hmmmm

Avatar has made a billion dollars and counting.

You would think they could have hired someone to teach Sigourney Weaver how to use an Eppendorf Pipette.

If you've seen it, did you notice? If you haven't, watch for it when they take the trailer to a remote location (you'll know what I mean).

Not to mention that since the film is set in 2154 it seems odd that Eppendorf would not have updated their design for about 160 years.

A lifelong dream realized

I've always wanted an ant farm. Why? I have no idea. Maybe it has to do with watching a tireless animal spend its few remaining weeks pursuing a fruitless endeavor. I don't know.

A lifelong dream has finally come true. The combination of doing something sciency for my kids and having vast amounts of disposable income inspired me to finally purchase an ant farm. And this is not your daddy's ant farm. This is a space ant farm equipped with LED lights and everything.

Behold:
The 'sand' is a gel. It reminds me of agarose. I took delivery of 30±2 harvester ants this morning and added them to the farm. I expect crops by Fall.

Here's another pic with flash:

Now, back to my stout and Easter eggs.

I need grant ideas

I really want to write a grant proposal, but I don't have any good ideas. Does anybody out there have any great ideas that I could use to put in a grant proposal? I want to get funding from the NIH or NSF so make sure your ideas are in line with the types of projects they fund.

I know I should come up with my own research ideas, but I can't really think of anything that hasn't been done. It's really hard thinking about that stuff. So I need your ideas. Send me your ideas to me soon. Deadlines are approaching.

****************************

Please note: the above note is completely sarcastic. I am not actually looking for research ideas (unless they're really good, of course and can guarantee millions in funding).

My point is this: Parents, stop asking me what your child should do for a science project. Yes, I have millions of ideas, but that doesn't help your child. Yes, some guidance is necessary, but the child must ask the questions.

I will gladly help if your child has a plan and needs assistance designing an experiment to doing an experiment safely. But for crying out loud, don't expect me to tell your child what project to do.

I get asked that a lot, usually from parents. My standard response is "no," but I do offer advice on how to guide the child to discover their own project. Get the child to look around and ask "How?" and then "what if...."

Isn't that what basic research is about and isn't that what a science project should be. It all starts with curiosity. Not all kids are gifted with or nurtured to develop scientific curiosity. They will be the ones that test laundry detergent for the science fair. The scientifically curious ones will take it to a different level.

Just don't ask me what they should do.

Irish Moss: A brief description

Clear beer is often a goal for many homebrewers, the standard being set by the commercial brewers. With modern brewing techniques and common industrial practice we have come to expect our beer to be crystal clear. When homebrewing, clear beer is not common. In reality, most homebrews are cloudy.

The two main culprits of cloudy beer are yeast and proteins.

As the yeast near the end of their job (i.e. when fermentation is ending due to lack of sugars) the single cells of yeast will clump together in groups of thousands and settle out. This is known as flocculation[1]. Different yeasts flocculate differently. Some yeasts settle out nicely and others do not. One strategy to get more yeast to settle out is to cool the beer (such as lagering) before bottling or kegging.

The other culprit of cloudy beer are proteins along with polyphenols and lipids (fats). While proteins are not necessarily small molecules, they are small enough to remain in suspension.

Beer can be clairified using Irish moss, a fining agent. Fining agents all work by making the smaller molecules aggregate into larger particles so they settle out of solution. This can be mathematically described by Stokes Law:

Where v is the rate of sedimentation, r₁ is the density of the particle and r₂ is the density of the wort, r is the radius of the particle, g is 9.8 m/sec² (a.k.a. acceleration due to gravity), and h is the viscosity of the medium. In other words, as the density and size of the particle increases it will settle out faster. In addition, a thinner wort will allow settling to occur faster.

Irish moss is Atlantic red seaweed[2] that contains k-carrageenan:
The k-carrageenan is a polymer of β-D-galactose-4-sulphate-3,6-anhydro-a-D-galactose. It is similar to starch or cellulose (i.e. comprised of thousands of carbohydrates). The negatively charged sulfate groups are thought to interact with the proteins in suspension. As the wort cools, more and more proteins interact with the k-carrageenan and the k-carrageenan adopts a more compact structure. The result is the molecular equivalent of marbles in syrup. After the churning of an active fermentation ends (4-5 days) the carrageenan-protein chunks settle out with the yeast.

Homebrewed beer is still often cloudy, but Irish moss does make a noticable difference.



[1] He he he he, I said flocculation.
[2] Yes, seaweed.

What do you want?

So, I've been really bad at posting on this blog. I'm not sure what my problem is. Oh! I know. I've been really busy at work with an impending accreditation review coming up in October.

So much for my summer.

Back in the day when I was pretending to be a premed, I had a med school interview. I was ready to answer all possible questions. So, I was taken aback when the doctor interviewing me asked me, "so, what do you want to know?" That was his first and only question. I didn't expect to be asked to ask questions. Perhaps I was naive. When all was said and done, I went to grad school. However, even before then, I was convinced I wanted to be a chemist. At the time I was just going through the premed motions.

So, I thought I'd ask you, my readers (both of you), what do you want to know?

What do you want to know about brewing beer? About teaching Chemistry? About holding your high school high jump record for 18 years (and running).

I know some things about these areas and will dispense whatever information I have about them free of charge.[1]

So, what do you want to know?

[1] I realize I'm overcharging you, but deal with it!

y=mx+b is for losers

Everyone who has mowed a lawn or watched professional baseball is familiar with the patterns a lawnmower makes as it cuts the lawn. Here is one example of what I am talking about:

Or here is an example from Minute Maid park in Houston:

The easiest pattern is a linear one, but this is boring. To prove how much of a nerd I really am, I decided to forgo the y=mx+b motif and employ a non-linear function. This week I mowed my lawn in a sin(x) manner. See:

OK, the picture isn't great and I couldn't fit my whole backyard into one shot. I am also too lazy tonight to screw around with Photoshop and merge them together, but you get the idea. The bucket was meant to be a point of reference. It looks better in real life, though one could easily tell I drew this with a lawnmower. It isn't a perfect sine wave.

I was originally going to do ln(x), but I'd still be mowing. *rim shot* (Get it? If not see: [1])

Next week, maybe a zig zag. First I have to figure out the function for a zig zag. Or I could do f(x)=|sin(x)|. hmmmmm, so many possibilities, so little lawn.

[1] Think asymptote.

Announcing....

Friends and others,

Do you like stuff?

Do you like stuff that is cool?

Do you like stuff that really lets you express your love of chemistry?

If you said 'yes' to any of these questions, then allow me to introduce to you:
This is bingo for chemists. Sure, there are other element bingo games out there, but none of them are called "LMNTO."

Some students and I developed this little game. Everything you need is available here. It is a great way to learn the names and symbols of all of the elements or just to pass some time with other people who appreciate chemistry.

It's simple.

1) print out the randomly generated cards
2) click on the other link to play the game.

This game is only for entertainment purposes. Please no betting. I'm kidding, go ahead and wager you paycheck away.

You may notice there is no "free space" in the middle of the card. That's because (with the same tone Tom Hanks uses when he says 'there's no crying in baseball' in A League of Their Own) there's no free space in LMNTO!!!!

Enjoy

Reading the literature

We are on Spring Break and since I won't be heading anywhere warm, I have decided to catch up on a few things.

For me (and many of my faculty colleagues) breaks are not about sitting at home watching the Price is Right and eating cheese puff[1]. It is about trying to catch up. An academic season is always frantic and busy and by this point, things have been sitting on the back burner[2] too long.

One of the things I try to do is read some literature. I am terrible at reading the chemical literature. It's not that I'm not interested. There are two significant limitations.

1) lack of access. The only journals I have access to are JOC and Org Let[3]. Our library is terrible in this regard. Oh, I've complained, but it is just too expensive. My only access comes from personal subscriptions. I'd love to have JACS, Angewandte Chemie, Chem. Comm, etc even Tet Let, but sadly, that is not possible.

2) lack of time. I will admit I am a bit unmotivated at times, but all of my time is consumed with my teaching and administrative duties. How does this schedule sound. I start teaching at 10:30AM and teach three classes in a row. I'm done teaching at 1:20. Then on 4 days of the week I have a lab at 1:30 until 4:20PM. That means I am in a classroom or lab with students from 10:30AM to 4:20 nearly every day. Add to that all of the prep time etc.... OK, I got a little carried away there. I didn't mean for this to be a rant....

So, I am spending some my break reading journal articles. Which brings me to the point of this post[4]: I cannot for the life of me, read journals on a computer. Unless I'm just scanning it in an attempt to get a summary idea, I must print the thing out and have it in my hands. Especially with synthesis papers. I have tried. I would prefer to save a few trees. But, I can't do it.

Having online access is great. It is also a lot cheaper, but I still print everything out that I want to read.

For those of you in the sciences, do you read journal articles on your computer?

UPDATE: Just my luck. When I do have time to read journals, the ACS site is down for maintenance:(

[1] both are actually things I don't like anyways.
[2] bunsen, of course.
[3] Journal of Organic Chemistry and Organic Letters
[4] it's about time, jerk!!!

Brewing is Biochemistry

Today in my Biochemistry class I got on a tangent[1]. We were talking about polysaccharides, such as starch. I got tangented[2] into brewing.

Briefly: in brewing, starch is broken down into fermentable sugars. This is a beautiful biochemical process. The alpha and beta amylase working so well together brings tears to my eyes[3].

But...should this (the science of alcohol production) be taught in a biochemistry course.....

Yes, I think it can (or should) be. I am not endorsing the use or abuse of alcohol, but I am admiring the biochemistry that has been utilized for thousands of years.

There is some cool stuff going on, I hope to continue to write about it in this blog. But, as usual, the more one learns about something, the more one realizes how little he (or she) knows about that something. I know a lot about brewing, but I realize I know so little. That is why we have experts.

[1] I easily get on tangents. Usually they are related to chemistry, but not always.
[2] It may not be a word, but I love verbing nouns!!!!!
[3] so much more could be said about this. I hope to do so in the future[4].
[4] near or distant[5]
[5] stop using endnotes in the endnotes, dumbass[6]!!!!
[6] sorry[7]
[7] it's just that psi star psi doesn't stop by as often since she got that super-cool job in that analytical lab[8]
[8] I miss her brief and insightful replies[9].
[9] Oh well, mjenks is always good for some quality replies[10].
[10] and at least he can use proper grammar real good and stuff to make for good writing...and stuff.

A research project worth doing

I wonder of NSF would provide a grant to study this.

...starting at center...E.J. Corey....

Yesterday I got an email from the folks at Wiley Scientific. They wanted me to know that the current issue of Journal of Pharmaceutical Sciences was available free of charge. The complimentary online access is in honor of Professor William Higuchi. I first thought to myself, "who the hell is William Higuchi." After further thought I realized, if a publication such as this is going to make such a fuss over someone, that someone is probably very important in that field. Perhaps I am a bit naive when it comes to the big players in the world of pharmaceutics. Well, to be honest, I should drop the "perhaps" in that last sentence.

I found myself in the same situation I find my students in. Most of my students (at least early on) have never heard of E.J. Corey, Woodward, Sharpless, Trost, Grubbs, etc... I had never heard of Higuchi but upon reading the article in the JPS and on his website, I realized he is quite the deal in pharmaceutics.

I'm much more familiar with organic chemists. A few years ago, as a way of putting the players in this field in perspective for my students, I started using sports analogies. This worked for 80% of my students. The other 20% were annoyed that once again I had boiled something down to sports [1].

I'll stick with the NBA since most of the players are fairly recognizable.
E.J. Corey is the Larry Bird of Chemistry
Grubbs is the Kobe Bryant of Chemistry
Sharpless is the Magic Johnson of Chemistry
Hoffmann is the Scottie Pippen of Chemistry
Nicolaou is the Karl Malone of Chemistry
etc......

These are fairly big names and they correspond to big names in the NBA. Frankly, the names get swapped around all of the time, but the point is made that if Chemistry was a spectator sport, we would know all of these names.

So, who are your superstar chemists and what sports figure are they analogous to? Who is the Michael Jordan of Chemistry? Better yet, who is the Luke Walton, Stephan Marbury, Vlade Divacs etc... of Chemistry?


[1] For me, most of my analogies involve sports or kindergarteners, but the kindergartener thing is another post.

OMG!!!! Beware the evil water

The video is about 10 minutes long and ends abruptly, but anyone with a basic understanding of chemistry (or anything, really) will be amused by this crap-filled video selling something to the ignorant.

My favorites: white copper sulfate and "only plants use inorganic minerals." There are many more.

There are a lot of blogs that address this type of thing (see Respectful Insolence for one high quality example). It is essentially, scam artists sucking money from the scientifically ignorant. I don't want to be that type of blog, but I couldn't pass this one up.

Fire!!!!!

Remember the good ol' days of Beavis and Butthead? They were, for good or bad (mostly bad), a cultural icon, albeit a short-lived one. The creators and MTV got into a lot of trouble for B&B's affinity for "fire" [I'm not sure how to type "fire" the way Bevis said it]. I remember people were up in arms because B&B were seemingly inspiring arson and the like.

Nonetheless, I couldn't help but think of them lately and their love for "fire."

Our Math and Science division is having a fall picnic this week, complete with bonfire.

I.... I, your humble crappy blog writer, have been asked to start the bonfire [OK, that's not really true, I simply usurped the privilege from my science colleagues].

I am going to ignite the fire using nothing other than chemistry!!! Now sure, lighting a match IS chemistry, but it is too traditional. I want to light the fire in a way that is dazzling.

At this moment, I am going to use my old standby reaction, thermite. I can do that with no problem. The beauty of it is that the fire would be started totally by the movement of electrons from one element to another. No covalent bonds would be broken [at least in the starting of the fire]. What a wonderful way of transferring energy to the wood and thus igniting it.

However, I'm open to suggestions.

And they're off....

Well, the semester is underway. All systems are go.

Today I taught my Chemistry of Art course, Organic Chemistry, and Instrumental Analysis. Plus, I did an organic lab today as well. It turned out to be a long day (I also mowed my lawn).

A few weeks ago, I was really nervous about the Instrumental Analysis course. Now, I'm starting to get really excited about it. I'm team teaching it with a colleague. I am going to focus on instrumental chromatography (GC and LC) and structural elucidation (NMR, IR, MS and UV-Vis). My colleague is going to cover what amounts to instruments used for advanced analytical analysis. In the end, I hope our students will have a general understanding of how instruments are used and what they can (and cannot) tell us.

I'm not going to get into the electronics of instruments. We will talk about signal-to-noise, but not about A/D converters and rectifiers or Zener-stabilized voltage regulators. I'd rather talk about J-couplings, COSY and McLafferty rearrangements.

Our first experiment will probably be the analysis of isooctane in gasoline using GC-FID. I'm going to have them change columns and everything. It should be fun.

Keeping beer cold.... A science project

There are a lot of ways to keep beer cold. But, what is the best?

Check this out to find out. I'm most impressed that they used PBR. It won a blue ribbon once!!!!

It turns out, a beer cozy made out of Rice Krispie bar is the best.

Don't ever tell me the internet isn't full of useful stuff.

Beer is bad? NEVER!!!! OK, maybe

A lot of chemistry blogs (many of them are very good) include updates from the literature. These are papers that are important in certain fields or just interest the blog author.

Recently, one of the (eh-um) "journals" I read had an interesting article about a dangerous chemical in beer. OK, the "journal" is Brew Your Own magazine, but it was still a well written and interesting article.

I'm a big fan of BYO magazine and BYO.com. It is a great publication for those of us interested in learning everything we can about our favorite hobby.

The article was part of the "Help Me, Mr. Wizard" feature. The articles in BYO magazine are great, but the "Ask Mr. Wizard" feature is my favorite. Mr. Wizard, Ashton Lewis, knows what he is talking about, but (and this is most important) he also researches what he says.

In the latest issue (which I have read completely and will proceed to read again), Mr. Wizard was asked about the dangers of tyramine in beer and the differences between draft beer and bottled beer.

For the most part, Wizard Lewis doesn't shy away from technical terms, but there is nary a chemical structure to be seen. That's OK. That's where this blog comes in.

Tyramine is formed when the amino acid tyrosine is decarboxylated by some bacterial enzymes, namely lactic acid bacteria.



Tyramine is not a problem for most people since monoamine oxidase enzymes catalyze the metabolism of tyramine. However, people taking monoamine oxidase inhibitors (MAOI) have difficulty dealing with tyramine.

The result is high blood pressure and possibly a stroke.

The Mr. Wizard response goes on to explain that tap beer has a higher chance of containing dangerous amounts of tyramine. Commercial bottled beer has a nearly zero risk thanks to pasteurization. Kegged beer and homebrew beer are not pasteurized and run the risk of harboring the offending bacteria.

Tyramine is also found in other foods.

The bottom line is avoid tap beers and homebrew if you are on MAO inhibitors.

Time. A precious commodity

Have you ever noticed how many times bloggers start a post with something like: "sorry for the lack of posts lately. I've been busy." Isn't that annoying? Well, here's another one.

Sorry for the lack of posts lately. I've been busy.

Seriously, I've been busy. I've been teaching summer school, installing ceramic tile in our shower, preparing for an institutional self-study and preparing for the summer science camp I am hosting next week.

The latter is the most interesting.

Two years ago, I decided to organize and host a summer science camp for Junior high aged kids. With the help of some colleagues, I put together a week of science fun for 7 students. Last year the number jumped to 9. Things went well last year. Word of mouth started. This year we maxed out at 30 with a number on the waiting list.

We start Monday. I look forward to the fun. I have the help of a very competent biology professor to focus on biology and I will focus on the chemistry. A few others will contribute to touch on math, physics and engineering.

This year in the chemistry portion I am going to have them synthesize paint pigments, synthesize aspirin, and do a forensic DNA analysis to solve a crime.

One of the pigments I will have them make is Prussian Blue. It is made from iron (III) chloride and potassium ferrocyanide.


(sorry for the small figure. I don't have time to figure out why it won't get bigger. )
After they make the pigment, we will mix it with some acrylic base and paint with it.

Mixed in with all of the serious stuff there must be some explosions. I have a number of demos planned. These include: hydrogen balloons, methanol cannon (mixed with a little boric acid for a green flame), gummi bears and potassium chlorate, and thermite.

I mentioned thermite a while ago. Well, it's time to go big or go home. I am going to do the largest thermite reaction I have ever done. Fear not, all safety precautions will be duly observed. I will also try to video tape it and upload the video.

It should be a fun week, but I have a lot to prepare.

PEG and me

Poly(ethylene glycol) is an interesting molecule. It is a polymer of ethylene glycol made by the polymerization of ethylene oxide.

Ethylene glycol is a dialcohol:



It is used in antifreeze and it toxic.

Recently it was discovered that a number of toothpastes made in China contained high amounts of diethylene glycol. mmmmmm minty deathpaste. DEG looks like:



When ethylene glycol is polymerized with itself it is know as poly(ethylene glycol) or PEG for short. PEG takes on a lot of different properties. The properties vary based on how big the molecule is. Ψ*Ψ at Carbon-based Curiosities recently posted about poly(ethylene glycol) (PEG) and it use in a hot bath.

I have been exposed to PEG in a number of interesting ways. In every instance it have been useful. I will relate three occurrences.

#1
My Ph.D. work in grad school dealt with the use of carbohydrate-functionalized dendrimers to study protein-carbohydrate interactions. A dendrimer is essentially a spherical polymer. I made dedrimers of different sizes with varying numbers of carbohydrates on the surface to see how they interacted with proteins. The goal was to understand more about how these important signaling processes occur.

OK, long story short time. No need to cover everything and bore you, the kind reader.

My first attempt used a phenyl ring as a linker between the dendrimer and mannose. It look like this:



This molecule shown had a molecular weight of about 28,000, and it had the solubility of brick dust. I needed a functionalized dendrimer that dissolved in water. This one did not. The solution turned out to be PEG. I replaced the phenyl group with a PEG group and voila, it was soluble in water. The structure looked a bit like this:



Granted, it's not really a *poly*ethylene glycol, but it is part of a larger molecule.

#2

Since I had laser eye surgery I have needed to use eye drops to keep my peepers moist. One of my favorite brands is Systane. The active ingredient is polyethylene glycol 400. The 400 means there PEG has an average molecular weight of 400 daltons, which translates to a molecule that contains 9 ethylene glycol molecules.

#3

A while ago my daughter was constipated. The doctor prescribed GlycoLax. GlycoLax is polyethylene glycol 3350. It's average molecular weight is 3350, which means it is made up of about 76 ethylene glycol molecules.


In all of these, the function is the same: hold on to water. This is done through hydrogen bonds between the water and the oxygens on the ethylene glycol molecules. It seems to work quite well.

I'm not dead yet!!!

Just to prove I have not dropped off of the face of the earth, here is a little post. During the weekend I destroyed a significant number of increasingly valuable hydrocarbons while I drove the family to the southern-most Dakota. I've been a bit detained by that incident.

Ψ*Ψ at CBC[1] recently[2] posted about poly(ethylene glycol) (PEG). This reminded me of the many ways I have use PEG in my life. From my Ph.D. research to eye-drops to laxatives and more. My next post[3] will detail all of the wonderful things PEG has done for me.

Until then, enjoy this:



"Dog's nuts!"

[1] That's Carbon-Based Curiosities for those of you just crawling out from under a rock
[2] OK, 'recently' is relative. It's been a while, but I've been busy.
[3] maybe

Beer and Celiacs

Yesterday, my family and I took part in the 6th Annual International Walk for Celiac Disease. My niece has Celiac disease and this walk is a great way to support her and help raise funds to support research of the disease. Most of the funds raised go to the University of Maryland Center for Celiac Research.

Very briefly, Celiac disease is autoimmune disorder that is caused by the ingestion of gluten. Gluten is made up of a number of proteins, but the main player seems to be gliadin. The main source of gluten is from wheat, but there are similar proteins found in rye and barley (more on this later).

There is no cure for the disease, but it can be treated with a gluten-free diet. That's the good news. The bad news is that it takes a lot of effort to avoid gluten. Anything made from wheat is out, and a lot of things are made from wheat. While it is tough, with a bit of education and training, people with Celiac disease can live completely normal lives.

The annual Celiac walk is quite the event. Over 1000 people show up, many of whom have Celiacs, but I would bet most do not but are there to support family members who have it. At the Minneapolis event, Rich Gannon (2002 NFL MVP) is Honorary Host. There are tons of food vendors giving away free samples of gluten-free foods. There are door prizes, raffles and then of course, the 5K walk. It is a lot of fun.

So, what does this have to do with beer? Well, beer is made from barley. For a person with Celiacs, that means barley beer is off the menu. Even a small amount of gluten can cause significant issues. The good news is that there is an alternative to beer made from barley. The alternative is sorghum.

Gluten-free beer can be made from sorghum. Beer made from sorghum is common in Africa where sorghum is a common crop, but until recently, beer made from sorghum has been rare. In addition, gluten-free beer made exclusively from sorghum has been very rare.

At the Celiacs walk yesterday, a vendor was supplying samples of Redbridge beer. Redbridge is made by Anheuser-Busch. I tried a few samples. My first impression was that it was not too bad. It had a decent flavor, but it lacked a malty body (it is from AB after all). It was also lacking in hoppiness, but that is normal for the macrobrews. I'm going to see if I can find some in my area. I need more that 2 ounces to get a good feel for it.

Homebrewing gluten-free beer is challenging, but entirely possible. It carries with it some unique challenges, but so did "normal" homebrewing back in the early days. I don't brew gluten-free beer, so I have no insights to give (sorry to anyone who googled "gluten-free beer" and got this blog).