Thursday, March 28, 2013

AskScience Live!

So I've got some amazing news. Many of you have heard of reddit, the "frontpage of the internet". In the past I mentioned as one of the greatest science resources that the internet has, and I still believe that. Sure, there are a lot of really horrible things about reddit, but if you're looking in the right places there are some really great conversations.

AskScience is one of those places. In the AskScience forum you can ask just about any science question you have and be almost guaranteed to get input from someone that is an expert in that field. AskScience has over 2,000 panelists in fields ranging from biology and chemistry to anthropology and psychology. Not anyone can be a panelist, though. You need to be at least a graduate student in your field and demonstrate that you can explain your field correctly and simply to a lay audience. Moderation can sometimes be pretty heavy handed, which makes the discussion usually on point and science based.

Doing something new: AskScienceLive
Over the past month or two I have been working with some of the other panelists to create a video podcast version of the forum. We are now pleased to announce AskScienceLive! We've gathered together experts from a few fields, and we're going to be doing a Google "On Air" hangout. Our first episode will be April 11th, 6pm EDT. We will be taking questions asked on Twitter and answering them live. This could really be an awesome event, so please mark your calendars and bring your toughest science questions!

Please check out (a current work in progress website) and stay tuned for more information and more episodes to come!

Monday, March 25, 2013

What does "Organic" mean, anyway?

"Organic" is a term that's thrown around a lot, and it means a lot of different things to a lot of different people. Sometimes organic means that a tomato has been grown without pesticides, other times it means anything derived from living things, and to a chemist it usually means any compound that contains both carbon and hydrogen. An "organic lifestyle" could either mean that you're attempting to live in tune with mother nature or it could mean you don't get out of the lab very often.

The internet (or at least the chemistry corner of Twitter) has had some great discussion over the last few weeks dealing with chemophobia. Today I read a great article on the blog "Behind NMR Lines" with a surprisingly un-chemist-like approach to chemophobia. The standard response from chemists who hear complaints about "chemicals" is to say something along the lines of "well, even water is a chemical". The author points out that, while this argument is completely true, it sidesteps the actual concern. When people say "chemical" they obviously don't mean "all matter, everywhere", they mean harmful chemicals.

What it means to me isn't what it means to you
I wonder if we make the same mistake by being too rigid with our definition of "organic". As a chemist, when I hear the word "organic", I immediately think of...well...chicken wire (the chemistry "shorthand" for organic compounds often looks a lot like fencing for a chicken coop). I think of the definition I know. I've had years of schooling that drilled "organic" into my head as meaning "a compound containing carbon and hydrogen". This definition works, but it makes things like "organic sea salt" sound like absolute nonsense.

So for years I have argued that the term "organic", as used by the general public, is not only ridiculous but almost meaningless. However, I wonder if I've been wrong. I wonder if it wouldn't be more appropriate to see organic (chemistry) and organic (food) as homonyms, similar to bark (dog) and bark (tree). Certainly the distributors of "organic sea salt" think so - their product description says:
"There are no chemical additives or processing aids used in Marlborough Flaky & Pacific Natural Sea Salt production and there is just one ingredient - seawater. The process fits in with organic principles and is Certified by Bio-Gro New Zealand" 
It seems, then, that we are using the same word to mean very different things.

Semantic Drift or Homonyms?
In response to the "Behind NMR Lines" post, @V_Saggiomo made the following point:

Which I think applies just as easily to "organic". You could easily argue that organic chemistry began in 1828, with the synthesis of urea. Prior to this synthesis it was believed that living organisms had a special property (vitalism) that couldn't be synthesized in a lab. The synthesis of urea, a compound found only in living organisms, sent that theory right down the toilet (a pun that is totally intended), and organic chemistry was born.

Now let's look at the other use of the word organic. Proponents of organic farming claim that organic farming has been practiced for thousands of years, but I think you could easily reject that claim - ancient farmers didn't use pesticides and other modern farming techniques because they simply weren't available. The term "organic farming" wasn't coined until 1940, and it was used to describe a farm as an organism.

The term "organic" in both cases was used because of the connection to a living organism, but that's about the only things they have in common. Organic (chemistry) was used to describe a family of chemical compounds while organic (food) was used to describe a type of farming that avoided "chemicals". Whether semantic drift is the cause for the confusion or the words were meant as homonyms from the start, one thing is clear: We're not saying the same thing.

Great, we mean different things. Now what?
I think it's obvious that organic farmers are not using the definition that chemists are, and vice versa. Organic farming is a technique that rejects modern techniques because the "chemical" treatments are either a potential health hazard or rob the fruits/vegetables of some nutrient. Instead of arguing about the word organic we should be refuting those claims. Specifically, I can think of two reasons why buying organic food doesn't make sense:
1. There's not much evidence of any health benefits from an organic diet.In fact, there's not even evidence that organic food tastes any better, either.
2. The requirements for an "organic" label are easily manipulated, and you're probably not getting what you think you are when you buy organic foods.
So maybe, just like with the word chemical, we should be focusing less on which words people are using and help them understand what they are really saying.

Tuesday, March 19, 2013

Living with chemicals: Retinal

The Chemical (IUPAC): (2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraenal
You probably know it as: Retinal
The structure:

Last week I wrote about betacarotene, the chemical in carrots responsible for their orange color. I mentioned that although betacarotene was necessary vision, eating a ton of it won't give you supervision. As I said, betacarotene is converted to Vitamin A, which is converted to retinal. Retinal is a cool chemical with even cooler chemistry. You may know that in your eyes you have light receptors called rod cells, or "rods". These cells are responsible for low light vision.  Your rods are so sensitive that in a perfectly dark room you would be able to detect a single photon! This is what  rod cell looks like:

You'll see that the outer segment has membrane shelves that are lined with rhodopsin. Rhodopsin is a protein containing 348 amino acids. Retinal sits wrapped neatly inside rhodpsin, bound to the amino acid lysine. In a completely dark room the retinal in your eyes will be in the "11-cis" conformation. This is a bent conformation which allows retinal to fit inside rhodopsin. When a photon is absorbed by retinal it changes the conformation to the "all-trans" conformation, and retinal no longer fits inside or rhodopsin. 

Rhodopsin then unravels and this sets off a cascade of chemical reactions that end with a signal being sent to the brain. What's even more amazing is how well we understand that cascade. But that's a story for a different day...

Thursday, March 14, 2013

Science Myths and Misconceptions - Part IV: Gravity in Space

#4 - There is no gravity in space
A common view of space is that it is a gravity free zone. I can understand where the confusion comes from (we do call it zero gravity, after all), but there is actually a lot of gravity in space. Gravity is the reason the moon orbits the earth, the earth orbits the sun, and the sun orbits around the center of the galaxy. Gravity is a force that any object with mass will create. We're most familiar with the gravity on earth, but even a small object (like you) will have an attractive force (you can read more about that here).

For an example of what "zero gravity" really is, let's look at Commander Chris Hadfield. Commander Hadfield has been on the International Space Station since December 21st, 2012. For those of you who aren't familiar with Hadfield's internet fame he's had a twitter conversation with Captain Kirk, given Reddit the best AMA of all time, and shared some amazing pictures. Now, why hasn't the ISS fallen from the sky in that time? Certainly if there were any gravity at all the entire station would come crashing down, right? The answer, which you already knew, is that the ISS is orbiting the earth. But what does it really mean to orbit?

Saying that the ISS is orbiting the earth is really just a fancy way of saying it's falling to the earth but hasn't gotten there yet. The ISS is traveling with a velocity horizontal to the earth of ~17,500 mph (Imagine a point 5 miles away from you. Traveling as fast as the ISS you'd be there in just over a second!). Commander Hadfield doesn't feel like he's moving at that speed though - he's falling to the earth at the same rate that the space station is so he feels weightless.

Here's a video of Commander Hadfield washing his hands in space:

You can see the rest of the the Science Myths and Misconceptions here!

Tuesday, March 12, 2013

Chemistry and Cooking

"Chemistry is just like cooking, except you can't lick the spoon!"

By training I'm a chemist, though what I do in the lab is far what most people imagine when they think of a chemist. When I say I'm a chemist, I'm sure most people imagine the mad scientist surrounded by glassware, odd colored liquids, and smoking test tubes (come to think of it, this is how I imagine organic chemists!). But the chemistry I do doesn't involve any of those things. I don't wear a lab coat, gloves, or safety goggles (though I do wear laser glasses). I haven't even synthesized anything in a lab in over 3 years. I think part of me misses that, which is why I find it very relaxing to cook. 

I don't like to follow a recipe, though. I cook in the style of "a dash of this" and "a pinch of that". If my wife really likes something I've cooked she knows to enjoy the moment because she'll never have that exact dish again. That's not to say my wife doesn't like my cooking, she just knows that every meal will be different. 

Usually when I'm cooking my mind turns to chemistry. In particular I've been thinking of the Maillard reaction. Though you may not have heard it of it before, I'm sure you've seen it. Just take a look at this amazing piece of chicken I fried up tonight: 

Ok, so maybe I wrote this as an excuse to post this picture. At least I haven't added a filter or something...

The browning on the outside of the chicken is due to the Maillard reaction, which happens when amino acids react with sugar in the presence of heat. You'll see it in toast, roasted coffee, maple syrup, caramels, and much more. From that list I'm sure you'll agree that the reaction can create a wide variety of taste. Understanding and utilizing the reaction is the basis of the food industry.

The following paragraph is written by a physical chemist. Like I said I haven't done "real" chemistry in years.

The process occurs in three stages. First, the carbonyl group of a sugar reacts with an amino acid to produce water and glycosylamine. Then, the glycosylamine pushes a hydrogen around (which is my simplistic - and wrong - way of describing an Amadori rearrangement, but I'll admit it I had to look that up) to produce a variety of aminoketones. In the final step a host of other products are produced depending on the pH, the temperature, and amino acids involved. These different products are why the Maillard reaction creates such a wide variety of tastes.

So my question to other chemists that read this is - do you enjoy cooking? For you synthetic chemists, does it feel too much like work to be enjoyable? Let me know in the comments!

Monday, March 11, 2013

Living with Chemicals: Betacarotene

The Chemical (Systematic name): 1,3,3-Trimethyl-2-[3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohex-1-en-1-yl)octadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl]cyclohex-1-ene
You probably know it as: Betacarotene
The structure:


In the next few blog entries for "living with chemicals" I'm going to be focusing on some of the amazing chemicals that make sight possible. We're going to start with the chemical betacarotene, which you've probably heard helps you see better at night. You may have even been told that eating carrots helps you see better at night because of the high betacarotene content.

While it is true that betacarotene is necessary for night vision (it's converted to Vitamin A which is converted to retinal which is necessary for sight), it won't help you see better at night unless you have a real deficiency. However, as is true with many myths, the story behind the myth is more interesting than the myth itself. During WWII, the Britain's Royal Air Force developed a new radar system (the Airborne Interception Radar). This gave them a huge advantage for shooting down Nazi planes. So, to keep the Nazi's from realizing they had a new tool they spread the rumor that their soldiers ate lots of carrots to help them see better in the dark.

And it worked so well that people believe it to this day!

Betacarotene is also interesting because it's a really long molecule. There are 22 conjugated carbon-carbon bonds (the alternating single and double bonds you see along the chain). This actually means that betacarotene is good evidence that quantum mechanics is a valid theory (that may sound like a leap, but let me explain). Some of the most simplistic models of electrons describe them as orbiting around a single atom. That may make sense, but it's wrong. In systems like betacarotene the electrons actually move freely down the entire chain. In fact, they exist as a wave that exists everywhere along the chain at the same time. We can model the electron system using the energy level diagram below:

Only two electrons can occupy each level, so in total 11 energy levels are filled. As the energy level gets higher the space between levels gets smaller and smaller. When light interacts with this system an electron is promoted from the n = 11 level to the n = 12 level. But this can't happen when just any light comes along, it must be light whose energy is equal to the spacing between the two levels - which turns out to be ~480 nm, a nice blue color. So that's why carrots are orange, they reflect orange light and absorb blue light. But we can still learn something cool if we model the system as a particle in a box. The energy of the particle in a box levels can be calculated by:

E = {n^2}\frac{{{h^2}}}{{8m{L^2}}}

Where n is the energy level, h is the Plank constant, m is the mass of the electron, and L is the length. The difference between level 11 and level twelve is:

\Delta E = {E_{12}} - {E_{11}} = \left( {{{12}^2} - {{11}^2}} \right)\frac{{{h^2}}}{{8m{L^2}}}

Which can be rearranged so that we can calculate the length of the chain in betacarotene:

L = \sqrt {\left( {{{12}^2} - {{11}^2}} \right)\frac{{{h^2}}}{{8m\Delta E}}}  = 1.89{\rm{ nm}}

Which is a pretty good answer for the length of that long chain in betacarotene, especially since we used a very simple model to get the answer. So next time you bite into a carrot, take a look at its nice orange color and remember that without quantum mechanics it wouldn't be orange at all.

Thursday, March 7, 2013

Zero Hour: Zero Credibility

A Bad Science on TV post by David Zaslavsky
(Check out his awesome physics blog here)

There's a new TV show on ABC, Zero Hour, whose previews really piqued my interest earlier this year. Highly skilled assassin, greatest conspiracy in the history of the world, something about clocks. Seems like good clean utterly ridiculous fun. I like horrible disaster movies, so I figured this should fit right in.

But only three episodes in, Zero Hour has already managed to butcher the science so badly I'm not sure I can stand it anymore. Let me set the stage: the main character, Hank, is searching for his wife, who has been kidnapped, and to find her he has to locate a series of clocks, each of which has clues leading to the next location. Clock number 2's clue was a map of the constellation Cepheus. Combined with the time and date on the clock (the hands were frozen in place), this supposedly led Hank to the exact location you'd have to be to view the constellation at that time: Chennai, India. But maybe you can see the problem here: a constellation is not visible from only a single location! By their criteria, Hank could be looking for any place in that entire hemisphere of the Earth. Sure, maybe the clue was supposed to identify where Cepheus would be seen directly overhead, but that's not anywhere close to India. Cepheus is a northern hemisphere constellation, very close to the north celestial pole, so the only places it appears directly overhead are in the Arctic. On the other hand, here's the view from Chennai at 8:15 AM on March 8, 1938, the date and time named in the show:

Cepheus is almost right on the horizon. The constellation that was directly overhead at the time was Aquila, which they could just as easily have named. To be fair, I guess that wouldn't make for very good TV because it's basically a nondescript rhombus, but then again, Cepheus is just a square with a hat, so you can't be too picky.

But that snafu with the constellation, which I could have lived with, pales in comparison to the next (and most recent) episode. The clue from the third clock leads Hank, after some floundering on the acronym IAS (which anyone as smart as he is should instantly recognize), to the Institute of Advanced Study in Princeton, NJ. Let's just bypass the fact that they managed to get almost every location in Princeton wildly wrong — I mean, if you've never been there, you probably wouldn't care. (For the record, the Princeton Public Library looks like an entirely normal public library, not a stuffy university library as it's shown in the show.)

What really irks me is the equation they found on Einstein's blackboard at the end. In the show, Einstein erased something from the blackboard he was working on just before he died, which was rumored to be the formula for a new power source that he considered too dangerous for humankind to control.
  • Real power sources come from engineers tinkering in workshops, not from equations on a blackboard.
In the show, the erased formula turns out to be a key to a coded message Einstein left on the rest of his blackboard.
  • Real physics formulas are neither keys nor coded messages.
In reality, you might recognize this formula:

Yep, that's the time-independent Schrödinger equation, an entirely mundane equation that forms the basis for nonrelativistic quantum mechanics. It would have had relatively little to do with what Einstein was working on at the time, and certainly there's no way it could have been turned into the key for a coded message which would also make sense as a physics formula.

Anyway, it's kind of a moot point by now. The latest news from the "TV gods" is that Zero Hour has been canceled after just these three episodes. Honestly, I'm not surprised. I only wish the lesson to take away from this would be that you can't get away with terrible science on television, and not just that sucky TV is sucky.