Aromatic compound names

We discuss a lot of very exotic-sounding compounds in class but one of the distinctions that had eluded me so far this quarter was the difference between something containing a phenyl group and something containing a benzyl group. At last, I returned to the old college organic chemistry textbook (McMurry 6th ed.) and there it was: phenyl is C6H5 (aromatic ring) while benzyl is C6H5CH2 (aromatic plus an alkylic (?) carbon). The naming of aromatic compound still remains, to me, one of the most idiosyncratic naming systems in organic chemistry--it seems like the root word "benzene" almost never appears--and yet there must be a good reason behind words like "styrene" and "toluene". Take phenol/phenyl for instance. McMurry writes:

The word is derived from the Greek pheno ("I bear light") commemorating the fact that benzene was discovered by Michael Faraday in 1825 from the oily residue left by the illuminating gas used in London street lamps. (500-501)

Rather poetic, isn't it? Unfortunately McMurry digresses at this point to discuss the ortho/meta/para system, but it would have been interesting to read a little more behind the unique linguistic history of naming aromatic compounds. Does anyone know about any of the others (for starters: toluene, styrene, aniline, cumene, xylene...)? Are there any other chemical naming systems that rouse people's linguistic interest?

Gene Goldwasser's account of the discovery of EPO

The pdf file of the article by Gene Goldwasser can be found here (click on 'EPO').  It is a great account of a major scientific discovery.

Thanks to Andrew Weber for this file.

Why do DNA gel shift assays work?

We discussed this a few classes ago, but did not resolve or pursue the topic.  

It is an example of something we think we understand, often a common phenomenon that we take for granted, but is not as it appears to be. There are many such: why does water (e.g. in the ocean, or a lake) appear to be blue?; why do gel shift assays work?  

For the latter (gel shift assays), I remain unconvinced by the explanation in the Wikipedia link - the linear DNA, which is huge, can move through the cross-linked gel, so a globular protein molecule (much smaller) should be able to diffuse away.

Any ideas?

Sedimentation equilibrium analytical centrifugation

measures protein mass. You can find out more here. 

Sam Goudsmit and Me

Samuel Goudsmit (1902-1978) was a Dutch-American physicist famous for jointly proposing, with George Uhlenbeck, the concept of 'electron spin'.  You can see the Wikipedia entry on Goudsmit here. 'Spin' is one of the most fundamental properties of subatomic particles; really, really fundamental: you know, the 'Pauli exclusion principle' and that stuff. 

What does Sam Goudsmit have to do with me? 

Well, in 1978 I was promoted to Assistant Professor at the Rockefeller University in New York  (the University of Chicago's sister institution, though neither acknowledges the connection) . At the first faculty social  function that I attended, being new I arrived at the stated time of 5pm, to be confronted by a very large room empty save for one other, older person. Since we were the only two people, we introduced ourselves, and Sam Goudsmit, for it was he, said he was on the adjunct faculty at the Rockefeller (at that point I had no clue who Sam Goudsmit was). He enquired where my accent had originated (New Zealand), and then said "I once nearly visited New Zealand", which seemed a bit odd so I asked: "Nearly? How come?"  "I was was invited for the celebration of the Centennial of Rutherford's birth. But they could not pay my fare, so I had to decline", related Sam. Hmm, I thought - why would they invite him?  "How come you were invited?"  "Oh,I was a post-doc with Rutherford".

Well, at this point I thought I had entered a time warp!  As far as I was concerned, at my then age, Rutherford was (approximately) a contemporary of Aristotle! I was dumbstruck and never uttered another intelligent word. Other people arrived, and we went our separate ways having found nothing to talk about . . .

Things I should have asked Goudsmit when I had the chance: "Wow! What was Rutherford like? Tell me some stories of working with him? How come he took you on as a post-doc?  What did you work on?What was the Cavendish Laboratory like?  What years were you there? Were there other well-known people there at the time, or people who went on to become well known? Etc., etc." 

I planned to ask him all these questions at the next faculty social function, but he died suddenly ~10 days after I had met him.

Moral of the story: we are surrounded by interesting people with stories to tell; be inquisitive; don't be over-awed; seize opportunity(s) when they happen.

Electospray ionization mass spectrometry of proteins

The principles of electrospray ionization mass spectrometry of proteins are described here in a fairly basic form. Anyone know of a better link?

'Correctness' of scientific papers

One topic that came up in Class#2 was that "not everything in a scientific paper is (necessarily) correct"; that led to the topic of why scientific papers are refereed  - reviewed by  (usually anonymous) professional colleagues.

A great overview of the history scientific journals and other forms of communication can be found here; naturally, it is a U of C production :-)  and also the first hit on Google for 'first scientific journal'.

So, why ARE scientific articles refereed?  Was the anecdote I gave in class correct? 

Give me your thoughts, questions.