The Science Thread

[winterfate]

Hello!

Over at the Hell is Real thread, a secondary debate started about creationism/evolution. There, I asked Corribus if he could indulge me on the principles of organic chemistry. He said to make a thread...so here it is.

@Corribus: You're up!

[jeff]

This can be a very lively topic, but it can also be a very emotional one as well. I urge caution on all parties, otherwise one of the 800 pound Gorillas will close the topic. I'll participate unless it gets nasty.

[asandir]

I was gonna ask how a science discussion could get nasty, then remembered the thread this came from ....

[jeff]

It's not the science part I was worried about, it's the creationist part. Some people get real touchy on that one.

[Corribus]

Alright, I'm game. What do you want to know exactly? Summarizing organic chemistry is a little too... broad.

Edit: this doesn't have to be a contentious thread, if we avoid science policy and philosophy. Certainly if someone wants to go there, I'm game for that, too, but we've got that going on elsewhere.

[winterfate]

@Corribus: Hmm...I don't know...how would the course in college start per se...what would be the first things the professor might touch upon?

[Corribus]

Well..

Organic chemistry is sort of a strange bird, curriculem-wise.

I'm not sure how it is in other countries, but here in the states it is typically taught the year after so called "general chemistry", so usually in sophomore (2nd) year of college. In general chemistry students are exposed to basic chemical principles, such as: conversions, stoichiometry, acid-base problems (titrations), equilibria, some lab techniques, as well as introductory level electrochemistry, quantum chemistry, bonding theories, thermodynamics, reaction dynamics, and some general information about the elements. So, it's sort of a survey of just about everything you will be spending a lot more time on if you decide to study chemistry as a discipline.

The way most curricula are set up is, as I said, to then take organic chemistry. Organic chemistry is, for lack of better words, the study of how organic (a rather loose word but generally any compound that contains carbon is organic) molecules can be made from other organic molecules. It is an important synthetic discipline but one that is really almost totally empirical. Generally you learn which molecules react to make which other molecules, but you don't really learn why anything works except in the most generally cartoonish sort of way. Organic lecture thus boils down basically into rote memorization. Literally hundreds of reactions are thrown at you and you are expected to know them all, and all the many intermediate steps along the way. There *are* some basic principles, but they really aren't that well defined.

After organic chemistry, if a student decides to go on, they usually take physical chemistry, the dreaded p-chem. I used to tell my p-chem undergrads (when I taught quantum mechanics) on the first day of class that p-chem was the study of why everything they had learned up until that point was wrong. They used to love that. But seriously, p-chem is essentially the study of the basic physics of molecules. (Chemistry itself as a discipline really boils down to the physics of electrons.) So in organic chemistry you are essentially learning the "effects" and in physical chemistry you learn the "cause". If you want a molecular biological analogy - organic chemistry is the phenotype and physical chemistry is the genotype.

Physical chemistry is usually broken up into three sections, quantum mechanics, statistical mechanics and spectroscopy. In days gone by, statistical mechanics (thermodynamics and chemical dynamics) was taught first and then QM/spectroscopy but these days things are moving towards the reverse, a true bottom-up approach. You start with QM which is really the foundation of modern chemistry, dealing with the structure of atoms, molecules and molecular bonding, and then move to stat mech, which discusses the physics of large groups of molecules ("ensembles") and thermodynamics --> moving towards gross chemical reactions. Spectroscopy (my discipline) deals with the interaction of molecules with light and draws on principles in both QM and stat mech.

Frankly, I think that o-chem and p-chem are taught in a nonsensical order. I feel it would be better to study WHY molecules react before looking at the outcomes of those reactions. But this backwards order persists to this day mostly because (A) historically, organic chemistry arose long before modern physical chemistry, (B) physical chemistry is much, much harder, particularly QM, and (C) o-chem is required for medical school. Don't ask me why.

There's also the branch of inorganic chemistry (technically this is what my doctorate is in) which up until about 15 years ago was sort of a dying discipline, until nanotechology exploded onto the scene. Sadly, many undergrad institutions haven't caught up yet with these events and inorganic chemistry curricula are severely lacking.

Well, there's a summary for you of undergrad chemistry curricula. I hope that didn't bore you too much. Personally I think o-chem was boring as hell, but it could be much more interesting if taught from a molecular standpoint. But, most organic chemists would not be equipped to do so.

[The Mad Dragon]

And some how, I understood all that.

I loved Chemistry back in high school. I had an awesome teacher and everything made sense.

But yea, that does seem weird that O-chem is taught first and P-chem comes after. You would think that they would switch it around in today's age.

[Corribus]

You'd be surprised at how hard it is to change a curriculem, especially ones as couched in tradition as natural sciences and involving many classes. Even within the discipling of physical chemistry alone, is has taken forever to get people to teach QM before thermo. Sad to say, until a lot of the older generation retires, more modern approaches will never become standard practice.

[The Mad Dragon]

Yea, I can understand that they would be hard to change with the older generations still around. Once your stuck in your ways, it's hard to change them. But, I think that eventually it will change.

[Caradoc]

To be fully appreciated, organic chemistry also need to placed into a context of biological systems -- eg. Citric Acid cycle or photosynthesis.

[jeff]

To be fully appreciated, organic chemistry also need to placed into a context of biological systems -- eg. Citric Acid cycle or photosynthesis.

Ah yes the Krebs and Calvin cycles, my students do not enjoy those.

[The Mad Dragon]

I didn't enjoy biology when I took it. I found it quite boring.

[Corribus]

To be fully appreciated, organic chemistry also need to placed into a context of biological systems -- eg. Citric Acid cycle or photosynthesis.

The funny thing is that a large percentage of the reactions learned in organic chemistry are not even used anymore, either because they are obselete or because they are just extremely dangerous. It's been a while since I took undergraduate o-chem, so maybe this has changed, but many modern techniques which are much safer and more efficient, such as those that use metal catalysts, are not even touched upon. And you're right, Caradoc, organic chemistry would be much more useful, particularly to premedical students, if it focused on biological reaction pathways, such as those in metabolism or the Krebs (Citric Acid) Cycle. (Photosynthesis is more of a physical chemistry topic.) But for some reason this is not usually done, and o-chem lasts a whole year!

The problem, and this is a general one, is that often times professors will teach the same class for 20-30 years, and do not like to change their syllabi, so while science changes, the material doesn't. Schools which rotate their teaching assignments do a much better job of staying modern.

[jeff]

I didn't enjoy biology when I took it. I found it quite boring.

Actually I did not enjoy bio either too broad a subject, but when I got to college studying Zoology, especially marine invertebrates became my main focus. Alas we don’t teach Zoology in high school.

[The Mad Dragon]

Heh yea. I wouldn't mind learning Chemistry again and maybe majoring in that...

[winterfate]

@Corribus: Cool! So that means o-chem is basically not fun.



So...for a logical order, I need to learn about p-chem first.

So, why do molecules react then?

Ah yes the Krebs and Calvin cycles, my students do not enjoy those.

Krebs...

We touched upon that cycle...ask me if I can remember (I can't ).
Cram sessions...

I didn't enjoy biology when I took it. I found it quite boring.

It's pretty fun, IMO...but then again my professors were a blast.

[The Mad Dragon]

Mine wasn't. She made it boring.

[Gaidal Cain]

Mod note: As this isn't the random thoughts thread, all the random stuff was done away with. There is nothing wrong with letting a thread lie unreplied to (well, unless it's someone who has a heroes question).
[size=0]And if you're thinking about replaying with some lame witticism to this, think again.[/size]

[Gaidal Cain]

To be fully appreciated, organic chemistry also need to placed into a context of biological systems -- eg. Citric Acid cycle or photosynthesis.

I'm eternally thankful to the Citric Acid cycle for making me sure that it was a good idea not to study chemistry, and to the Physical Chemics course I took last year for reminding me about it. I can't understand how someone can take something as cool as quantum physics and turn it into something so boring.

And if you don't find quantum physics cool, that's probably because they're focusing on all the electron-around-atoms part, which while important, isn't very interesting, as, say, tunneling.