Greg’s Place

I received an email from Dr. Eric Lander today about his appointment as co-chair to the President’s Council of Advisors on Science and Technology today. Then I noticed it on CNN as well. As an employee at the Broad Institute, I’m both thrilled and proud of his achievement. I still remember one of the first “Broad 101″ lectures I attended - and I had not met Dr. Lander yet. I kept thinking, ‘who is this strange guy asking all these questions?’ I’ve learned a lot from those questions and I’m thankful to him, his questions, and the poor presenters who tried to answer them.

Had a great conversation last night with a very informed friend about torture, whether waterboarding is or not, how useful it is, etc. First thing I see this morning is a great essay by Matthew Alexander on the subject. Alexander is a 14 year Air Force vet and interrogator. I’ll let him make my argument - he does a much better job.

I learned in Iraq that the No. 1 reason foreign fighters flocked there to fight were the abuses carried out at Abu Ghraib and Guantanamo. Our policy of torture was directly and swiftly recruiting fighters for al-Qaeda in Iraq. The large majority of suicide bombings in Iraq are still carried out by these foreigners. They are also involved in most of the attacks on U.S. and coalition forces in Iraq. It’s no exaggeration to say that at least half of our losses and casualties in that country have come at the hands of foreigners who joined the fray because of our program of detainee abuse. The number of U.S. soldiers who have died because of our torture policy will never be definitively known, but it is fair to say that it is close to the number of lives lost on Sept. 11, 2001. How anyone can say that torture keeps Americans safe is beyond me — unless you don’t count American soldiers as Americans.

It’s a good read, and thoughtfully done. Here is a list of other editorials that I have kept over time. I stopped collecting them some time around the summer when the volume became too much to keep track of.

• My favorite, a 30 year vet in interrogation: Two problems with torture
• A prominent Catholic viewpoint: Be Not Afraid II
• Tom Rick’s, another Army intel vet
• Malcom Nance, a SERE instructor who teaches the technique, is pretty adamant about the subject.
• Here is the unequivocal view of a Commandant of the Marine Corps and Commander of US Central Command.
• The story of Yukio Asano, sentenced to 15 years hard labor for waterboarding (among other torture techniques) American soldiers during WWII.
• A Natiional Guard JAG discusses the criminality of waterboarding.
• And the now-famous CIA officer Kiriakou who admits that it is torture, but equivocates on the necessity of it.
• Some helpful sourcing of the phrase “Verschärfte Vernehmung“, i.e. enhanced interrogation, and how some of the practices of convicted WWII war criminals are precursors to what has happened at the hands of US interrogators.
• Lieutenant General John (”Jeff”) Kimmons, the deputy assistant secretary of Defense for Detainee Affairs, explaining that: “No good intelligence is going to come from abusive practices. I think history tells us that. I think the empirical evidence of the last five years, hard years, tell us that.”
• 5 myths about torture and truth. Darius Rejali, a political science professor, has studied the issue in a clinical manner and gets to the heart of some details. Bottom line: it doesn’t work. Here’s a key quote from a WWII era Japanese field manual: “the clumsiest possible method of gathering intelligence.”

Listening to the kids rehearse the Polar Express movie today, one would thing that the Hot Chocolate song has this line:

“Santa spit it in the pot”

when the lyrics are actually:

“Keep it cookin in the pot”

Well, it’s hard not to stop laughing at this one.

Here are Peter and Lex enjoying the first real snow this season. We had a sprinkling earlier this week, but it didn’t amount to much. Today, we had about an inch to an inch and a half to work with.

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I wasn’t going to post these pictures, but since Henry and Mike set up an entire website for her, I think it’s OK. In fact, they have their own set of pictures from this event. They brought Minh back to Boston for a visit this summer. My boys had a blast visiting up in Milford NH that day. It was just a couple weeks earlier that we had been to the same place for my wife’s aunt’s 50th wedding anniversary.

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This year was the first time I heard about this crazy tradition. Jake and the crew seem to have found every excuse in the book to hang out with old college friends and share a drink. It was amazing to get back in touch with some real good friends that I haven’t seen in over ten years, and some more than that. My old boss and eternal pal Jake, Dante Varrasso, Jamie Gahan, Brian White, Rob Pine, Neil Joyce, Dave Stordy, Lew Conley, Dan Dulaski, Rich Conley, Tommy Winston, Bob Miller, and a host of others attended that night. It was a fascinating time to catch up and find that everyone is doing so well in life. Here’s to everyone there, and to everyone that couldn’t make it. I’m already counting down the weeks until next Thanksgiving.

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This Halloween, Peter was an ice cream cone and Lex was a firefighter. Lex still wears his costume from time to time around the house … and to firehouse tours … and to friends’ houses. At one firehouse tour, someone asked who the shortest firefighter was. Lex raised his hand and said that it was him. Stephanie hand-made Peter’s costume. The sprinkles are cut up straws and the ice cream is white tights stuffed with batting and appropriately arranged.

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This summer, we filled in our pool. There were lots of issues - but the biggest one for me was the maintenance. I spent more time with the pool than I did my family. Ok, that’s a bit of an exaggeration, but it was a lot of time spent for relatively few hours of fun.

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It’s been far too long since my last blog post. I guess a year and a half isn’t so long in the overall scope of things. And so many things have happened that the time seems to be about right. In random order, I’ll attempt to cover the following items over the next as-yet-to-be-determined-time-period.

• Reconnections from the past
• House work and my attempt at plastering
• Family life, photo albums, and all the fun stuff
• Work life at the Broad Institute
• Friends and their lives
• Technology
• Politics
• Religion
• Anything else likely to cause agita amongst my family

Hat tip to Andrew Sullivan. This post by Tom McMahon is just plain amazing advice to live by.

So, Eclipse was driving me nuts today. While trying to load up the hibernate console in the JBossIDE, it kept failing with a class cast exception due to incompatible javas versions and telling me it was using java 1.4.2. I had upgraded to 1.5 many weeks ago and this was frustrating. I googled a bit and found this page on switching the CurrentJDK link. I was unaware of this pesky problem. I had set JAVA_HOME to 1.5, used the apple java switcher to point to 1.5, but apparently that’s not enough. This link also has to point to 1.5. That resolved my class cast exceptions … now to resolve some others

cd /System/Library/Frameworks/JavaVM.framework/Versions

sudo ln -fhsv 1.5.0 CurrentJDK

Well, another year is over with. I haven’t blogged in quite a while, but I did put up new pictures of Christmas this year. We had the Bindas and D’Angelos over the weekend before Christmas weekend, then we visited my sister’s condo on Christmas Day. So, these pictures span a week.

On the work front, I’ve been enjoying my new job tremendously. I’m working for the Broad Institute which is affiliated with Harvard and MIT. I came in under the MIT side of the house, so I’m officially an MIT employee. I’m working as a software engineer doing web-based applications for the labs. My first project revolves around a brand new biological sample tracking application. The app is all java 1.5 on jboss. They use all sorts of technologies, mostly hibernate/struts. We’re using Stripes for the presentation layer, which is much easier to work with than Struts. I like the idea of using event handlers as annotations … i.e. a form submission in a jsp can be mapped directly to a method in a java class.

So far, the work is reasonable and there’s plenty to do. I’m very impressed with the level of intelligence of just about everyone I’ve met. Most of the java folks are well-versed in genetics and lab management. My biology background is pretty weak, so I’m a bit over my head in that area, but I’m finding the work to be just about perfect. It’s the first time I’ve been able to work with java 1.5, so that is a blessing now.

The downside is that I miss my walk across the common and the public garden each day, and I also miss my former co-workers. There are some real talented folks back at Pearson that I’m glad I had the chance to work with, and I already miss them. I might be able to alter my commuting routine to get some more walking in, but it’s hard to make time to get together with folks from the old office. Bernie and Ed did drop by a couple weeks ago and we had a blast. I hope we can make some time to get together again.

Another big change is that I’m working on a mac laptop now for all of my development. I love the fact that I can just take the laptop with me when I have to catch the train and pick right up where I left off when I get on the commuter rail. I’m finding development pretty comfortable with Eclipse for the mac and BBEdit. JBoss and Tomcat run perfectly. I found this great utility (from YouSoftware) that lets me create multiple desktops and then you can switch between them from the menu bar. This helps a lot with the cluttered desktop that is a hazard with macs. If there is one thing I don’t like is the lack of a decent window management system built into OSX. There is the F9 and F10 thing, but that’s a still a little awkward if you have more than ten windows open. So far, I like to have one desktop for development and one for email.

Well, today’s my birthday, and also the first snowfall of the season. It started out pretty light, a mix of rain and snow really, but by nightfall, we had about a quarter-inch on the ground.

The other batch of news revolves around work. I’ve been searching for a new position for a little while now, since early September, really. It’s been a tremendously enlightening process compared to all of my previous searches. I started out focusing in the academic arena after a good friend of mine had recently moved from an administrative position to a faculty one.

From the very beginning, I received lots of calls from recruiters and head-hunters. I’ve worked with many of them before, and had very poor luck. This time, however, two companies really pulled through. So far, I’ve had second interviews with four companies through these two recruiters, and it looks like two might make offers.

It was my first round of efforts, though, that have delivered. Although the academic world is a bit slow at taking these steps, the Broad Institute at MIT made a very decent offer yesterday. I’m very excited about the opportunity … it’s definitely my top choice at the present.

These companies that I had second interviews at seem like very solid places in case anyone else might be interested:

• Rapid7
• XRefer
• PHTCorp (they still have the typo on their home page)
• Shoebuy

So, some of the concerns I’ve had and things I’ve been looking for revolve around quite a few factors. My current position is as a lead web developer for a product that was built over four years ago and a significant portion of the code is from that era. Over the years, newer technologies like hibernate and struts have been bolted on which have helped quite a bit, but the underlying architecture is fairly dated. Not much is going to change either, so it’s really fairly limited in terms of developing in newer architectures.

Another factor for looking is the current work situation. It looks more and more like our division is looking to shed the development operations here in Boston. We were re-org-ed from Prentice Hall and Scott Foresman to a group that is based out of Mesa AZ. From that point on, it’s become more and more clear that remote operations (i.e. Boston) are less and less viable. For instance, our supervisor moved to Mesa this summer. One of the other two developers left for another company too. That left me and one other in the office. There is no new development now as well. There is only bug fixes and updates to the legacy system until the newly re-architected version is released next year.

More later … it’s getting late

(Updated 10/30/05) A third consideration revolves around development itself. We are two developers, a remote development server, and QA/stage environments. There’s not too much in the vein of refactoring old code, learning from one another, automated testing routines, or significant support for the various server environments. It’s becoming more clear that there’s little money to put into this part of the ’system’, so it has steadily devolved to its present point. In publishing, the budget is based on the discipline. That discipline has the cash … so they call the shots. Not too many folks care about what’s required for a solid development environment, so few resources go that route. Instead, all efforts are focused on the feature that department X is paying for, and lately, to the detriment of the existing code. It’s also clear that for me to move beyond this, I need to be in an environment that takes this part of the process more seriously.

Lastly, how can I estimate the impact of old friends? Steve Tello, a good friend and mentor from UML, has moved to a faculty position after many years directing the helm of the UMass system’s online education program. His dedication to academia and personal commitment to education were very strong motivators for me to return to the world of education.

Here we go!

Here are some wish lists for the family. Hopefully, this will make holiday shopping a bit easier. In the meantime, I’ll look at adding these as a list in the left-hand nav panel.

• Peter and Lex
• Greg

I subscribe to the Dilbert newsletter for a random laugh. Turns out, there is a blog for this: http://dilbertblog.typepad.com/. My favorite line in the newsletter was in the intro:

Dogbert’s New Ruling Class boasts 475,000 members. Each of you is so intelligently designed that you can survive a Category 5 hurricane via a process known as running away.

I liked this CNN article on feeding young children. It’s good to see that some of the things we did … i.e. giving our children pizza, for instance … wasn’t such a bad thing. If we do have another child, I’ll be sure to recall this advice.

I’ve long been worried about the turning of the markets. I was pretty sure the local housing market would turn by the end of this year and I was a little late on that prediction. My prediction about the overall economy is that our country’s present spending plan is insane and will see a serious reality-slap within a year or so. It was with great laughter that I read James Cramer’s (of The Street) recent article on how to survive the coming crisis (via Andrew Sullivan).

“Our only hope that financial disaster won’t strike sooner lies with the Chinese, who actually fund our deficit by buying our Treasuries—$242 billion worth, or 12 percent of all foreign holdings. If the Chinese decide to be good communists and stop buying our bonds, the Feds will have to raise rates to attract new investors and the reaper will be at our doorstep with interest rates more akin to those of South than North America. Right now, it’s not a problem. But in a year or two or maybe less, I perceive that the government will throw a bond auction and nobody will show, including the Chinese, until rates shoot up dramatically.”

He’s a bit more optomistic than I am. I think the interest rate scene will be starkly different in the spring … more representative of the early 90’s than anything else.

I’ve been too far out of the loop lately with recent technologies. However, I’ve been rapidly making up for lost time now that I have some solid reading time on the commuter rail. TechCrunch is a great site for keeping up with all sorts of new applications coming out, but this page just lists Ajax applications. I just looked at the Kiko calendar app and it’s pretty slick for a beta product.

That, some updates to the AppFuse project and a newly discovered Trails project left me with quite a bit to read through and digest. I’ve spent quite a bit of time reviewing the JBoss demo apps as well, as they are all built on java 1.5 and use EJB3. Unfortunately, my current project is still java 1.4 and very old (over 4 years now), so I usually delve into the demo apps to get a grip on them. I’m quite envious of the simplifications to J2EE webapps and the new features like Annotations and Generics. The simplified for loop is also quite nice. It’s good to see the language gurus weeding out the syntactic obstacles in these updates.

Wow! It looks like the McCain amendment passed … overwhelmingly! This has to have something to do with Captain Ian Fishback and his courage. Here are a few links that cover the details. This is one of the unfortunately rare times I’ve felt like our government truly has a moral conscience. Let’s hope it continues.

• Washington Post story on the amendment.
• Another WP article.
• Today’s NYTimes story on the vote.
• The record of the senate vote on McCain’s amendment.
• NYTimes story on Captain Fishback.
• Andrew Sullivan’s extensive coverage of the vote and the issue.
• The Belgrade Dispatch blog item on the subject. This is interesting because the author quotes from sworn interviews.

An email I sent this morning to supportfishback at aol dot com. This man deserves everyone’s support for standing up to the unbelievable pressures of corruption.

Dear Captain Fishback,

I am a former Marine, one of many I’m sure, who truly does believe in the principles you outlined in your letter to Senator McCain. As a private citizen now, I have been saddened and disheartened by the many reports of abuse by our servicemen and women. While it would be easy to dismiss them for many reasons, it would be the wrong thing to do in a time of crisis for this country.

Therefore, it is with great pride that I read about your letter. Your actions are above commendation. Please know that many, many Americans stand with you in your attempt to restore traditional American values when our leadership seems to have forgotten them. It is the duty of all citizens, private or those committed to government service, to ensure that the actions our country are in alignment with our values. To the world, and to ourselves, we are what we do. Please keep the faith.

-Greg Rushton.

More on the subject here.

And then a message to my two senators:

Dear Senators Kenedy and Kerry,

I am writing to you to express my hopes that you will support the efforts of Captain Ian Fishback who recently sent a letter to Senator John McCain (link: http://www.washingtonpost.com/wp-dyn/content/article/2005/09/27/AR2005092701527.html). As a former Marine, his efforts struck a chord with me. His courage against the overwhelming obstacle of bureaucracy is nothing short of heroic. He deserves every ounce of support from every citizen of this great nation. Please do whatever it is that a senator can do to support Capt. Fishback in his efforts to expose the truth of his story.

Thank you sirs for taking the time to read this.

Gregory Rushton,
Randolph, MA

We had a fantastic time this afternoon at the Boston Children’s Museum. I left a little early from work and met the family there. The kids loved everything there. Lex was just crazy … running back and forth and crying out in joy … you’d think we kept him locked up judging from how happy he was to run free! They both loved the water thing where you put sponges and boats onto a sloped ring in which water is pumped. It was near impossible to drag them away from that one. After a McDonald’s break, they both went crazy again with the extra energy. Alisa, from my office, says McDonald’s is crack for kids. I think she’s not too far off!

I finally bit the bullet and moved to a full-featured photo gallery tool. In my case, I chose Coppermine. It has quite a few nice features, and I’ve liked the other sites that have implemented it. So, I spent a little while moving over the image folders to the coppermine directory, re-linking the posts with gallery links, and deleting the old qdig installation. While qdig is quick and dirty, there are just too many things that it doesn’t do.

The other reason I decided to do this was that I accidentally blew away a bunch of pictures from old posts that used to be part of a separate ‘photos’ section. I tried finding back-ups, but could only come up with about a quarter of them. So, I’ll be digging up the original photos and re-organizing some of those posts so that they point to the coppermine gallery.

Lastly, I’d like to update the coppermine theme with one that looks like the coffee cup theme I use for the main site. That shouldn’t be too much work … we’ll see. I did find quite a few coppermine themes at Shuttertalk.com.

After downloading it, uploading the package, and trying to configure it to use ImageMagick, I had some trouble so I went to my hosting provider’s support site … almost. I use totalchoicehosting.com, but instead went to totalhosting.com and pestered their tech-support people. To their credit, they did answer my queries promptly, politely, and accurately … despite the fact that I didn’t have an account with them. It turned out that totalchoicehosting has a nice feature where they will auto-install several packages for you. Coppermine turned out to be one of them … so I never had to go through the trouble in the first place.

My brother’s band, Thirsty, got a pretty decent review for their album, A Taste Is Not Enough. Go get ‘em Billy!

We had a fantastic time at Edaville Railroad yesterday! The kids both had a blast on the various trains and especially on the Thomas train. They have a huge assortment of trains and rides for kids.

We were quite nervous about the weather as Ophelia was supposed to drench us. It turned out to be a great day, nice and cool, for playing outside. Stephanie arranged the outfits, which was pretty cool. Everyone commented on how cute they looked. There was only one other boy dressed similarly, and he had a whistle and a stopwatch as well.

These pictures are from early last fall or late last summer. We had a blast taking the kids to the playground on Castle Island. It brought back all kinds of childhood memories for me. We’ll have to go back and enjoy some Sully’s clamstrips.

This little group of pictures is from last January when my mother called and invited us out to Chili’s. It seems she had about thirty $5 gift cards that she received from various mortgage brokers and banks over the past few months. So, from all of us at the Rushton household, thanks!

You can date these pictures because of Lex’s teeth. Note that he only has four at the moment in this picture, but has a good eight now and a few more cutting.

Here are some pictures my sister, Lauren, took last time she went to Taiwan back in the summer of ‘02. I’ve yet to send them to her after she returned my camera with all of these pictures. So, Lauren, here is a belated gift. I think the first picture in the gallery, the rainbow one, is one I took from the back door of our old house on DeCota Drive. I’m not sure though, and since it was in the same bundle as Lauren’s pictures, I’ll just pretend she took it!

Great editorial in the NYT today. Frank Rich really hits the nail on the head on so many issues. I finished reading that one after reading this in the Sunday Globe. I think, with all of the declining support for the war, the 2006 elections will see a pretty big change in the power structure of this country.

So, I’ve been painting the house for about a year now. I first started last summer with the chimney side and front sides of the house. I was able to scrape, sand, and lay two coats of primer on before the week I set aside ended. This summer, I’ve been able to squeeze in the same on the back and other side of the house. Yesterday, I finally put on a coat of the finish body color. It looks great! So, after many, many, many hours of stress and strain, the payoff is worth it. With the primer on, the finish coat goes on extremely easily. The only thing left to do after this is the porch … which I’ve left as a separate project because it has so many sliding doors. I have one more week off coming up in September, so I’m hoping I can finish up the body of the house and then do the porch.