Here's a problem for you

When I took over this teaching gig, my predecessor left a fold behind labeled "Diabolical Organic Problems." I love the word "Diabolical" but some may argue that that title is redundant with "Organic."

I have on occasion given my students diabolical problems to hone their skills. Today in preparation for the cumulative final exam, I gave my General Chemistry class the following question:

A 21.0 cm³ piece of dry ice is placed into a sealed 5.0 L container at STP. The dry ice is allowed to sublime while the temperature is held constant at 0°C. The container also contains 12.7 grams of sodium hydroxide. Sodium hydroxide reacts with carbon dioxide to form solid sodium carbonate and liquid water. What will the volume of the dry ice be when the pressure in the container is 2.5 atm? The density of dry ice is 1.5 g/cm³. Assume the volume of the container is 5.0L.

I'm kind of proud of this question as it incorporates several concepts we covered in the first half of the semester. I'll give anyone who answers this 50 extra credit points.

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.

Annoying frustration

As a teacher, I occasionally experience situations that make me wonder if I am the worst teacher ever. There are times when, despite what seem to be my best effort, the point I am trying to make never sinks in. Sometimes after a bit of contemplation, I can figure out what went wrong and do something to correct the situation. But, occasionally there seems to be no solution. It is even more frustrating when the topic is fairly simple.

I recently had one of these frustrating episodes. In my Organic Chemistry class we have been covering substitution and elimination.

***disclaimer: To any non-chemists out there, much of this may not make sense. I'm not going to try to explain what I'm talking about, because based on the response of my students, I'd fail miserably.***

I put the following reactions on the board:

Many of you will recognize this as a classic question posed to organic chemistry students since Alexander first described his ether synthesis. One route will work quite nicely as written, but the other route is fraught with failure. Do you know which is which? If you've read this far, I'm sure you do.

Route A will work. Route B, however, will fail to make the desired product because elimination (to form 2-methylpropene) will predominate.

I put both reactions on the board and asked my students which one will work and which one won't.

Dead silence.

I rephrase the questions to something like, "one of these is a valid strategy and one is not. Which one will work and which one will fail to make the ether?"

More dead silence.

I start asking leading questions, but nothing is clicking. I finally get annoyed and ask, "how many carbons do you need to form a double bond?"

A student timidly answers, "2?" I say, "exactly. Which reaction will undergo successful substitution?"

Nothing.

It went on like this for about 15 minutes. I could not get them to realize that in route A, elimination is impossible. Or, if they did, they could not explain it to me.

This has really annoyed me, because if the entire class fails to figure something out, the most likely culprit is me. Besides, the example I describe above is NOT a difficult concept. I spent about half of a class period describing the difference between the two.

I'll find our tomorrow if it worked. This is the first question on tomorrow's exam.

UPDATE: Only 20% of my students got the answer correct. The others chose B. This is preposterageous!!! They will learn.

Learning things...twice.

Have you ever learned something twice?

Have you ever learned something, forgot it, and learn about it later only to realize you already knew that?

Sometimes, it can be kind of embarrassing. Especially if you tell something you are convinced is true only to find out you knew better. That happened to me today.

At The Curious Wavefunction, Ashutosh posted about an article in the New York Times about radio signals and early stars. He identified a rather curious statement in the article:

Dust grows over time as stars manufacture heavy elements called metals, like carbon, silicon and oxygen, that make up dust and then spit them out into space.

I checked out the article and found the offending sentence and it offended my delicate chemistry teacher sensibilities. Carbon, silicon and oxygen are most decidedly NOT metals, nor are they "heavy elements."

I decided I had finally found my purpose on this planet and decided to send the author an email and personally advance his education. This is what I sent him:

Mr. Overbye,
In a recent article you wrote: "Dust grows over time as stars manufacture heavy elements called metals, like carbon, silicon and oxygen, that make up dust and then spit them out into space." Carbon, silicon and oxygen are most certainly NOT metals nor are they heavy elements.
Best wishes,
Eric Woller, Ph.D.

I added the Ph.D. part to make sure he knew I wasn't messing around. I felt good. I had taught some big shot NYT science correspondent some damn fine chemistry. He was nice enough to reply. This is what he sent me:

Astronomers refer to anything heavier than helium as metals.
Thanks for writing,
Dennis

That was when I slapped my forehead and realized...I knew that. I'm such an idiot.

While one can argue that labeling anything heavier than helium as a metal is silly, that's what astronomers and the like do. I knew that, but it didn't stop me from displaying some degree of ignorance.

So, I learned that little fact...again.

"BBA" is for...

Bad Bond Angle!

There are a few things I insist on in Organic Chemistry. One of the big ones is that I expect students to draw realistic bond angles. I am always reminded that this must be very hard for students to do. Even my best students draw impossible bond angles.

Things look like this:

These present teachable moments. I don't bring the sledgehammer down. Just a calm and stern correction. What they have drawn is wrong, and they can learn from their mistakes with proper guidance.

Eventually, when they should know better, I take points away. I once had a student ask me why I took points away. I told her it was because her answer was wrong. She didn't like that. Apparently she felt her ability to put something onto paper was worthy of credit. I had to convince her otherwise.

The year begins

So, Milkshake asked me to tell a little about the start of the school year here at my institution.

That is a great idea. Here it is:

OK, it's not supposed to be this stressful, and it usually isn't. However, the summer for me has been loaded with (as I have alluded to before) the Great Crap related to an impending accreditation review for my school. That's a bit of a big deal if you are in the business of higher education. And, it's an even bigger deal for me because I'm in charge (partially) of getting everything ready. I am really ready for summer vacation fall break winter break.


OK, I'm feeling better. This is very therepeutic tharepeutic theraputic therepuetic STUPID F-ING SPELL CHECK!!! JUST TELL HOW THE F*CK TO SPELL THERAPEUTIC BEFORE I BREAK YOUR FREAKIN SILICON!!!!!

OK, sorry, I'm better now. really. honestly.
So, how does the school year start at my school?

Students move into dorms on Saturday (yesterday).
Girls spend that night figuring out which tank tops to wear during the week.
Boys spend the night trying convince dorm mates that they where the shit in high school.
Matriculation service on Sunday afternoon followed by a campus picnic.
Girls wearing tank tops meet boys who think they were the shit in high school.
Monday is orientation day. All first years report for two hours of blah, blah, blah very useful information.
After that I meet my new advisees, all of whom are probably delusional pre-meds. Oh well, a bit of Organic Chemistry should take care of that.
The rest of the day is spent by me prepping for classes.
On Tuesday, classes officially begin. Lives start to change, for better or for worse.

OK, through most of this post I have been a bit cynical, but that last sentence is true. I've been heavily involved with non-teaching activities related to academic policy during the summer. Right now, I just want to teach. I realize accreditation is important, but (here comes the cynicism again) so much of it comes down to budget. Yes, a school needs to financially stay afloat, but we get paid crap to do what we love to do and what we love to do is why the school is here. This is a place of learning and not just teaching. It's not just about the bottom line.

I am very excited to see my returning students and to meet the new ones. I can't wait to help them learn new things. I can't wait to help them see how cool the molecular level is. I can't wait to torture them with Organic nomenclature teach them about carbon.

I love teaching and I love my job. There are still sooooooooo many non-teaching things that must be done that detract from the teaching, but I still love to go to work.

Thanks Dr. Phil. I feel much better.

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!

We've all been there

I have a student who has been working on a "research" project for me. The project is to extract a protein called concanavalin A from Jack beans. I use quotes because this isn't a novel area of research by a long shot. My goals for this project were to #1 develop a method of extraction that I could use in my Principles of Biochemistry course and #2 teach my student a variety of laboratory methods.

Concanavalin A (con A) is a lectin from the Jack Bean. A lectin is a protein that binds carbohydrates. In the case of con A, it binds with glucose and mannose but not galactose (or other carbohydrates). It does not have enzymatic activity, and its role in the plant is not clear (as is the case for most lectins).

My student has been working on this project all semester. Briefly, the Jack beans are soaked in pH 4-5 buffer and then blended in a blender. The supernate is removed after centrifugation. It is saturated with ammonium sulfate. The precipitate is collected and dialyzed against 1M NaCl. The protein solution is passed through a sephadex column and the Con A binds with the sephadex. It is displaced by glucose. The solvent used in the sephadex column is 1M NaCl (that's important to remember for this story).

Through trial and error and up the steep learning curve that is undergraduate research, my student eventually got enough sample to the sephadex column part. She loaded the sample onto the column . However, instead of running 1 M NaCl through the column, she used 1 M HCl instead. ugh! There is a big difference between a pH of 7 and a pH of 0. It wasn't good for the protein which, for the most part, appeared to cease to exist intact.

I should point out that she is NOT a bad student or a lab disaster waiting to happen. She is a very good student and one who absolutely knows the difference between NaCl and HCl. But these things happen. Unfortunately for her, that meant the end of her project.

We've all been there. If you've spent anytime in a lab, you've probably made a stupid mistake. I'm not talking about the frustration of dealing with things that don't work. I'm talking about the things that you ruined by a stupid mistake. It happens. The goal is to never repeat it.

Chicago

I spent this last weekend in Chicago at an accreditation conference. My school is up for accreditation review during the next year. I somehow accepted the request to co-chair our self-study review. I have not regretted the decision to accept the responsibility, but I sure would love to have this time for other things.

The conference was very informative. I learned a lot of things I needed to know. I'm glad I went.

However, I sadly was unable to enjoy Chicago. I went with 3 colleagues. We spent all of our time going to conference sessions or working on our self-study (usually over a drink in the hotel bar). We had no time to explore Chi-town. This really sucked because one of my colleagues lived in Chicago for 5 years and knows everything. He would have been a great guide.

That is my only regret. I wanted to essentially explore Chicago, but never got to.

I'm smart

OK, maybe I shouldn't claim to be smart, but I do know I'm not dumb.

As a way of assessing how well I have been teaching and how well my students have been learning in Organic Chemistry, I am going to administer the ACS Standardized Exam for Organic Chemistry. This way, I can measure my students to their peers around the country.

What I want to know is whether my teaching is effective or not. Are my students learning?

I received the exams a week ago and as they sat on my desk I became more and more curious. I wondered what I would score if I took the exam.

Well, I took the exam. There are 70 questions and I didn't have a 2 hour block to devote to it. So, I took the exam 15-20 questions at a time when I had some free time.

Of the 70, I got 69 correct. The one I got wrong was a result of me being stupid. I should have gotten it right. I can't and won't divulge what was on the exam or what I got wrong. That would violate something, I'm sure. But, the one I got wrong was me thinking a nucleophile was going to act as a base when it was just a nucleophile...I was stupid for screwing that up.

The good news is that I am in the top 100%ile for organic chemistry students. All I can say is that I better damn well be in that bracket or I have no business teaching organic chemistry.

Moron...I mean: more on textbooks

Ask any Organic Chemistry teacher and they are sure to have an opinion on textbooks. I would guess that 98% of those asked would say that there is no perfect text out there. The 2% would include those who have written texts or work with those who have.

We teachers are all different, but I suspect what we have in common is that we tend to teach the way we learned. This may not be true all of the time, but my anecdotal evidence[1] suggests it is true more often than not.

The text I used when I was learning Organic back way back in the olden days was written by Stanley Pine. This book can't even be found on Amazon.com.


My ideal (and evolving) approach to teaching Organic is this:
1) Review bonding, orbitals and hybridization.
2) Teach functional groups and nomenclature of almost EVERYTHING.
3) Teach physical properties of almost EVERYTHING.

The reason is that Organic is like going to a different country. If you can't speak the language, you can't communicate. So, basically the first two weeks are spent learning the language and basic "customs" of Organic Chemistry.

After learning the basic language, we can talk about mechanism. I emphasis the fact that everything in organic comes down to Coulombs law: opposites attract. If you can tell where the electrons are most likely to be, you can tell a lot about how the molecule will react.

Basically, I've adopted the philosophy of a grad school prof I once had. He said[2] "If you want to understand organic synthesis, you must fully understand physical organic chemistry first." I think he was right.

Now, to find the perfect text that presents the material how I want to teach it.....stay tuned....


[1] I regularly remind my students that "anecdotal evidence" is NOT evidence. It only suggests a trend that is worth investigating scientifically.
[2] I'm paraphrasing.

Not so unrealistic after all

I've been a bit under the weather lately. Nothing serious and nothing 4 mg of loperamide HCl couldn't fix. I wanted to blog about the cyclopentene post I made, but I haven't gotten around to it.[1] Now I'm feeling better.[2]

Enough about me. Let's talk about the dehydration of cyclohexanol. As it turns out, I probably should not have been too surprised at the results. From the comments and an email I got from my brother including an attached paper from Industrial and Engineering Chemistry Research[3] it is clear that the formation of methylcyclopentenes during the acid catalyzed dehydration of cyclohexanol is entirely reasonable.

In hindsight, I should not have been so surprised. Before divulging my ignorance to the world, I should have mulled it over. Oh well.

What I've learned is that having colleagues in Organic chemistry would be nice. I teach in a 2 person department. My colleagues is an Inorganic chemist. He is great at what he does, but we find it difficult to have discussions on advanced topics in organic or inorganic chemistry. Neither of us knows enough about the other's area to be any good.

I love teaching where I teach, but I miss the impromptu discussions that occur between chemists. My substitute for that is this blog. I may continue to post questions that could easily be resolved with a discussion with another organic chemist. My goal is to learn even at the risk of exposing my ignorance.

[1] I also wanted to bottle all of my beer, but I only got 2 of the 3 batches done.
[2] Sadly my 2-year old is not.
[3] I gotta be honest, I'm not a regular reader of what I'm sure is a fine journal.

On the basic nature of Organic Chemistry

During the first day of my Sophomore Organic Chemistry class (the second semester portion) I waxed philosophical. We were reviewing first semester stuff just to get everybody's brain (including mine) back into gear.

Occasionally, I like to put this class into some sort of context for my students. Organic Chemistry at this level can be bewildering. Organic Chemistry can be bewildering at ANY level, but I've noticed that at about two-thirds of the way through the first year, students start to get really weighed down by the subject.

This course is the typical 2nd year Organic Chemistry course. It covers all of the basics, from nomenclature to physical organic to reactions etc.... We cover a ton of material but only cover the tip of the tip of the iceberg.

I try to put this course into context using an analogy. Doing Organic Chemistry is like learning to write.

To learn to write, one must learn about all of the grammatical pieces and what purpose they serve (i.e. nouns, verbs, adjectives, prepositions etc...).

Students first learn what a noun is and how a verb makes it "do" something. The boy walked.

After mastering that, the student can add prepositional phrases. The boy walked into the store.

Eventually, through the employment of many different grammatical elements, the simple sentence can convey a great deal of information. The young boy slowly walked into the pet store and bought a dozen goldfish.

With the proper practice, this sentence can be combined with others to create a paragraph. Eventually, a number of paragraphs can be combined to form a story. The quality of the story can certainly vary, and writing a good story requires great skill.

This process is the same in organic chemistry. Right now, I am teaching my students how to use the nouns and verbs of organic chemistry. Eventually we will be able to use prepositional phrases. However, even though we cover a ton of material in this class, we will not get beyond that stage.

That is unfortunate (albeit, necessary). In my Advanced Organic Chemistry course we finally get to "read" a story: a total synthesis. Towards the end of that class, they learn to write their own paragraphs.

It is usually in grad school where they will get the chance to write a story (i.e. a total synthesis) on their own (or at least contribute significantly to one).

There is great beauty in organic chemistry. Sadly, it is hard to see during the early days of ones education. I never truly appreciated organic chemistry until Advanced Organic Chemistry during my senior year. There we read the "stories" and I was greatly impressed.

"Diastereomers"

During my first semester of grad school long ago, I took a Physical Organic class. It was a great class. The teacher was from Poland and spoke with a moderate accent, not thick enough to be indecipherable, but occasionally some words were totally different.

One day we were talking about diastereomers. Now, for the non-chemists out there, I'm not going to try to explain it. It would take more time that I want. For those of you who need refresher, Eliel defines diastereomers as: "Stereoisomers that are not related as mirror images. They usually differ in physical and chemical properties."

The correct (or at least most understood) pronunciation is: die'-ah-stair'-e-o-merz. OK, not the way Webster would have written it, but you get the point. Well, on day in class, my Polish prof pronounced it: dee-ah'-stur-oh'-murs (note the accent on the second syllable). Say it out loud. It sounds quite different than the "normal" way of saying it.

We were in class when this happened and it took a few minutes to figure out what he was saying. Yet, since we were familiar with diastereomers, we eventually figured it out.

However, this prof also taught Sophomore level Organic Chemistry. The students in that class had never heard of diastereomers before. As a result, the class of about 300 all learned to pronounce it as dee-ah'-stur-oh'-murs. It was hilarious to have a student come to the chemistry help center and ask for help on "dee-ah'-stur-oh'-murs" from the TA. I wonder how many of them still pronounce it wrong.

E.J. and Roald will have to wait

One of my goals of the ACS was to get an autograph from E.J. Corey and Roald Hoffmann. I got neither. I was stricken with guilt when the time of their appearances coincided with a couple of talks I really wanted and needed to go to. I gave in to my guilt and went to the talks.

The registration fee for the ACS convention is a rather steep $385. Throw in a hotel for 4 nights for at least $800, travel at about $200 (from MN) and food etc... The final total can end up close to $2000. Granted, my employer picks up the tab, but for my small school, $2000 is a significant amount of money. I could use that $2000 in a lot of different ways (like research).

The bottom line is that, I couldn't squander the (expensive) opportunity to learn and advance myself as a teacher, just to get a few autographs. The autographs would be really cool, but in the end, they are just ink on paper. I chose knowledge in my head over that.

Why I was able to become a chemist

Paul at one of the premiere chemistry blogs just wrote a post on why he became a chemist. This got me to thinking, "why did I become a chemist?" Well, that got me to thinking about not why I became a chemist, but why was I able to become a chemist.

Sure, having a brain helps. Having parents who encourage you to read instead of watch TV really helps[1]. Having parents who encourage you in general to study and learn really helps.

I always had a natural interest in science. I was amazed at how things worked, natural and man-made. By the third grade I was determined to become a neonatal surgeon. Obscure choice for an 8-year old? Yes, but true nonetheless. I would wear my pajamas backwards because they looked like scrubs. I never changed my mind until I was lured away in college by the mistress that is "Chemistry."

Yes, I was one of those pre-meds we in academia all really love to love[2]. I was slowly lured away by chemistry, but the final nail in that coffin was when I took Advanced Organic Chemistry during J-term. Brutal and hardcore, but I loved it.

But, how did I get to that point? Well, I was prepared very well. Here are a few of the most important individuals in my academic training that made it possible for me to become a chemist.

Mr. Willems in high school. I had him for Biology, Chemistry and Physics. He did a lot with a limited budget. He was very well organized and orderly. He didn't just teach us facts and trivia. So much of today's HS curriculum deals with learning about facts and trivia[3]. Mr. Willems taught us to think through problems using basic principles. This is a skill that has helped me greatly. Of course, there are some facts that must be memorized. One of the most valuable things he forced us to memorize in Chemistry was the names and formulas of the common polyatomic ions. This proved to be incredibly valuable later in my college career.

Mr. Bolda in high school. I had Mr. Bolda for most of my HS math. He was also my track coach. He was your prototypical nerd that many HS students tend not to embrace, but he was a very good teacher. One that, despite his mannerisms, any reasonable student would respect[4]. I did respect him. This was in the days before every HS in the world offered AP calculus. What Mr. Bolda did offer was a solid foundation in trigonometry and problem solving. I still use the problem solving skills he taught us in HS. I got to college with the skills need to breeze through most of a math minor.

Mrs. Kjeer in college. Staying with the math theme, I had Mrs. Kjeer for almost all of my college math (calculus I and II, differential equations, multivariable calc...). It was my very first day of college, 8AM class. We walked into our classroom and were met by this young and attractive calculus teacher who seemed to be hopped up on too much caffeine. This was NOT what we were expecting. When we got into the class, we learned quickly she knew what she was talking about and she wasn't hopped up on an alkaloid. She loved what she was doing. This coupled with uncompromising standards, an infectious excitement for calculus and the ability to back up what she said inspired us. I took as much math from her as I could. This helped me in ways I don't even realize.

Mrs. Weberg in college. Finally, I get to an actual chemistry professor. Mrs. Weberg inspired many students to become chemists, and provided the tools to do so. I had her for General and Organic. Mrs. Weberg was a great teacher. She knew what she was talking about and knew how to get students to learn. However, most importantly, she was like a mother to so many students. She was a very nurturing person and it wasn't always in the lovey dovey way. She was a mother after all, and she knew that every now and then, the best way to motivate a student is to kick them in the butt. She was stern when she had to be and compassionate when she had to be. We learned as much about life as we did about Chemistry. What she did was create a situation with clear standards and the motivation to reach those standards.

There are others to be sure, but these are four of the more important ones for me.

In retrospect, all of these individuals had some common traits. They loved what they did. They had high and uncompromising standards. They provided as much support as a student may need or request. They realized there is life outside of the classroom.

I try to model how I teach and interact with my students around what these individuals did. I usually fall far short of what they did, but I try.

They are why I was able to become a chemist.


[1] Don't get me wrong, I watched a lot of Transformers and He-Man back in the day...
[2] Some of the words in this sentence are inaccurate.
[3] Read your states expected education outcomes.
[4] Of course, not all HS students tend to be reasonable in this regard. Mr. Bolda eventually quite teaching. I do not know where he is now.