other companies in the index have similar departments.

Pricing Tiers and Product Needs
Twelve of the twenty companies have a tier pricing program. These programs are designed to bring low cost drugs to developing countries. One problem with these programs is that while drug companies may provide a low cost, third party companies often sell the drugs at the standard retail price. This means that companies, not patients, benefit from these tier programs.

Contract Research Organisations
Pharmaceutical companies have come under fire recently for their transparency (or lack thereof) in clinical trials. This report is no different. Contract Research Organisations (CROs) are third party companies used to oversee clinical trials, drug recalls, and research. The Access to Medicine Index points out that Big Pharma needs to improve transparency regarding their collaborations and obligations to CROs.

Overall I think the Access to Medicine Index is good news. Out of the 20 drug companies, 17 companies scored higher in 2012 than in 2010. Although clinical trial practices remains an area that needs improvement, it's promising that the index brings the issue to the forefront once again.

[1] For a more in-depth analysis of what Big Pharma actually does wrong (instead of wild conspiracy theories) I suggest this book by Ben Goldacre.

Tuesday, November 27, 2012

Facebook's "Copyright by status update"

This is primarily a science blog, but I'd like to change the topic for today. I'm probably justified writing about this topic, though, since it involves critical thinking (that and it's my blog I can do what I want, thank you very much).

In the past few days an old hoax has been making the rounds on Facebook. The idea is that since Facebook is now a privately traded company your pictures, status updates, and any other personal information is now freely available unless you post the following status update:
In response to the new Facebook guidelines I hereby declare that my copyright is attached to all of my personal details, illustrations, graphics, comics, paintings, photos and videos, etc. (as a result of the Berner Convention). For commercial use of the above my written consent is needed at all times! 
(Anyone reading this can copy this text and paste it on their FacebookWall. This will place them under protection of copyright laws. By the present communiqué, I notify Facebook that it is strictly forbidden to disclose, copy, distribute, disseminate, or take any other action against me on the basis of this profile and/or its contents. The aforementioned prohibited actions also apply to employees, students, agents and/or any staff under Facebook’s direction or control. The content of this profile is private and confidential information. The violation of my privacy is punished by law (UCC 1 1-103(a) and the Rome Statute). 
Facebook is now an open capital entity. All members are recommended to publish a notice like this, or if you prefer, you may copy and paste this version. If you do not publish a statement at least once, you will be tacitly allowing the use of elements such as your photos as well as the information contained in your profile status updates…
 Every time someone posts this status I can't help but think of this similar declaration:

Just as Michael Scott can't declare bankruptcy just by saying the words, you can't do anything about your privacy on Facebook just by posting a status update - no matter how many important sounding words and legal codes you mention in it. That's just not how it works. I'm almost positive that nobody posting these statuses has even read the legal codes they're referencing. For example, UCC 1 1-103(a) states that:
(a) [The Uniform Commercial Code] must be liberally construed and applied to promote its underlying purposes and policies, which are: (1) to simplify, clarify, and modernize the law governing commercial transactions; (2) to permit the continued expansion of commercial practices through custom, usage, and agreement of the parties; and (3) to make uniform the law among the various jurisdictions. 
In other words (or at least how I understand it) the commercial code must be written in a way that allows it to be modernized, allows the expansion of commercial practices, and to make the laws uniform. I'm not sure what that has to do with punishment for using your Facebook status.

The Rome Statute, on the other hand, is a treaty that establishes the jurisdiction of an International Criminal Court (ICC). This ICC investigates war crimes, genocide, crimes of aggression  and crimes against humanity. Your picture may be important to you, but its misuse doesn't have anything to do with the Rome Statute. Furthermore, if you're in the United States it's even more ridiculous to claim copyright protection since the US hasn't even ratified the Rome Statute. 

Sometimes people will post one of these statuses and then in a comment below say something like "It may not be true, but what could it hurt?" 

Well for one thing it can hurt my respect for you. Before writing this I didn't know what the Rome Statute was,1 but it doesn't take long to do your own research. A critically thinking person will take the time to ask "does this make sense?" or "could it really be this easy to copyright something?". There are lawyers who get paid millions to understand copyright law. If it were as easy as posting a status update they would be out of a job. These same critical thinking skills should be used when you see any "Share this picture and this child gets a free {insert medical procedure here}" scams.2


The real way to protect yourself online is to realize that you're online. Don't post something you wouldn't want others to see. Know, and control, your own Facebook privacy settings. If you don't like Facebook's privacy settings don't use Facebook. Take the "postcard" approach to your online interactions: You can write to a specific person, but assume that it will be seen by others as well. 

[1] I've proofread this post several times, terrified that I wrote "Rome Statue" instead of "Rome Statute" somewhere. If I did, let's be clear: Yes, I know the difference.  
[2] I say scam instead of hoax here because the people that post those pictures do have a financial gain when those pictures are shared. An active Facebook page (a page that has lots of likes and gets lots of shares) is a commodity that can be sold. The "scam artists" will post some picture that generates a lot of attention (likes, shares, etc) and then sells the page to a company looking for quick attention.

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Monday, November 26, 2012

Science: The MythBusters Way

I just finished watching the latest MythBusters episode: Explosions A to Z. Even though this was pretty much just a "clip show", it was MythBusters clip show so of course I watched it. It was a great episode with a fun look inside the MythBusters process, and it got me thinking.

I've been critical of the MythBusters in the past. They rarely use a true, scientifically valid control group, their method development is almost always fundamentally flawed in one way or another, and I don't think many things they do would pass any diligent peer review. But does that even matter? I have 3 reasons why science, the MythBusters way, is an important and necessary innovation.

1. They're entertainers.
The MythBusters team isn't just the well known Adam, Jamie, Kari, Tory, and Grant. Their team includes cameramen, writers, producers, directors, stuntmen, and departments for art, costume, animation, and lots more. Why do I point this out? Because the MythBusters are first and foremost entertainers. They have a huge supporting cast that works hard to put together a television show - not a science textbook. They do make an entertaining television show about science, and they know a lot about what they're doing. In the end, though, they are entertainers. This means that they may occasionally take some creative liberties with the scientific method, and that's okay. They're not promoting pseduoscience like many celebrities or others in the entertainment industry. They're never misleading about what they're doing. In fact their methods, while often flawed, are available for public scrutiny. In other words, their approach to the scientific method is readily accessible to be over analyzed by just about any pretentious internet troll.1

2. They know their audience.
Because they're entertainers they are distinctly aware of their audience. That audience (as a generalization) doesn't work in a lab. They don't design experiments that will be submitted to peer reviewed journals, and they may not have even heard of a control group before watching the show. If the show's approach were to rigorously describe the details of every experiment needed to correctly proclaim a myth as Busted they would lose that audience very quickly. I know I wouldn't be as interested in watching, would you?
Instead, the MythBusters approach is to quickly explain the science behind what they are doing and (between explosions) the basics of the tests they are using. Instead of faulting them for using an incomplete control group we should be applauding them for showing millions of viewers that a control group is necessary. Instead of pointing out the flaws in their method development we should be pointing out that for some of their viewers the idea of experimental design is completely new. While other entertainers promote the newest fad diet the MythBusters are introducing viewers to the basics of the scientific method.

3. Science advocacy starts with a BOOM!
Science is AWESOME. No really, everything in the universe that you could ever call awesome can be explained by - or is a direct result of - science. However, sometimes you have to look pretty deep to see just how awesome it is. The great thing about the MythBusters approach to science is that they bring the awesome of science to the forefront. They're very clear about how awesome science really is. I'm talking of course about explosions, but that's not all. The experimental methods that the MythBusters use may be flawed but those experiments allow them, as entertainers, to show that an experiment can be designed to answer a question. This combination of science and entertainment is an important innovation in science advocacy. An explosion may look cool, but if it gets someone to start asking real questions about the world around them that is truly awesome.

[1] Fun story, I got my first piece of hate mail over Thanksgiving weekend. Some of the last sentence is a direct quote from that soul-crushing feedback. Thanks, you'll always have a special place in my heart.

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Sunday, November 25, 2012

Infinity and Beyond

by Angela Calchera

By my estimation, scientists are the modern-day equivalent of the explorers in the days of Magellan and Columbus.  Back in the third grade, I read a book about Christopher Columbus and promptly changed my career goal from fire fighter to explorer.  As I continued through my school days, however, I became more and more convinced that all of the lands left to discover were outside of earth, and  I dropped that career goal for something more practical, like being a doctor.  Then, after "exploring" the world of medicine by shadowing an ophthalmologist for a day, I realized that I didn't like needles and sick people very much and decided to pursue the hard sciences instead.  Now that I am nearing a terminal degree in Physical Chemistry, I realize that I have come full circle in a way, and that, not only do many "lands" remain to be discovered without ever leaving the Earth, but I am one of the explorers seeing them for the first time.

Today in  my lab, Chad, the originator of this blog, stopped by my office to complain about the irritating sounds that his lab equipment makes.  He uses a pulsed laser that flashes five times or so per second, making a really grating clicking noise as it does so.1  During the conversation he made a remark about our laser not making that noise because it is continuous.  In reality, the laser we use in our lab is also pulsed, but instead of getting five pulses per second, we get 1000 pulses per second, which is faster than human eyes can detect.  It makes noise when it pulses on and off as well, except instead of hearing clicks, we hear a hum that has a frequency of exactly 1 kHz.  Since Hertz is a unit of "per second" and the "k" stands for "kilo," meaning 1000, that is a frequency of "1000 per second," so essentially it is the sound of our laser clicking on and off 1000 times per second.

The amazing thing is that these one thousand pulses each only last for 120 femtoseconds.  Why is this so amazing?  "Femto" is a prefix that means 10-15, which is one millionth of a billionth of a second.  Another way to think about it is 0.000000000000120 seconds.  So, it starts and ends pretty darn fast.2  How fast?  Well, we get 1000 of these a second, which seems really fast already - so fast that your ears cannot hear the individual "clicks."

Even though we can appreciate that a femtosecond is a very short period of time, it is difficult to truly appreciate just how very short it is, so let's stretch our 120 femtosecond pulse out to one second.  That means that on this new scale, one normal second would now equal 264,000 years.  Since there would be just a thousand pulses during this period, the laser would only actually be "on" for one second every 264 years.  So, the laser that to human eyes and ears appears to be continuously "on" is actually "off" most of the time.  This should disturb you, and maybe even hint that there's a lot going on in the world that your senses are not showing you.3

Just about every physical and chemical phenomenon has a "lifetime," which is to say, that very rarely does anything actually happen instantly, even if it sometimes seems that way.  For example, shining infrared (pronounced: infra-red) light on some molecules causes the atoms in bonds to vibrate like balls on a spring.  In this way, we can "see" (or understand) something happening on a molecular scale.  This motion lasts for a finite amount of time, and we can use a second quick pulse of light to see how long this motion lasts, as well as how it changes over time.4  The shorter the laser pulses, the faster the phenomena we can study and measure.  This technology opens up a new world of the ultrafast and ultra-small that before these lasers were invented were impossible to study on this level.

Every day when I fire up the laser and begin an experiment, I travel into the unknown world of the very small and the very fast.  I am exploring the world around me, and seeing things that, although they've been right under our noses the whole time, we have just never seen them before.  Although I am not facing the possibility of bloodthirsty sea creatures or sailing off the edge of the earth, I am still pushing boundaries and learning to see new "lands" never seen before. And like the discoveries of the explorers of history, the discoveries made by scientists like me open up whole new worlds to human the human mind.

That's not the only irritating noise in his lab.  He'd want me to mention that.
"Ultrafast" is the term used by people who work with lasers to describe that regime of pulse duration.
I once met a Mapuche man in Argentina who told me that his religion taught him to believe in all things seen and unseen.  He said that one of his most spiritual experiences in his life came when he read about an electron microscope and saw some images recorded using the instrument because he felt that that particular technology was allowing the seen and the unseen to become one.  I think that is a beautiful way of describing that sense of wonder I feel when I ponder the infinity right here around me.
In my lab we do something called Vibrationally-Resonant Sum Frequency Generation Spectroscopy, which takes advantage of this lifetime.  The first pulse is in the infrared and causes molecules to vibrate, and the second pulse comes in and converts the vibrational energy into a generated pulse of light that has a frequency equal to the sum of the frequency of light that started the vibration and the frequency of light that hit second.  We use optics and a detector that are only capable of steering and detecting the higher frequencies, so without both pulses interacting with each other and the sample, we can't pick anything up.

Saturday, November 24, 2012

Saturday Links: November 24, 2012

Wow, Saturday ended sooner than I'm used to. Here are the links for this week...

Friday, November 23, 2012

30 Second Science: The Wiimote

One of the most innovative gaming systems in the last few years is the Nintendo Wii. The Wii is designed for interactive gameplay that hasn't been seen since the Power Pad.

I can proudly say I own one of these.
But how does it work? In today's 30 second science I'm going to give you a quick tour of the gaming system and explain how a few things work.

The Wiimote
It may be one of the most childish names for a controller, but the Wiimote is actually a pretty advanced piece of technology. Inside it has a speaker, an infrared sensor (we'll get to that later), a microphone, bluetooth, a 16 kB memory chip (which isn't by itself impressive at all), an expansion slot for accessories, and most importantly an accelerometer. 

Now an accelerometer is cool enough technology to warrant it's own article, but we'll just state the obvious: it measures acceleration. It can also measure the angle of the remote relative to the ground as well as roll (movement around the Y-axis), pitch (movement around the X-axis), and yaw (movement around the Z-axis).1

The Sensor Bar
The Wii Sensor Bar may be one of the biggest misnomers in all of gaming. The Sensor Bar actually doesn't do any sensing at all. Sure, when you're playing the game you'd like to imagine that you're pointing the Wiimote to the Sensor Bar which then sends information to the Wii, but that's not what actually happens.

The Wiimote can know everything about its position (from the accelerometer) except where the TV is - and that's an important piece of inormation. The Sensor Bar is actually just a source of infrared light.2  The Wiimote has a filter on the front that blocks all light except the frequency that the Sensor Bar emits.  When it "sees" the light it knows that it's pointing at the TV.3 The following examples shows what the Wiimote "sees".

When you point the Wiimote down

When you point the Wiimote up

When you point the Wiimote left

When you point the Wiimote right

Because the Sensor Bar isn't actually sensing anything at all, you actually don't even need it. You just need two IR sources (Using one won't work, the Wiimote needs two to triangulates its position). Candles work fine as an IR source, and I do suggest you try it at home, but I think it would be cool to try and play the Wii while being fired at by a pair of high power Nd:YAG lasers...

Now THIS is how you play the Wii...
Trying to dodge lasers makes playing Mario much more fun.

[1] Of course I should mention here that X, Y, and Z are completely arbitrary. I'm using the labels on the picture. I really wanted the blue pictured axis to be the Z-axis to fit with the convention I'm used to, but whatever...
[2] Pronounced "INFRAred" not "INFAred". Start mocking people that say it wrong; it's the new "Nuclear". 
[3] In the direction examples, notice that the directions are inverted from normal vision. When you point the Wiimote all the way to the left, it sees the IR light move to the right of it's vision. 

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Tuesday, November 20, 2012

Turkey makes you sleepy, right?

Hey! So Thanksgiving is upon us, and I wanted to answer the question: Does eating Turkey make you sleepy?

Partial transcripts
Happy Thanksgiving!

Today families across America will gather with relatives they dislike to eat food they love. What's on the menu? Turkey, of course! After feasting on the bird, most of us want a long nap. It's a common belief, then, that turkey makes you sleepy - but is that true?

The chemical in turkey that supposedly makes you sleepy is tryptophan, an amino acid. Remember that amino acids are the building block for protein, and therefore, life. But does the tryptophan in turkey make you sleepy?

The answer that most chemists would give you right now is NO! Of course not! They will point out that turkey has just about the same amount of tryptophan as chicken, salmon, lamb, and beef. There's nothing special, they'll tell you, about the tryptophan in turkey that makes you sleepy. The real explanation, they'll tell you, is that you eat lots of carbohydrates with your turkey. Those carbs take more to digest and your body shuts down to get busy digesting.

That's a fair point, most chemists, but the truth is the tryptophan in your turkey is responsible for your sleep coma. It's just responsible in an indirect, and much more interesting way.

(Insert Something Exciting Here) discovered on Mars!

In a recent press release John Grotzinger, chief scientist for the Mars Curiosity rover has said they have made a discovery. Not just any discovery, though, this discovery is "one for the history books".

We don't know yet what that discovery is and that may upset some people (if you know something why don't you just tell us!!?!!), but that's how science works. Discoveries should be verified and peer-reviewed before an announcement is made. Otherwise we end up with a Pons/Fleischmann cold fusion debacle.

However, this isn't a peer-reviewed blog, so I can speculate all I want. I have a couple ideas of what could be announced and what I think that could mean - in order from least likely to most likely.
SAM (Sample Analysis on Mars) instrument

1. Evidence of current microbial/bacterial life
Ok, this would be awesome. From what I know of the rover's capabilities the evidence they would find of current microbial or bacterial life would things like large peptide and protein fragments. The Mars rover has lots of fancy instruments, but Grotzinger has said that the discovery was found using SAM, or Sample Analysis on Mars, which has a mass spectrometer. If some form of life is on Mars right now the mass spectrometer would most likely respond with peaks for all sorts of amino acids, peptides (several amino acids bound together), and proteins (lots of amino acids bound together). To be honest, this isn't looking very likely. If bacterial life was currently on Mars I think we would have seen evidence already.

2. Amino acids
Another possibility is that Curiosity has found individual amino acids. Amino acids are the building blocks of life. Finding them would be interesting because it would say something about how prolific life in the universe really is. The basic building blocks of life being found on two separate planets in the same solar system would be huge. I don't think this one is very likely either, though.

3. Methane
We know that Mars has an atmosphere of mostly carbon dioxide with some water, carbon monoxide, and oxygen. Finding methane would be a big deal as well. You may wonder why I'm just glossing over the fact that there is water in the martian atmosphere and focusing on methane. The reason that methane would be such an important find is that methane is the product of many carbon decomposition reactions. If life once existed on Mars, we should see methane. Living organisms would be broken down to their component parts, proteins would be broken down to peptides, peptides to amino acids, and amino acids to methane and other products. Finding methane would be a big deal, and if I were a betting man I'd put my money on methane.

4. Minerals
Minerals may sound like a boring thing to find, right? So what, you found a few rocks, what's the big deal?
I've been waiting to make a Breaking Bad reference. I just didn't think it would be this one...
Minerals have already been seen on Mars. We found hematite, the mineral form of iron (III) oxide. The presence of minerals on Mars would suggest that at one point there were large bodies of water on Mars. This wouldn't necessarily mean that life existed, but water is obviously one of the things needed for life.

4. Something else
Okay, let's face it. I'm not an expert. I know chemistry and I'm interested in Mars. I could be completely wrong and something very different has been found. The truth is everything I've written is speculation. "One for the history books" could mean something very different to a scientist than to the author of a real history book.

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TED Talk Tuesday - Kevin Slavin: How algorithms shape our world

In this TED Talk, Kevin Slavin talks about algorithms and how they are used.

Bloodletting makes a comeback?

In a recent search for science news that I could write about, I found this recent article in BMC Medicine titled "Effects of phlebotomy-induced reduction of body iron stores on metabolic syndrome: results from a randomized clinical trial". Metabolic syndrome is a collection of risk factors generally related to obesity. Phlebotomy-induce reduction of body iron store is basically bloodletting.
Schematic of common bloodletting points

If you've never heard of bloodletting, the idea is that you cut someone and let them bleed for a while. This was thought to heal a wide variety of illnesses including seizures, fevers, stroke, heart attack, gastrointestinal problems, and more. If you fell ill in the late 18th century it was almost a guarantee that your physician would try bloodletting. Although it sounds like a gruesome treatment today, it actually has some ties to some modern alternative medicine ideas.1

Bloodletting originated at a time when the circulatory system was not understood. Physicians before the year 130 thought that veins carried blood and arteries carried air. Since the blood in the veins doesn't circulate, they reasoned, it can become stagnant in the extremities. The cure was to bleed a person to get rid of the stagnant blood. 

Even after the circulatory system was understood, though, the practice continued. Eventually physicians would only prescribe the treatment - barbers would do the actual procedure. In fact, bloodletting is the origin for the well recognized barber pole; the red signifies blood, the white a tourniquet, and the pole itself a rod the patient would squeeze to dilate the veins.

Bloodletting continued well after science based medicine should have put a stop to it, but it continued for the same reason that modern alternative medicine is popular - it had a good story. Your body has toxins that need to be removed. Bloodletting is a rejuvination for your body. It restores your body's natural state and energy. But it's all wrong - no matter how good it sounds.

Of course, modern medicine still has real uses for bloodletting (or at least a similar practice). The treatment for hemochromatosis (too much iron in the blood) and polycythemia (too many red blood cells) is venesection.The study I cited at the beginning of this article suggests that patients suffering from high blood pressure may benefit from regular removal of blood. Does this mean that bloodletting was a good practice after all? Not really. Bloodletting was used extensively as a cure for just about everything. Getting it right in one specific case does not validate the idea as a whole. If a patient in the 1850s suffering from symptoms related to high blood pressure was treated with bloodletting, their situation may have improved. However, high blood pressure is often subclinical (meaning you don't notice you have high blood pressure. Instead you notice something that the high blood pressure causes, like headaches for example).

We don't need to revert to bloodletting as a cure all. You may wonder why I'm stating the obvious, but many alternative medicine practices make comebacks. With the right story I wouldn't be surprised to hear Oprah, Dr. Oz, or some other celebrity telling you how bloodletting (they'll call it something more appealing) can cure cancer, rejuvenate you, or restore your body's natural energy state. After all, they've told us stories crazier than that.

[1] I actually found this article while writing a post about some crazy medical practices of the past and how they are similar to modern alternative medicine. Just you wait, it's gonna be good!
[2] Venesection sounds so much better than bloodletting, right?

Monday, November 19, 2012

Clarity and simplicity in science!

The most common response I get when I tell people I'm a graduate student studying chemistry is "Wow, you must be really smart!"

Pictured: Me as a child

I really hate that response. 

There are two main reasons I hate that response:
1. No, I'm really not that smart! 
I don't say this as a point of humility. I'm really not that smart. I found a subject that interests me so I was willing to put the time needed into studying. I never finished an advanced placement class in high school (I dropped out of AP calculus).1 I've written before about my slacker, no direction lifestyle in my post high school years, but it's worth repeating. I missed 85 days of school my senior year. I had no plans for a career, and I definitely had no interest in science or math.

I'm a little embarrassed about my first math class when I finally decided to go to college. I took the placement test and was put in the correct class for my math abilities. On the first day of that class we were given an assessment to make sure we had the math knowledge needed to succeed in the class. Questions for the assessment were things like:
What is 107+24? 
What is 25+81?
To this day, I still use a calculator for simple arithmetic like 8+5 (My calculator is just much cooler now). So no, I'm not really smart. I'm not too far from average and I definitely don't have any special or magical ability for math and science. I had an excellent chemistry professor that showed me how amazing science is and a few really great mentors. Once I saw how amazing the universe is it was an easy decision to learn more.

2. Science isn't difficult!
I also hate that response because it gives the idea that somehow science is difficult or unclear. That's far from the case, and I'm not just saying that because I have a "brain built that way" (see point #1). Yes, to become an expert in some area of science it does take years and years of studying, but isn't that true for anything? I don't think most people would be taken aback by how incredibly smart their plumber is, but it took him years to learn his trade. In the same way, it has taken me years to understand quantum mechanics (and I'm probably not much closer to understanding it than your plumber is).

Journalists have a knack for making science sound difficult, and I think they are partially to blame for scientific illiteracy. Some of them joke about how hard it is to understand science and make a special effort to point out that they don't understand what they're reporting on. This, among other reasons, is why I hate science reporting. As a science reporter it's cool to  be scientifically illiterate. Imagine if a field reporter was uneducated about the war they were covering, and instead of studying up and correctly reporting the situation they just joked about not understanding it. In all but a few cases, I'm sure that reporter would be fired. But for some reason it's okay for a science journalist to joke about not understanding the thing they are reporting on!

Science is meant to be clear!
In a odd twist, the point of science is to make things easier to understand. Science was developed as a way to understand the universe, not as a way to separate the smartest people in the world into a class of their own. Science takes complex ideas and simplifies them. We look at questions about the universe, test them, and come away with an answer! Science is supposed to be clear!

As an example of the opposite of clarity, take a look at this picture:

Now, the correct answer to the question is 8. But the real question I have is why write it like that in the first place? By writing it like that you're just being unclear for the purpose of being unclear, and that's not what science or math (especially math) is about. Here's an analogy of why you shouldn't feel stupid if you got the answer wrong:
Calling you stupid for getting that math problem wrong would be like me writing a really really long drawn out sentence without any punctuation and trying to put a bunch of ideas together in the same sentence and then I'd be really upset at you because you didn't understand what I was trying to say but you should know what I'm saying because the words are right there just read them what are you stupid?
There is a much easier way to write the question:

Mathematically I'm asking the same question, but by adding parenthesis you make the question much easier to understand.2 Sure, there are rules in math to define where those parenthesis are supposed to be placed. Sure, we could answer the question without them, but why make it harder than it needs to be?

The person that originally posted the picture wrote an article on why it was alarming that 74% of Facebook users got the answer wrong. It may be alarming that so many people got the answer wrong, but that doesn't tell me that 74% of Facebook users are stupid. It tells me that we're only being clear enough for 26% of Facebook users to understand us. That's a number that we need to work on.

[1] My thoughts on calculus since then have...changed (Get it? Calculus is math all about infinitesimal changes? Right? Anyone? Ok, never mind, I 'll keep my dumb jokes to myself).
[2] There is one reason to use an unclear problem. If you're trying to teach the mathematical order of operations it can be helpful to make a ridiculous problem. That way you force students to really think about what the order should be. In the real world, though, it's not necessary.  

EDIT: I forgot to add the obligatory XKCD reference.

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Saturday, November 17, 2012

Saturday Links: November 17th, 2012

This Saturday I only have two links, but they're the coolest I've posted in a while. Enjoy.
  • Students at MIT have created a game to model what would happen if you started to move close to the speed of light. The game works by collecting orbs. Each orb you collect lowers the speed of light until you are able to run close to the speed of light. Very cool stuff. Download it now, it's free!
  • Some very unexpected science advocates. A very cool video.

Friday, November 16, 2012

Science Term of the Week: The Doppler Effect

Today I'm going to be explaining the Doppler effect. The Doppler effect is what happens when the sound of a fire engine seems to change as it passes you.

Now, common sense tells us that the siren's frequency didn't really change when it passed us. We've heard it happen so many times and it always happens the moment it passes us. So what's really happening? Why does it sound different?

Sound travels in waves. When something emitting a sound is moving forward the waves are compressed in front of it, and spread out behind it. The faster it moves the more compressed they are and the more obvious the Doppler effect is to our ears. Here's another example, this time with sound waves drawn in to help visualize the effect.

The Doppler effect is seen in any wave phenomenon. You may notice it more with sound waves, but it is also very important to light waves. When something that emits light is moving very fast (more exactly, moving fast compared to your frame of reference) the light waves are compressed in front of it and drawn out behind it, just like airplane example above. 

This effect is very important in astronomy. It's one of the main reasons that we know the universe is expanding. Stars near the edge of the visible universe look much redder than they should (we say they are red shifted). The explanation is that the universe is expanding very rapidly and those stars are moving away from us at an appreciable fraction of the speed of light. This makes them appear red due to the Doppler effect.

If something is moving towards you very fast it will be "blue shifted". If you were moving
close to the speed of light the Doppler effect would make this red bumper sticker appear blue.

Wednesday, November 14, 2012

Why Send a Robot to Mars?

A few months ago I went camping with some friends. We talked around the campfire until about 2 in the morning - a little about the Utah Jazz, a lot about politics, a little more about the Jazz (one of my friends is arguably the most avid Jazz fan to ever live), and even a little about NASA and the Curiosity rover. One of my friends asked the question "Why did we send a robot to Mars, what was the point?" Although I think I did an OK job answering the question on the spot, I'd like to take a second to answer the question more thoroughly now. I'd like to give 5 reasons for us to send a robot to mars.

Reason #1 - Because it's there
 President Kennedy once said "We choose to go to the moon in this decade and do the other things, not because they are easy, but because they are hard…"
The same attitude is applicable to an unmanned mission to Mars. A lot of hard work went into getting a robot on Mars. Was that time and money wasted? It is human nature to climb high mountains, run long distances, and explore the unknown. We push ourselves to the limit just to find it. Mars is a perfect example. In the night sky, Mars is barely visible to the naked eye. It is, on average, 125 million miles away from us. We look up at the night sky and it becomes a challenge. And so we go to Mars, not because it is easy, but because it is hard. 

Reason #2 - Improve our knowledge of the universe
We've already learned some pretty cool things about the universe. The Curiosity rover will tell us even more about the universe. Yes, we're sending it to find evidence of life on Mars, and that would be really cool to find, but we've also sent it with a wide range of analytical tools to tell us all about Mars. Many people see science working in a question/answer process. That is:

  1. Ask a question
  2. Design a test
  3. Get an answer
  4. Ask another question
But that's not how it usually works. Usually it works more like this:
  1. Ask a question
  2. Design a test
  3. Get some really weird results
  4. Explore those weird results
  5. Get more weird results
  6. Design new tests
  7. Get the answer to a question you weren't even asking in the first place
This is one reason to explore Mars. We are looking for life on Mars, but we're sure to learn lots of other things about our universe as we explore deeper.

Reason #3 - Technologic advances
This is somewhat related to Reason #2. When we get really weird results we have to design new ways to study those results. Science in general, and NASA specifically, has asked some really interesting questions in the last 50 years. To answer those questions we've had to develop new technology. That new technology then becomes available to benefit the rest of humanity. Some notable advances that have come out of NASA are:

  •  Improved computer software
  • Enriched baby food
  • Portable cordless vacuums 
  • Solar energy
  • Water purification
  • Carbon Monoxide detection
  • Wireless headsets
  • Flame retardant materials
  • LEDs
  • Diamond coating
  • Artificial hips/limbs
  • Food safety
  • Electronic advancements
In other words, almost everything you interact with on a daily basis can be at least indirectly tied to advances it the space program. Many can be tied directly. If you want a more complete look, check out this really cool interactive website. An interesting note: Velcro was not developed by NASA. It's often listed as something NASA has developed, but that's just not true.

Reason #4 - Pave the way for human visitors
About a year ago my son and I were at a used bookstore looking through old books. My son found a large, space themed picture book. He looked through with wonder (remember, his favorite book before then was Cosmos by Carl Sagan), until he came to a picture of Mars. He asked a few questions about Mars and then exclaimed, "Dad, some day I'm going to walk on Mars!" To this day he talks on and on about Mars. We watched the video of the Curiosity rover landing and now he's excited to see the rover in person some day.1
My son's excitement to someday walk on Mars isn't necessarily overanxious. I believe that he may in fact walk on the surface of Mars some day. That's pretty amazing. Sure the first trip to Mars may be a one way trip - it's much easier. That may seem crazy, but explorers throughout history have always left their homes without a guarantee of returning. Many knew they wouldn't return. I would take the opportunity without hesitation, and I know I'm not the only one. I'm excited to see the spirit of exploration is alive.

[1] My son is excited to see the rover, but he has told me that he hopes "that robot is dead by then. I don't want it to shoot me with its laser". Maybe I shouldn't have shown him this picture.

Tuesday, November 13, 2012

TED Talk Tuesday: Bobby McFerrin plays...the audience

In this TED talk, Bobby McFerrin plays...the audience. The pentatonic scale is very interestingly ingrained in our minds.

Ok, so it's not specifically a TED Talk, but I did find it on the TED website, and it is pretty cool.

Monday, November 12, 2012

Standing on my Soapbox: Scientific Literacy and The Unscientific Scientific Committee

I've been accused of treating this blog like a soapbox. I've gone on and on about certain pseudosciences, I know, but I don't really think I've stood on a soapbox.

Until today.

In the past I've written on the importance of science education. I feel strongly that one of the most important things we can do for our country is cultivate science learning. That doesn't just mean we need more scientists, it means we need a scientifically literate citizenry. Science literacy doesn't mean knowing basic science facts. Sure, it's alarming that 33% of Americans don't believe the earth goes around the sun, 14% think that sound travels faster than light, and 49% think that only genetically modified organisms contain genes. But those are just facts. Facts can be corrected. I don't think anyone is stupid if they don't know something. After all, for everything you know today there was once a day that you didn't know that. It's perfectly okay to not know something.

"Saying 'what kind of an idiot doesn't know about the Yellowstone supervolcano' is so much more boring than telling someone about the Yellowstone supervolcano for the first time."

So, not knowing facts is okay. What's not okay is a targeted disinterest or even disdain for learning something new. Scientific literacy is not a working knowledge of facts, it's a way to approach learning. A scientifically literate person doesn't need a science degree, they need to know the process of analyzing evidence.

A frightening outcome of scientific illiteracy is that the scientifically illiterate will elect the scientifically illiterate. In the US the House Science Committee makes important science related policy decisions. Many of those members are far from scientifically literate. Consider the following examples:
Those that make decisions in Washington are becoming less and less scientifically minded. To better promote scientific literacy we need scientifically minded leaders.

When I initially started this blog, I was writing it because I needed to improve my writing skills. Since then I have developed a real passion for science advocacy and promoting science literacy. Thank you for reading. Thank you for your comments, e-mails, and every other way you've been supportive. Please share with your friends even (and especially) if you think they aren't interested. Remember, I don't care if someone doesn't know a science fact - I care if they refuse to hear about it.

Update (November 29, 2012):
Recent news has me bringing this up again and, unfortunately, adding one more name to the list:

  • Lamar Smith - Chairman Nominee: House Science Committee. Smith denies global warming. In 2009 he said: 
"The [ABC, NBC and CBS television] networks have shown a steady pattern of bias on climate change. During a six-month period, four out of five network news reports failed to acknowledge any dissenting opinions about global warming, according to a Business and Media Institute study." 
Of course, there's a reason not to acknowledge any dissenting opinions: they're mostly political. There is a consensus among scientists that global warming is not only real, but man made contributions are real.

Now, I'm not saying that it's wrong to question global warming, but it is wrong to unilaterally dismiss the scientific consensus without very strong evidence in your favor. We need leaders that make science based decisions, not decisions that are politically or socially appealing. There is a silver lining, though. Lamar Smith thinks funding for STEM programs (Science, Technology, Engineering, and Mathematics) needs to be extended, saying "If America is going to remain competitive in today's global economy, we need to remain innovative and focused on exploring science and expanding new technologies." Of course, if Lamar Smith really supported science education he wouldn't be denying what scientists are trying to tell him...

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Saturday, November 10, 2012

Saturday Links: November 10th, 2012

Only four links today, but they're good ones!
  • Discovery of a nearly complete Mammoth skeleton, that's great, but there's one serious problem with the science reporting in this article. Can you find it? Leave your answer in the comments. 
  • What do you do when a young earth creationist runs unopposed? You write in Charles Darwin, of course. Around 4,000 votes were cast for Darwin in the town of Athens, Georgia. An interesting story, but not only is this guy a member of the house of representatives - he's on the house science committee! This man is not qualified to make scientific decisions!
  • And finally, this video, where Hank Green tells you more about apples than you'll ever, ever, ever want to know.

Friday, November 9, 2012

Science Term of the Week: Laser

A guest post by Angela Calchera

Lasers have been used by scientists, surgeons, evil villains, the Jedi, and by non-technical non-evil non-Jedi people, but what are they really, and how do they work?  The first thing you must understand is that the word "laser" is really just an acronym for what a laser does.  It stands for:

Amplification by
Emission of

So a laser amplifies light in much the same way that an amplifier at a rock concert might amplify the sound of the guitars on stage, and it does this by a process called Stimulated Emission of Radiation.

It's kind of a mouthful, which is why they packaged it all up in an acronym.  And actually, a lot of those concepts could use some further explanation.  You need four things to make a laser:
  • Light Source
  • Gain Medium
  • Cavity
  • Output Coupler
Let me walk you through each of these components, using the titanium sapphire (Ti:Sapphire) laser I use for my research as an example.

Light Source
Every laser has a light source.  Lasers don't  make light, they amplify light.  That means you have to have some light to put into it in order to get something out, just like you need some sound in order to make it louder with an amplifier.  The light source is said to pump the laser, promoting electrons in the gain medium from the lowest energy state into higher energy states.  In the first laser, the light source was a flash lamp, which produces bright bursts of white light like a camera flash.  In the Ti:Sapphire laser in my lab, the light source is actually another laser.
Figure 1. Generalized laser diagram
Gain Medium
The gain medium is where the "magic" happens.  At room temperature nearly the entire population of electrons in a given material are in the lowest possible energy level, also known as the ground state.  In order for the laser to operate, it must achieve a population inversion, meaning that more electrons need to be in an upper level than in a lower level.  In some materials, this is impossible.  For example, if a material only has two energy levels, the best we can do is to put half of the electrons in the upper level and half of the electrons in the lower level; the population of the upper level can never exceed that of the lower level as we need it to in a laser gain medium.  It turns out, three levels is the minimum to make population inversion possible.

In a titanium sapphire laser, the gain medium is sapphire with (intentional) titanium impurities.  In this material, there are four levels the electrons can occupy.

Figure 2: Energy Diagram of Ti:Sapphire
Step 1. First, light comes in from the light source, and that promotes some electrons from the lowest energy level into the upper-most energy level.

Step 2.  Electrons don't stay in that level for long at all, and very quickly move down into the second-highest state.  The electrons lose this energy without any light being produced.  Because this step is very fast, and the next step is very slow, many more electrons end up in this level than in the level below it, which is the population inversion we needed.

Step 3.  This step is the one that gives the laser its name.  Photons (packets of light energy) of the right energy cause (stimulate) the electrons in that level to go down to the lower level.  As those electrons "fall," they release (emit) light energy.  The photons coming in did not get absorbed, their only purpose was to stimulate the emission of more photons, so the emitted photons add to the total number of photons coming out of the gain medium.  So, you see this is the amplification step because the total number of photons is amplified here.  Also, this amplification came by the stimulated emission (as opposed to spontaneous emission, which would occur without the photons coming in to get it started) of radiation (light waves/ photons are a form of radiation).

Step 4.  Electrons very quickly return to the lowest energy state without emitting any light.

The name of a laser pretty much always comes from the type of gain medium used.  In a titanium sapphire laser the gain medium is a nice pink crystal.  You may find it odd that the sapphire is pink and not blue.  Sapphire without impurities are actually completely colorless - the colors come from impurities in the crystal structure by changing the energy levels that electrons can occupy, but that's for another post.

Figure 3. Ti:Sapphire gain medium

Cavity and Output Coupler
A mirror is placed on each side of the gain medium so that the light passes through the crystal multiple times, and with every pass that light is amplified.  The two mirrors make up the ends of the cavity.  If both mirrors reflected all the light, the amplified light would be useless because it couldn't escape the cavity, and so one of the mirrors in the cavity, also called the output coupler, is not as reflective and allows some light to be transmitted out of the cavity.

The invention of lasers and their improvement have led to many advances in physics, chemistry, materials science, environmental science, manufacturing, medicine, and media storage, among other areas.  However, it is interesting to note that when they were first invented, they were considered a novelty that had no practical applications.  For this reason, lasers are a great example of why it is important that we invest in fundamental research, even if it doesn't have an apparent practical application.  You never know what lab project will turn out to be yet another versatile tool to enhance your life.

Also, no, I can't make you a light saber.