Bif's Birth!

My pardon, noble readers for the extended delay between this and the last post. I beg your pardon, partly because I wished to leave the last post up for as long as possible but also because I had absolutely nothing interesting to write about. Oh I could have blathered on about any number of things, I assure you, but I spare you this by blathering to myself on my exceptionally long commute. In any case, something exciting happened a few days ago (the 19th) that was easily of sufficient magnitude to get me blogging: Biff was Born!

For those of you scratching your heads, Bif is the fetal name of my new nephew, Benjamin! He weighed in at a little under 8.5 pounds, had a full head of hair and all fingers and toes. My brave sister was forced to deliver without the usual calming sea of Novocaine and opiates due to an exceptionally quick labor which lasted a grand total of 3.5hrs! Ben was in a bit of a hurry! In fact, things were so hectic that one might almost forgive K for getting his new son's name wrong! That's right. Jane and I found out about the birth as we were going to bed and uncovered a message each on our cellphones. We were ecstatic to hear from K that little Sebastian had been born and quickly phoned the H & K residence to offer our warmest congratulations at the birth of Sebastian. The next day there was an email from my mom - 'Re: Benjamin not Sebastian'. The theory is that Karl's (understandably) addled brain was already making plans for his little boy based on his middle name: Johan. Yes... those musical types among you have probably already made the connection - Johan Sebastian Bach.

In any case, we have high hopes for Ben too, him being the product of two such extraordinary people. I have little doubt that my sister H and husband K will make really excellent parents. That kid will grow up in an environment enriched with learning and music! Here's to H, K and Ben! Here's a couple pictures:

Maga

Well, after a few weeks of teetering on the brink, the inevitable: My grandma on my mother's side (we call her Maga) has died. I think she was comfortable in the last few days, and she was in very good hands. After telling her sister and a nurse that 'her bags were packed', she basically fell asleep.

From the moment it started to look like her latest slide was one-way, my memories of her have been getting sharper. I think that knowing I wasn't going to see her again was causing me to sortof 'finalize' my impression of her. In any case, here are few facts (which might be a bit wrong) and recollections:

- She grew up in one of those little towns on the French-German border that was sometimes French and sometimes German. I think for her it was mostly German.
- She came to the US with my grandpa (who died before I was born) fleeing the second world war
-There she and her husband built up a dedicated group of friends founded primarily on the love of chamber music, but also on intellectualism and nascent liberalism. All of these emphases were passed on to their three children. I think they were perfect examples of the 'New England Liberal Intellectual', a group that the US has been ignoring recently, to it's detriment.
- My first impression of her was the feeling that she was a little eccentric and quite no nonsense. This, and her preferential treatment of my sister, was explained to me as arising from the fact that she didn't know quite what to do with little boys, having herself only had girls.
- She ate the brown bits of bananas, claiming that this was 'the best part'
- The comforter in her bedroom (the only room in the house with air conditioning) was freakishly soft and smelled of flowers
- If she thought you were trying to pull a 'fast one' on her (which I often was), she had a characteristic 'ah a' (her way of saying 'no you don't') which, if you were being especially bad, was accompanied by a wagging finger.
- On the other hand, she gave me candy. To the consternation of my mother, this was typically just before bed after teeth had been brushed!
- She had remnant german words for all kinds of things. The one I remember most was something like 'hast du genugh gegessen?' which basically means 'are you full?'
- She was quite well off indeed, and was able to fund three major family trips. The first of these was to Martha's Viniard. I don't remember too much about that trip except that I was quite good at the 'ring grabbing' merry-go-round, I really wanted to go to the arcade and a family bike ride (my bike was vastly inferior, as I recall). The second was to a coastal house in Main. It was there that I discovered a Bill Cosby comedy record, which I memorized word for word. The third was to a castle called 'Mohonk' in upstate New York for her 80th birthday. Later I would discover that this was a favorite escape for my favorite science fiction author, Isaac Asimov!
- I once went to stay with her for what I think was a month one summer. There I went to a camp called B B & N. I also remember watching a documentary on Troy, discovering the Teenage Mutant Ninja Turtles about 6 months before any of my peers in Canada and exploring her seemingly endless basement among many other little things.
- In her later years, she lived at an old folks home called Kendall and where she was eventually joined by her two brothers and her sister. Jane and I visited her twice there, once when she was quite well and living in her own apartment, and once when she was still somewhat active, but having trouble mentally. While active, she was 'getting into all sorts of stuff' as my mom put it, joining various committees etc.

So if you were wondering where I get my little quirks from, I can only say that it is likely from this side of the family. My grandma was eccentric, extremely intelligent and committed to the cause of amateur music. I didn't see her much, but I'm going to miss her.

What the Heck I am Doing Over Here

WARNING: This post contains scenes of extended pontification on a scientific subject. It is unsuitable for pretty much everyone.

It occurs to me that I haven't yet bored all of you by explaining exactly what it is I am doing over here. No doubt you have wondered on many occasions: What is this thing called Nuclear Magnetic Resonance that he goes on about for a second or so before start to drift off?

Maybe it would be better first to say what I'm using Nuclear Magnetic Resonance for and why anyone would even bother. I study proteins. Proteins come in all shapes and sizes, but they are all 'just one thing after another' as my very weird advance organic chem prof used to say. They are made up of a chain of small molecules called amino acids. There are 2o 'standard' amino acids. Each one has the same basic structure except for one of their 'arms' which varies. This arm can be long, short, acidic, basic, hydrophobic (water-hating) or hydrophilic (water-loving) and, when you make a chain of them, things start to get interesting. First, the non-variable part of the amino acid structure causes the chain either to want to twist into a sortof spiral (called an alpha-helix) or fold back on itself (called a beta strand, two or more strands side by side make a beta sheet). Whether the chain forms a spiral or a strand depends on the variable part of the amino acids, some are 'spiral friendly' and some are 'strand friendly'. The variable part of the amino acids also causes the spirals and strands to fold around each other in a specific way. Parts of the chain where there is a prevalence of amino acids with hydrophobic arms, for example, will try to minimize their exposure to water by clustering together in the middle of the protein.

And once you know how a protein is shaped, you know pretty much how it works. You can imagine that, depending on the sequence of amino acids, they can form pretty much any shape. Some will be long and and stiff like the stuff in your fingernails and hair, some are round-ish with hydrophobic pockets to ferry hydrophobic molecules around in your blood. So if we're going to mess with them, i.e. interfere with proteins we don't like or get proteins we do like to work better, we are going to have to know their shape. Lots of drugs work by messing with proteins. I'm on one right now. Omeprazole (Losec) is a molecule that fits into the protein that make acid in your stomach by pretending to be the molecule that it normally works on. The protein starts to work on Losec, but gets permanently 'jammed' in the middle of the job, taking it out of commission. So knowing the shape of a protein can help us find drugs like losec. But that's tricky, really, because for being so big, proteins are actually very, very small.

Enter Nuclear Magnetic Resonance (NMR). It wasn't an obvious choice at first. NMR is actually kindof like a radio. What you do is you take a sample and put it inside a coil of wire. This coil, it is important to note, is sitting in a very strong, permanent magnet. What does this do? Well, nothing, chemically, but it makes the nuclei in your sample (say hydrogen, H, or nitrogen, N) have a slight preference about the direction in which they are spinning. They are spinning, incidentally, at different speeds. Different nuclei (like H and N) spin at very different speeds, while nuclei that are the same spin at slightly different speeds because they can be shielded from the magnetic field to various degrees by the cloud of electrons that surrounds them. So basically every proton in a protein (and there are a lot of them) has a distinctive spin. What good does this do? Well, none, actually because we have no way to measure this spin. What we need to do is change the preferred alignment of the spin so that is 90 degrees to big huge permanent magnetic field. But how do we do that? I mean we're competing with a big huge permanent magnet here. Well, it turns out you can cancel out a really huge magnetic field with a really dinky one if you ensure that the field oscillates at the same frequency as your nuclei are spinning. That's resonance, baby, and it works.
Now we could apply our '90 degree' field and then vary the oscillation frequency so that we 'excite' (and thus detect) our spinning nuclei one at a time. But that would be boring. Instead we'll hit the nuclei with a very quick, high power field and excite them all at once. That way, we can measure them all at once. To visualize what the signal that we get, imagine a lighthouse light spinning around. As the light spins toward you it gets brighter and brighter, then fully bright, then dimmer then dimmer then fully dim, then brighter, then brighter etc. So we get a wave that goes up and down in intensity. Now imagine there are hundreds of lights in the tower and they are all spinning at different speeds. That is a very complicated set of waves and it doesn't really tell us anything to look at it. Fortunately, there is a neat trick in math called a Fourier Transform into which we can plop in a wave of any complexity and come out with a 'spectrum' of all the spin speeds that made the wave. I know, I know... way cool.

So now we can see all these spinning protons. So what? What does this tell us about the shape of a protein? Again, nothing. To get information about the shape, we have to take things two steps further. First, we have to limit the number of hydrogens we are looking at cause if we tried to look at all of them, we won't be able to tell one from the other (because their spin speeds are too similar). We do this by 'isotopically labeling' the Nitrogens in the protein. Every amino acid has one nitrogen in it's non variable part, and that nitrogen is attached to one hydrogen. So using some NMR magic, we can limit the spins we excite only to those hydrogens that are attached to our labeled nitrogens. Then we get really clever and do all kinds of NMR magic to measure the effect that one excited spin has on another. This is perfect because, if the spins are close by, they will affect each other really strongly, while if they are far apart, they'll hardly affect each other at all. So, by measuring the strength of this effect, we can get a series of inter-hydrogen distances. From these, using a computer, we can figure calculate all of the possible chain shapes that satisfy all of the hydrogen distances. We then take the average of these shapes (weighted average, actually, because some chain shapes are better than others) and do some more calculations to figure out in which direction the variable 'arms' are pointed. And voila! We have a protein structure!

New Link

We must be having sortof a midlife crisis. We seem to be trying to use the internet like the youth of today. I have a blog, I have a myspace profile (which I never use) and we now are into facebook. All we need to do now is buy skateboards and start cruising youtube. In any case, the advantage of facebook over myspace is that it lets you upload as many pics as you like. And she's uploaded a fair few. You'll need to register to follow the link to Jane's profile on the right, but it's not too bad and free and they do appear to manage to avoid spam. Just make sure to use your 'junk' email account.

The better half of the UK

While we were back home over christmas, I think it's fair to say that there was alot we didn't miss about the UK. I've said it before before and I'll say it again: The minute I stepped off the plane, people just seemed to be a little happier and much more efficient. I have a number of theories about why people seem a little more 'stretched' here, but I think most of them boil down to climate. It may not be as cold as Canada, but most UK-ers live farther north than most Canadians (who all huddle around the US border for warmth) and we find that the lack of sun in the winter is actually quite tough. In Northampton, on the shortest day of the year, the sun is right down at about 3:30 pm. Combine that with omnipresent cloud-cover, and you have a recipe for depression. And how do the brits respond to this? Well, with three things: Beer, dogs and cigarettes. Smoking, drinking and walking the dog are as much national pass-times as football.

But you've all heard me whining about this stuff before. What I'd like to do is point out a few of the things that we did miss while back in Canada. So here they are:
1) Open air markets/high streets. Jane and I have gotten into the habit of going down to the market on Saturday for a coffee and a walk around. In every british town of significant size, you will invariably find two things in the city center; a 'high street', where you'll find stores of every size and description, and a market, where you'll find everything else. The thing is that high street are, compared to where Canadians shop, much much prettier. The streets are usually cobble stone, there are no cars and the buildings are invariably reconstructions of victorian (sometimes pre-victorian) buildings with all kinds of nice architectural features. Especially the pubs. This ends up being more efficient and infinitely more attractive than the closest Canadian equivalent, which is the strip mall (yuk). By the end of my trip home, I was feeling a nostalgia for the Northampton market that rivaled that I had for Tim Hortons before I arrived (gasp).
2) The trains. Brits complain about their current rail system all the time, and justifiably. That is because, about ten years ago, the british government privatized (read: sold) their trains and tracks and, in spite of whatever controls they put in place, the inevitable slide in quality for the sake of profiteering has begun. Nonetheless, the rail system in this country is a million-fold better than Canada's (which barely exists). The commuter trains are integrated with the London underground, which is itself an amazing system. I never really understood how the brits managed to 'get back on the horse' after the attacks of July 7th '05 until I came here. Now I see there are two reasons: A) You can't scare Brits with bombs (the terrorists could have saved themselves alot of trouble/death by asking the Germans if that works). B) The underground is massive. You have really have to experience it to appreciate the immensity.
3) Really old buildings/castles: For the first year of our bring here, Jane and I went to visit a whole lot of old houses/buildings. We did have English heritage passes, which got us into all sorts of sites for free, but these have since expired, and, having to travel ever farther afield to find new sites, we have slowed down enormously. We are planning a major trip up to Hadrian's wall, Edinburgh and Glasgow in April, but we won't be doing nearly as many little trips over the next month or two. I should add that English heritage is a truly excellent organization. We really enjoyed having those passes! For 40 pounds they were well worth it.
4) Movie passes: One of the major cinema companies here (Cineworld, the other major one is VUE) has a program of 'see as many movies as you want for a flat monthly fee'. Up until just before we left, we had these passes, and it was really great just to be able to go see a movie whenever without 'paying'. I'm thinking cinemas in Canada should follow suit: They make most of their money from concessions anyway.
5) A housing market that keeps going up and up and up. OK, there's no good reason to like this, except that it motivates brits to be very intense about their property market. Which results, in turn in lots of high quality shows about house buying/house renovations etc.

There's probably plenty of other stuff... I'll keep adding things as they come to be. But you can see that, the longer we stay here, the more 'balanced' our view is becoming of the differences between this home and that home.