Archive for December, 2005

Fun For Science Geeks

December 30, 2005

My wife gave me a most excellent book for Christmas this year: The Discoveries by Alan Lightman. The format is simple: Lightman has chosen 22 seminal scientific papers of the 20th century and reproduced them here, each with a nicely written forward that explains the context and significance of the paper, some biographical information on the authors, and additional background to help the reader navigate through the paper.

You’ll find some obvious choices included: Einstein’s 1905 paper on special relativity, Heisenberg’s 1927 paper describing uncertainty, Watson and Crick’s paper on the structure of DNA, Hubble on the expansion of the Universe.

But there are other treats as well. I was thrilled to see Krebs’ paper on the Citric Acid Cycle (AKA, the Krebs Cycle) included as it brought back the sense of wonder I felt in high school physiology when we studied how energy is produced at the cellular level by continuously converting ADP to ATP via the transitions of the Krebs Cycle. The Krebs Cycle rivals the workings of DNA in importance and in elegance.

The Krebs section seems relatively typical of Lightman’s overall approach so I will describe it in more details. The reprint of the paper (The Role of Citric Acid in Intermediate Matabolism in Animal Tissues) is preceded by about ten pages of introduction by Lightman. In it, he first outlines briefly the evolution of scientific thought around biological energy use and production, touching on the major names involved. He then introduces Krebs and sets him and his work in the context of other contemporary work–concentrating on work by others that Krebs will unify and extend to describe the basic cycle of energy production in the body. He also covers enough of the basic chemistry and lab methodologies to make the paper understandable to the reader. He ends the introduction with a sort of play-by-play that describes the overall structure of the paper as well as the significance of each of section as Krebs builds to his final conclusions.

If you or someone you know would enjoy a guided tour through some of the most important scientific breakthroughs of the 20th century, then take a look at this book.


NYC Transit Strike: View from the Street

December 22, 2005

My brother Jon works for the YMCA in New York City–he commutes by bus from New Jersey. Here are his impressions from the first three days of the transit strike.

Amazing how quickly the novelty has worn off.

Day 1

I thought I would give you a first hand account of the NYC Transit Strike. As you would imagine, the streets are very busy with people who would normally be taking the subway. My walk to work (12 blocks) was very crowded, I barely had to move my feet as I was swept along with the crowd. Roads are closed to private vehicles below 98th street so all that you see are people fighting for cabs (which are taking as many fares at once as possible), charter buses trying to get people to Wall Street (to keep the financial machine moving) business people riding bicycles and roller blades and lots of police cars.

As for the YMCA, we are trying to keep all 19 branches open using all available staff. I may be off to the West Side Y soon to relive my days as a program director!

My commute was easy as the roads into the city are restricted to buses and passenger cars with at least four people.

Day 2

Things getting pretty tense on the streets, yesterday’s good humor and novelty have give way to today’s frustration. You may have seen clips of folks walking over the Brooklyn Bridge, one of my colleagues did that walk yesterday (9 miles from her home to the office). I, on the other hand have had a very easy commute, no cars on the road. Imagine traveling on 93 into Boston and being the only car on the road at 7:00am, bizarre! My commute today was just about 70 minutes (20 less than normal)

Day 3

As we enter day three of the Strike, anger and defiance seem to be the mood of the day. On Days One and Two, although the sidewalks were very busy, there was a sense of order. Today, people are simply walking in the streets among the grid locked cars. Things are so congested that it is hard not to bump into people. The common terms of “excuse me” and “sorry” have been replaced by more colorful and perhaps even seasonal phrases like “Jesus Christ” or the very common, “what the F***”!

It is best summed up a scene I witnessed on 34th Street. Despite the police officer waving cars through the intersection, people just started walking across the street (surrounding the cars and stopping the already slow moving traffic) Over the sounds of horns blaring I heard the Officer say, “Are you people F***ing crazy, these cars will crush you!”

Also, because of the overcrowded sidewalks, street vendors have not been able to set up. What this means is that I am without my 60 cent bagel this morning and it will be unlikely that you will each be receiving a very special $5.00 Rolex watch from the City!

Finger of Hope

December 15, 2005

Melville Got It Right

December 14, 2005

It is six degrees Fahrenheit here in Sharon, MA this evening. Which puts me in mind of a delightful passage from Herman Melville’s Moby Dick:

“…because truly to enjoy bodily warmth, some small part of you must be cold, for there is no quality in this world that is not what it is merely by contrast…But if, like Queequeg and me in the bed, the tip of your nose or the crown of your head be slightly chilled, why then, indeed, in the general consciousness you feel most delightfully and unmistakably warm. For this reason a sleeping apartment should never be furnished with a fire, which is one of the luxurious discomforts of the rich. For the height of this sort of deliciousness is to have nothing but the blanket between you and your snugness and the cold of the outer air. Then there you lie like the one warm spark in the heart of an arctic crystal.”

Some frosted window glass in the bedroom–my own arctic crystal.


December 12, 2005

It’s not popular to talk about nuclear power these days and even less popular to discuss nuclear malfunctions, but I did see an interesting tidbit in Ken Silverstein’s The Radioactive Boy Scout that I’d like to pass on.

In 1942, Enrico Fermi achieved the first sustainable nuclear chain reaction using a primitive reactor constructed in a makeshift laboratory under the stands of the football field at the University of Chicago.

Silverstein describes the origin of the term “scram”, which refers to the emergency shutdown of a nuclear reactor:

The chain reaction took place in a small reactor, which Fermi called an atomic pile. One of the control rods made of cadmium–which blocks neutrons, which are used to split the uranium atom and initiate the chain reaction–was attached to a rope over a pulley and suspended above the reactor. Should something have gone wrong, a scientist named Norman Hilberry was to cut the rope with an axe, thereby dropping the cadmium rod into the reactor and, it was hoped, halting the chain reaction before a meltdown occurred. Hilberry’s job title was Safety Control Rod Axe Man; hence, ever since then, an emergency nuclear-plant shutdown has been called a scram.

Go, Sparky, Go!

December 8, 2005

Open-source hardware? Yeah, open-source hardware. I mean: YEAH!!! Open-source hardware!! If you missed it, we announced earlier this week that we’ll be open sourcing the UltraSPARC T1 processor early next year. In other words, our latest and greatest, coolest and hottest, SPARC processor. Downloading a chip–and for free–kind of a funky idea. OpenSPARC.

For those not familiar with how hardware is designed this may seem an odd concept, but it is actually pretty straightforward. At least conceptually. Hardware designers write pile and piles of code in a hardware description language (HDL) which is then essentially “compiled” and used to create an actual, physical chip. We used Verilog for the UltraSPARC T1 design. Here’s an example of what Verilog looks like from the Wikipedia.

So who’s going to play in this new sandbox? I don’t think we know for sure yet. I’d expect universities to give it a serious look since students don’t often get to look at a full, industrial-strength, cutting-edge microprocessor design in an academic environment. It would be cool to see someone offer a course in which students make interesting modifications to the basic framework. With all of the framework already there, I’d expect to see some pretty funky and creative mods, even within the span of a single semester.

On his blog David Johnson says he doesn’t think hobbyists will have too much use for OpenSPARC, but he does allow that someone could take it as a base and, by ripping out a lot of instructions, create a simpler custom processor design that they might then burn into an FPGA. Interesting idea. I could imagine some three-letter agencies I know thinking the same thing.

One thing is sure. If you give people a hugely powerful and flexible tool with all the knobs and buttons exposed, there’s no telling what they’ll come up with. And watching that is going to be tremendous fun.

CoolThreads and HPC

December 6, 2005

Today Sun is announcing its new CoolThreads servers–a huge technology innovation that we believe will change the rules in the datacenter. You will undoubtedly see press and announcements that trumpet the higher levels of achieved application performance, at significantly lower power than competing servers, in significantly less space, and at a lower price point than competitive machines.

But what does this mean for High Performance Computing? Should you run out and buy a rack full of CoolThreads servers to run your next LINPACK or maybe a car crash simulation?

Hell no. Please don’t. These servers use the UltraSPARC T1 processor, which has been carefully designed to be highly efficient in serving throughput workloads centered around web infrastructure–running workloads like web and application servers, for example. The T1 has very little floating point capability (one floating point unit to serve all 32 hardware threads.) This isn’t a bug—this was precisely the design point we targeted with this first radical CMT (chip multi-threading) processor. We set the dial here on purpose. So don’t go running a Monte Carlo simulation on one of these babies— that’s not what it’s for.

Will these CoolThreads systems be useful for HPC customers? Sure, in the sense that HPC installations have infrastructure requirements like any other IT-intensive business. You’ve got web tiers and grid middleware and other non-FP workloads that may benefit significantly from a CoolThreads approach. Plus you have some of the biggest, fullest datacenters on the planet and could probably use some lower power, denser systems. Just keep thinking web infrastructure and integer workloads and you’ll be okay.

Does this mean that CMT as a concept is irrelevant to the computing part of HPC? Again, hell no. Don’t confuse the UltraSPARC T1, a CMT implementation, with the CMT concept itself. You’ll see us set the knobs in a different place with our ROCK CMT processor, for example. We haven’t talked much about this chip in public yet, but you’ll see a very different (and more interesting) computational profile from that CMT implementation. Stay tuned.

[ T: ]

The Radioactive Boy Scout

December 5, 2005

A friend lent me a copy of The Radioactive Boy Scout by Ken Silverstein, which I read last night while flying to the Bay area. It’s the true story of a teenager who built a model breeder reactor in his mother’s backyard that was radioactive enough and dangerous enough to be declared a Superfund cleanup site in 1995 when it was discovered. Moon suits in Michigan.

It’s the story of a troubled kid who develops an obsession with chemistry and, eventually, atomic energy. Despite the author’s attempt to portray David Hahn as a whiz-kid science type, I didn’t buy it. His failure to use all but the most rudimentary of safety procedures, and his poor handling and understanding of the dangerous substances he was using speak to a real lack of intellectual depth. And his stealing and receiving stolen goods speaks to a real lack of character as well.

I don’t recommend reading the book to gain insight into David Hahn’s psyche. What I found fascinating was how easily he was able to obtain his radioactive materials — radium, thorium, americium, polonium, and uranium. Fascinating and extremely disturbing. Which leads me to my final point. This book was written in 2004. I found it odd in the extreme that the author makes not a single reference to terrorism or to the construction of dirty bombs. The story illustrates how, with a little creativity, a determined individual could procure and produce a variety of radioactive materials in a large enough quantity to build a dirty bomb using this material and conventional explosives. THAT is a lesson worth understanding.

A Very Expensive Bird Perch

December 2, 2005

[Photo courtesy of AM, the Navel’s San Diego correspondent]

I saw the above while visiting San Diego recently and wrote the following note to the Driscoll Mission Bay Marina:

Hi. I was visiting San Diego recently and someone pointed out an amazing site that I think was in your marina–a boat with an osprey’s nest on top of the mast. My friend told me that the boat hasn’t been used for 3.5 years because the bird and nest are protected. Is this true or just an urban legend? It certainly is a great story.

Here’s what I heard back from Mary-Carol Driscoll:

It’s no urban legend – it’s true (much to the owner’s dismay). The boat has been in our marina since 2000. It was about 2001 when the osprey spied the tall mast and made their home. Osprey like to have a high perch and the mast is the tallest in the basin, hence the attraction. The boat can be moved when the birds aren’t “nesting.” The owner did move the boat once and removed the nest, but the birds returned within a month. It is quite fun to watch when the birds are nesting. They are excellent hunters, but messy eaters. Hopefully your next visit to San Diego will be during the mating season.