Tuesday, February 18, 2014

Proteins and PEGylation: Sam's Thesis

It's a new podcast episode! This is the first episode that we've got Dorea Reeser as the newest permanent co-host of the podcast.

In this episode we're interviewing Sam about his Masters thesis. He studied protein stabilization using polyethylene glycol (PEG).


2:30 - A general introduction to proteins and amino acids. Complete with the start of an analogy by Sam. Comment below if you can finish the analogy for him.

4:00 - Sam's thesis title: "Investigation into the effects of PEGylation on the thermodynamic stability of the WW domain". We discuss what thermodynamic stability means, what PEGylation means, and how both of these ideas apply to protein therapeutics (using insulin as an example).

18:00 - How does Sam make his proteins? (Hint: Sam does it the hard way)

20:00 - Chad asks a synthetic question. Chad's children join in with their questions about synthetic chemistry.

25:00 - What are the big objectives of Sam's research?

28:00 - "30 Seconds of Jargon" a new feature for the podcast. We give our guest 30 seconds - and only 30 seconds - to explain their research with all the jargon they can muster.

30:00 - The Fortnightly Scientist: Primo Levi

Sunday, February 9, 2014

Hypothetical Homework #2: Sitting in a room. Waiting to die.

This week's question comes from @fxcoudert on Twitter:

"When sitting, your head is in the lower half of a room's volume. Estimate the frequency at which you will asphyxiate because all air molecules have spontaneously gone up to the higher half? Interpret the results."

Statistical Mechanics. My favorite (said with 0.0001% sarcasm). When I asked for homework problems I knew the day would come that I would be a bit stumped. I didn't know it would happen on the first submitted question. Thanks to @fxcoudert for the question. I hope I don't mess this up too much.

The first step in this question is to find the probability that all of the air molecules will be in one half of the room. Statistically this is simple; it's just:

So, partial credit at least. For this last part I know I have the right answer. At least correct to within a several orders of magnitude (and you'll see soon that a few orders of magnitude is close enough).

For the rest of the problem I'm going to be employing the ergodic hypothesis; I'm going to be assuming that over long periods of time the system will be in a particular state for a time that is equivalent to the probability of being in that state. So here's what we'll do. We start by putting all of the particles in a random position:

Then, after a certain amount of time we move all the particles to a new position:

The benefit of this approach is I can ignore any actual movement of the individual particles; we'll just assume that they move instantaneously from one state to another. This obviously doesn't happen in the real world but it's an assumption that is valid when you're looking at large numbers. 

So how long is "a certain amount of time" that we leave between switching states? The best approach is probably to consider a state changed every time there is a collision. Depending on the pressure I'll estimate that at somewhere around one collision every microsecond. We can calculate how long it would take  for all the particles to be in half of the volume by multiplying the time between changing states by the probability of that happening:

N is incredibly large (~1024). The age of the universe is ~1017 seconds. The amount of time it would take for all the molecules to be in the higher half is 21024 (and actually you wouldn't asphyxiate because they'd start moving away from each other to fill that empty space pretty quick, but I'll assume the question ignores that point).

Interpret the results? Well, you're safe to sit down. It won't kill you.

Wednesday, February 5, 2014

The Real Damage of Chemophobia

I root for the underdog.

I'm not sure why, really. Maybe it's because I watched Rudy too much growing up or because my city's Minor League Baseball team couldn't win a game for a "Make-A-Wish" kid even if the other team was in on it. I cheer on the Miami Dolphins and go to Utah Jazz games. Lately I've noticed that I've been backing another, much more unfortunate, underdog: Chemistry.

Chemophobia is an irrational fear of chemicals. It can (and has been) debated that the word itself creates more of the same irrational fear; that it drives the fear deeper by making it a point to ridicule. Whether that is true I'm not completely convinced. What I am convinced of is that an irrational fear of chemicals runs deeper every day. This fear is seemingly unchecked by the chemistry community at large. I don't mean we don't talk about it. We do. We talk plenty about it. But what are we doing about it?

In early January General Mills announced that it will no longer be using genetically modified crops in Cheerios. You may have heard this but unless you've read it straight from the source you probably missed the part where vice president of Global Communications Tom Forsythe admits that the move actually changes nothing in the Cheerios recipe and is nothing more than a new marketing strategy:
"We did it because we think consumers may embrace it...it’s not about safety...And it was never about pressure. In fact, General Mills’ position on GMOs hasn’t changed."
General Mills' position, by the way, is very reasonable. It's just unfortunate they have tried so hard to hide it from consumers. They admit that 20 years of rigorous testing has shown GMOs to be safe, that not a single disease can be linked to GMO crops, and that a host of benefits come with the technology. So why hide this evidence-based, rational position? Because they see that consumers embrace the opposing position.

Another company, Johnson & Johnson, recently made some radical changes to appease consumers (changes that brought with it some serious chemical misinformation). The famous amber colored "No More Tears" shampoo recently got a new formulation. In the past the well known shampoo contained formaldehyde. Actually, to be more accurate it contained preservatives that over time produced low levels of formaldehyde. How low? You would need to drink 15 bottles of shampoo to get the same exposure to formaldehyde that you get from eating one apple. You heard that right, an apple (and why in the world are you drinking shampoo?That's for washing babies). But Johnson & Johnson went through an exhausting process to reformulate the shampoo and remove the preservatives. All this because it makes them look good and consumers demanded it.

Finally, this morning I read a petition by the self described "Food Babe" to Subway. In it she demands that Subway stop using the chemical azodicarbonamide. She claims that eating a Subway sandwich with azodicarbonamide is the same as eating a yoga mat. This claim isn't new. Chemistry blogger Derek Lowe handily debunked the claim nearly 8 months ago. Azodicarbonamide has been documented to cause respiratory problems but only in high concentrations. The dough contains very, very low concentrations. The bread is made even more safe by the fact that none of the chemical even exists in the bread; it breaks down when heated (a process that I'm pretty sure all the bread you've ever eaten has gone through. Bread needs to be baked after all). Azodicarbonamide is completely safe in your bread and there is no need to worry. Imagine my surprise, then, when just 24 hours after posting the petition on her website the Food Babe gets a direct reply from Subway. It took only one petition and 24 hours for Subway to begin changing their recipe.

So what's the harm? Cheerios don't have GMOs, baby shampoo still looks and works the same, and I don't really like Subway in the first place. Big deal, right? I can keep eating the food I want and using the products I choose because companies will work just as hard to please me as the "chemical free" crowd. Why do I even care what health choices someone else makes? Aren't they making healthy decisions? If Subway removes azocarbanomide from their bread it will only make it more fresh and healthy, right?

The reason this is such a big deal has nothing to do with those individual products. The real damage of chemophobia comes when little by little the word "chemical" becomes a bad thing. The harm comes when people believe that if you can't pronounce an ingredient you should never put it in your body. Ingredients like thiomersal, monosodium glutamate (MSG), and formaldehyde. You'll find these ingredients in vaccines. Vaccines that save lives. Vaccines that - if avoided - will cost lives. So yes, chemophobia kills. I'm not just a pedantic chemist. An irrational fear leads to irrational decisions and every corporate concession legitimizes that fear. When General Mills goes against their own policy to appease the GMO free crowd they misinform the public. This misinformation leads to third-world countries banning GMO crops; the very crops that can help produce a thriving farming industry.

This is all very disheartening but I'm a perpetual optimist. I think chemophobia is something that can be overcome. If the Food Babe can bring about change in as little as 24 hours with one petition then so can we. I challenge organizations like the American Chemical Society to be more vocal about chemophobia. Do it in a way that educates. Do it in an open way, not behind a pay wall or trapped behind the safety of the chemistry blogosphere. Do it in a way that the American public won't be able to ignore. Do it in a way the American people will love you for. Chemistry doesn't need to be scary, but it doesn't need to be boring either. It won't be easy and it won't be cheap. But it is necessary and I think we can do it.

Because I root for the underdog.

Sunday, February 2, 2014

Hypothetical Homework #1: The Amazing Eli

I'm in a very awkward stage right now - I'm neither teaching nor taking any classes. This hasn't happened to me in almost a decade. Many (and probably most) of you would say this is a happy time and I should just enjoy it. Instead I've felt absolutely lost. I'm not taking, grading, writing, or studying for any tests. So I've decided to start a new series on this blog I'm calling "Hypothetical Homework". It's basically the questions I wish I could either ask students or answering questions that others send me.

Here's the deal: I'll answer at least one question per week. I do not guarantee the questions will be answered correctly - in fact I suspect I'll get some very, very wrong - but discussing why I'm wrong can be part of the fun (that's what we call fun at least, right?) Submitted questions will take precedence over questions I write for myself, so please send questions to chad (AT) thecollapsedwavefunction.com or ask them in the comments or on Twitter. Any topic is allowed, but chemistry and related disciplines will likely get picked first unless the questions are really awesome.

So, without further ado I present to you:

Hypothetical Homework #1

Eli, an orangutan at the Hogle Zoo has correctly predicted the Super Bowl winner 7 years in a row, the latest being the Seahawks victory over the Broncos. Is this statistically surprising? Why or why not?

The result is not surprising. Eli has correctly predicted the winner of Super Bowl from 2008-2014.1 The probability of him choosing the winner in any given year is 1/2. For Eli to pick the winner correctly 7 years in a row is a bit more surprising:

That is, there is a 0.78125% chance that Eli would pick the winner of the Super Bowl 7 times between the year 2008 and 2014. Or you could say that there is a 99.21875% chance that Eli would have gotten at least one of those years wrong:

So far it actually seems like we should be amazed at this ape's ability, and this is probably where most people would stop. But here's the deal: we also need to ask ourselves what makes Eli so special? Was he chosen from birth and raised with the expectation that from 2008 to 2014 he would correctly predict the Super Bowl Champions? Probably not. So the question we want to answer is, "What is the probability that a captive orangutan (of which there are ~350) could correctly predict the winner?" For that I pull out a special trick in statistics that I like to use: calculating the probability of the opposite outcome. In this case I want to find the probability that all 350 captive orangutans would predict the wrong team at least once:

There is only a 6.42% chance of all orangutans getting at least one pick wrong. This means that there is a 93.58% chance that at least one of the 350 captive orangutans would have picked the winner correctly from 2008-2014. A counter point may be that not all 350 captive orangutans were asked to predict the winner, but that doesn't really matter given the number of animals asked about any number of sporting event. And we haven't even begun to mention the probability of this happening during any other 7 year period (2007-2013, 2006-2012, etc). The point is you should not be surprised to hear an animal has predicted the future because it's all a confirmation bias: Only the animals that pick winners make the news.

[1] - Why didn't Eli pick his brother's team for the win? (It's a sport's joke, nerds. Peyton Manning, Quarterback for the Denver Broncos, has a brother named Eli who also plays football)