Getting crabs in B’more

DSC_0009Perhaps the destination I’d most been looking forward to on this journey was Baltimore. To most people in the UK right now, Baltimore means the Wire. Hannah and I are massive fans, we finished the last episode of this incredible, multi-layered drama the day before I left for the US and plan to start watching it again when we get back.

Of the many themes covered in the Wire, crime, drugs and murder are probably at the fore. It seemed wise to have a local guide when exploring. We’d already been told that this is a city where you can end up in some gritty areas simply by walking a block over from a “decent” neighborhood.

Luckily, Karen Nelson from JCVI and her husband Tony were willing to take us around. Tony, a builder and architect, grew up in DC and went to school and college in Baltimore.

P1020761First stop was the harbour. This is the tourist-friendly side of Baltimore. A large area with pleasure boating, the National Aquarium, huge Hard Rock Cafe etc. Over the water is Fort McHenry – Tony was keen to point out this was were the Battle of North Point took place: or where “you blokes” got whupped by US forces. Instantly recognisable to Wire fans is the iconic Seven Foot Knoll Lighthouse. Do you remember the scene where Lt. Sydner makes the call from the ‘serial killers’ phone, prompting police helicopters and squad cars to flock to the scene?

We visited the aquarium which was fantastic and nicely-laid out. A strange throwback was a dolphin show – I haven’t seen one of these since they closed down the Brighton Dolphinarium in 1987. These creatures do seem still too intelligent to be wasting their time entertaining us with facile tricks. At least put them to work I say, perhaps they could patrol the Baltimore Docks.

P1020796Something about the aquarium had worked up an appetite for some sea-food. A missed opportunity to put a traditional crab house in the aquarium meant a short trip down to Obrycki’s for lunch. The neighbourhood had obviously seen better days, and taking happy snaps of the corners apparently was a bad idea.

Obrycki’s was exactly what I been looking for in a Baltimore crab house: dim lighting, funereal curtains and wooden tables and chairs. We were served by a proper B’more waiter. He spread brown paper over the tables, got us a pitcher of the local brew and told us “A dozen crabs in a bushel is $46”. The answer from Tony and I was clearly yes, bring that right now – before we had even consulted the ladies present who may have wanted the more delicate concoctions on offer. The bushel was up-ended onto the table and dinner commenced.

Crabs here come steamed (rather than boiled), in copious amount of Old Bay seasoning. Old Bay seasoning is black and red pepper, celery salt and various spices which encrusts the shells. The crab variety are Maryland Blue Crabs. They used to come exclusively from the Chesapeake Bay, but demand has increased and supply diminuished such that they are shipped in from the Gulf states which also get the crabs but don’t have a crab culture of their own.

P1020800Compared to British restaurants, the tools employed to help with dinner are rudimentary: a wooden mallet, a fork and a sharp knife. First bash open the claws and devour the sweet meat inside. Then use the knife to prise open the abdomen, rip off the dead man’s fingers and discard, and then work your way through the flesh inside.

The crabs were really sublime, perfectly cooked, deliciously sweet and with just the right amount of seasoning. I really could have spent all day eating these.

DSC_0046Full of crab, we made our way to the car and Tony took us on a quick tour of Baltimore. As with many cities there is a “good” and a “bad” bit, but in Baltimore the juxtaposition is stark. He showed us the complex of correctional facilities in the centre of the city which were dismal looking. We spotted some corner boys. The houses were once proud, now often boarded-up and allowed to degenerate.DSC_0035

A couple of blocks over, north of Downtown the picture changes completely. Imposing pre-Depression mansions show the wealth that flowed through Baltimore, once a more significant port city than New York and as important as Philadephia. Verdant, open spaces house the John Hopkins buildings and various other presitigious academic institutions.

Drivin’ the East Coast

DSC_0041The Mustang I picked up on Saturday had a slow puncture so we ended up replacing him at Richmond Airport. The new one we’ve nicknamed Maurice is in working order, but even with a 4.0 litre (!) V6 on board, this car doesn’t really shift as I’d hoped. That’s probably because it looks like it weighs 3 tons. There is a GT model which develops 300hp, and the Shelby with 500hp, but neither can be rented from Avis. It does make a pleasing noise though, and looks great from the rear.

Driving around you can see that the American motor industry is suffering: Japanese cars are the dominant species on the road. The desirable cars are the European and Japanese brands.¬† The US cars spotted tend to be large SUVs and massive pick-ups (usually with nothing in the back).DSC_0110 Petrol is still laughably cheap here, going at around $2.30 a gallon (37p a litre), although their standard stuff is 87 octane, which I wouldn’t put in a landmower back home. The super-premium is 93 octane, less than our standard stuff.

Heading down the coast in Maurice, we stopped in Jackson Ward in Richmond. This neighbourhood is great for Soul Food, church shops packed with gospel records and pawn shops. A sign on the bail bondsman’s window offered a $600 reward for the capture of “Cleveland Peoples”.

We stopped in at Croaker’s Spot for lunch. Seafood is a big deal on the East Coast and in the South. Shrimp, clams, catfish, whiting, fried oysters and crab are the typical bill of fare. Sometimes these are dumped into a baguette with some salad and sauce to make a po’boy sandwich. The portions are of course way too much for even my now-stretched stomach. The carbohydrate highs (and lows) I’ve experienced here are out of control, and I find myself hugely hungry but then satiated in just a couple of mouthfuls. Last night I had such a bad starch craving I considered eating an Arby’s burger. Sense prevailed and we dined on cheese and crackers in the hotel room.

DSC_0089Croaker’s spot offered the motherlode of fish fry: their legendary fried fish served with crab cakes and fried shrimp came with a pancreas-busting assortment of sides: cabbage, corn bread, cheese grits and potatoes. And of couse, it wouldn’t be a Southern meal without¬† a load of hot chilli sauce.

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On The East Coast Trail

Apologies for slowness of updates for a while. This has mainly because I’ve had some work to do for a deadline yesterday and so blogging and posting pictures of food could to the untrained eye be been construed as procrastination!

Much has happened since I last wrote. I met up with Hannah at Dulles Airport on Saturday night as planned, although she took 2 hours to get through customs. That gave me just enough time to pick up the Mustang for this 2nd leg of the journey, a tour of the East Coast.

After reuniting, we swung South to Fredericksburg deep in the Civil War heartlands of Virginia. Fredericksburg was a Confederate stronghold and an important strategic site on one of the most inland rivers navigable from the Atlantic Ocean, the fast-moving Rappahannock, where locals fish out catfish and bass and the occasional person foolish enough to try to swim in it.

Fredericksburg is achingly quaint and picturesque; the colonial buildings have been kept in pristine condition by the local preservation society. There are tons of antique shops and a few nice pavement cafes and restaurants.

This is famous for being the home town of George Washington, who lived here from the age of 6 until 20, and the stories of him throwing a silver dollar into the Potomac are interpreted locally as a rock into the Rappahannock. It is also the home of Mary Washington who lived on here until her death.

We stayed at the rather quirky Richard Johnston Inn B&B, the architect of whch was an original signee of the Declaration of Independence. Breakfast, always a fraught affair in a B&B on account of the other guests was pancakes, whipped cream, blueberries and sausage balls. Other people staying in the inn were a selection of East Coasters from Connecticut, Massuchussets and New York. One was curious to know whether Gordon Brown was going to survive the next few weeks.

Right now we’re holed up in Virginia Beach which is decidedly more low-brow destination, with the sounds of Americans enjoying their holidays on the beach punctuated by low-flying fighter jets on manouevres.

Will keep you more up to date hopefully from now on!

Pujoles and Busch (Stadium)

Hi all – just updating from Midway Airport where I’m about to fly to DC to meet up with Hannah and start the East Coast leg of this journey. Just time to update quickly…

I know that title sounds very rude, but it isn’t. All will become clear. Earlir in the week I got 4 tickets to the ball game from a dodgy bloke on eBay and on Thursday we went to see the St. Louis Cardinals (go Cards!) play the Cincinnati Reds at Busch Stadium (there ya go!).

Now as all the world knows, baseball is an excuse to turn up on a warm evening and drink weak beer and eat hot dogs (or foot-long brats) in the company of other Americans.

Any sport based around eating and drinking is right up my street as you know by now.

So, we had a blast at the game. The dodgy bloke came through and we had a great view of 3rd base and the rest of the action. The expensive seats go up to $250 per ticket.

That’s a lot to pay for the risk involved – sit too close to the ‘batter’ and you run a good chance of getting a baseball straight in the face if the guy lets go by accident.

And indeed that’s what did happen, smacking a poor spectator right in the chops. The crowd stood up, presumably hoping to get a view of some blood, and over rushed a bunch of medics. I jested that they were followed closely by an army of litigators.

Steve, Pam’s husband assures me that the disclaimer on the tickets (not our fault if you get killed by a bat) is water tight.

Perhaps there is a movie plot there, someone deliberately tries to kill an audience member (say, an unloved relative) by releasing the bat at the right moment. The twist would be that they’d miss and kill their wife instead.

Anyway, great times were had and the Cards won 3-1, with the local star, Albert Pujoles (pronounced poo-holes) getting not just a ‘homer’ but also a ‘double’ I’m reliably informed.

Pictures to follow!

Drowning in data at the Wash-U Genome Center

P1020221So, how about a little bit more info on the Wash-U Genome Center where I am visiting until the end of this week.

Walking past the guard into the anonymous-looking building, past the drab physical therapy suites to the elevator, you would be forgiven for not twigging that this was the hub for some of the most exciting work in science right now.

Things look up when you hit the 4th floor. Reading the placard next to a first-generation ABI sequencer you will find one of the first machines used on the original Human Genome Project. Another one in the corner serves as a table for a vase. Moving down the corridor, genome nerds will get a frisson of excitement as the tantalising sight of large, blue machines can be glimpsed through the small square windows. To the genome nerd, those blue machines mean just one thing: data.P1020212

Here, genome data is being produced on a scale which would have been unimaginable even a few years ago.

Those blue machines are Solexa machines, what we used to call a “next-generation sequencer”. Wash-U has 29 of them (soon to be 35). There are also 8 454 machines, the competing technology from Roche.

My original calculations figured that these machines were producing around 1 to 2 gigabases of DNA sequence per run, as per the manufacturer presentations. However, a customer as big as Wash-U works closely with Illumina, the manufacturer, and these numbers have already been rendered obsolete.

P1020220Each machine routinely produces 10 gigabases per run (running 75 cycles to make DNA fragments 75 nucleotide bases long). Each run takes around 10 days to complete. So, with it all running 24/7, that’s about 1,200 terabases a year.

With a human genome commonly quoted as being 3 gigabases long, you are looking at 400 human genomes (or cancer genomes, or chimpanzee genomes) per year when sequenced at 10-fold coverage (i.e. every nucleotide in the genome sequenced 10 times on average, to improve accuracy).

And that’s just the tip of the iceberg, sequencing throughput is out-pacing Moore’s Law right now by some margin, and there is no reason to think that the amount of data being pushed from each machine will not continue to increase.

With all that data generated, you need some pretty serious IT infrastructure. The genome center this year completed building a dedicated data center which is located over the road. It is connected to the machines through a dedicated 10-gigabit fibre connection. The data center is spacious with plenty of room for expansion. In common with data centres in the commercial world, it is stocked with resilient power and air-conditioning.P1020218

What’s inside? The big numbers are 3 petabytes (3 thousand thousand gigabytes) of storage, connected to 3,000 processor cores! That’s a lot of hard drives when you see them all lined up. Gary Stiehr told me that at least one disk failed every 2 days.

So, all those sequencers and all that storage and processing capacity. What have I missed? Of course, people – there are around 300 staff in the genome center.

I’ll tell you more about how all this is co-ordinated, a huge task, in another update.

I’m not dead (or on Coronary Care)

Don’t worry, I am still alive. Have been getting really stuck into the genome analysis work in the past few days, plus going out each evening, leaving little time for blogging. However, I will give myself a little break later and tell you more about what I’ve been doing. Tune in later for chicken dinners, biker bars, lesbians, and some more hard-core genomic nerd chat.