Posted by: Jamie | November 9, 2011

West Coast Adventures, Part 1


Well, here I am. I’ve got my badge and my keys and now I feel like a “real” scientist. Tomorrow night I’ll for real and true move in to my California apartment.

This is the third day of the BaBar collaboration meeting. I have met a bunch of colleagues in person, and I’m a bit overwhelmed by all the physics.

The time change treated me well, although it is causing me to have to rethink my raiding schedule. :) Tonight will be the first meal I have to locate on my own.

There’s nothing very exciting to say yet, but it’s good to set the stage. Here goes!

Posted by: Jamie | August 24, 2011

A bit on the large side.

So I am finishing up a little project for the ATLAS experiment at CERN. Part of what I’m doing involves making minor calculations of the detector geometry. I’m sitting here looking at the numbers for the size of this detector and I’m just a bit overwhelmed. The outermost edge of the outermost muon detector is 13 meters from the center. 13 meters is big. I am having trouble getting my mind around how big. Here are some things I looked up to help me get an idea of the size of 13 meters:

  • For starters, anything that is 13 meters is 42 feet. (Can we just switch to the metric system already and join the rest of the civilized world?)
  • 7 people over six feet tall, standing on each other’s heads, add up to 13 meters.
  • The wingspan of a Cessna 172 is 11 meters.
  • Four lanes of US highway add up to 14.5 meters.
  • The tallest male giraffe ever recorded stood “only” 6 meters.
  • The dinosaur Giraffatitan is believed to have been able to raise its head 13.5 meters in the air.
  • Depending on the height of the rooms, a 4 or 5 story building is about 13 meters tall.
  • The letters in the iconic Hollywood sign are each 14 meters tall.

Hmm. So that’s 13 meters. The radius of this muon detector. So, you know, double all that for the actual height from the ground. Sheesh.

Posted by: Jamie | April 7, 2010

Bad Science Journalism, Episode 1

I have decided to keep track of instances of bad science journalism that get my hackles up. Usually, the things that bother me most are very simple things, and are probably even covered in the AP Stylebook. I should check that… Anyway. From FoxNews:

“Freaky Physics Proves Parallel Universes Exist”

ZOMG NO WAI!!!!!!!!!1!!!1111!

You’re kidding me, right, Fox News*? Now, for starters, don’t get me wrong. This experiment? It is badass, amazing, and way freaky.

Scientists in California have done something astounding. They’ve shown that physical laws thought only to rule in the mysterious realm of atoms and electrons can also apply to stuff you can actually see. (NPR)

They managed to get a visible object to exist in a superposition of quantum states – essentially behaving two different ways simultaneously. Those two ways – moving and not moving – would be mutually exclusive under classical laws of physics.

But back to the thing that annoyed me. Let me list, for you, the headlines from some other news sources.

  • Macro-Weirdness: “Quantum Microphone” Puts Naked-Eye Object in 2 Places at Once | Scientific American
  • Scientists supersize quantum mechanics | Nature
  • A Mechanical Device Behaves as a Quantum System Right Before Your Eyes | Popular Science
  • Quantum Physics Used to Control Mechanical System | Wired
  • Tales from the quantum frontier | MSNBC
  • Team’s quantum object is biggest by factor of billions | BBC
  • Quantum Physics Leaps Into The Visible World | NPR
  • UCSB Researchers Have Created a Visible Mechanical Device That Behaves as a Quantum System | Convergence

Do any of those say anything about parallel universes? No. Do any of them use the word “prove”? No – they sure as hell better not!

Let me explain what the Fox News article does that the other articles don’t, which they seem to think justifies their ridiculous headline and narrative. This article devotes a single paragraph to a description of the experiment (emphasis is in the original):

UC Santa Barbara’s Andrew Cleland cooled that paddle in a refrigerator, dimmed the lights and, under a special bell jar, sucked out all the air to eliminate vibrations. He then plucked it like a tuning fork and noted that it moved and stood still at the same time.

Then they take a quote from Cleland:

“When you observe something in one state, one theory is it split the universe into two parts,” Cleland told, trying to explain how there can be multiple universes and we can see only one of them.

And then they run off to talk to a couple of other physicists who are willing to provide quotes that can be mined to support this pet narrative about proving parallel universes. I think my favorite part is where they directly contradict the headline within the text of the article (emphasis is mine, this time):

Sean Carroll, a physicist at the California Institute of Technology and a popular author, accepts the scientific basis for the multi-verse — even if it cannot be proven.

Yes, this research is awesome. Does it prove the existence of parallel universes? No. It is the first in what I hope will be a long series of experiments replicating and verifying this result.

Fox News’ headline is problematic because it is misleading about what science can and cannot do, and has and has not done. You know how annoying it is when the media jumps on the latest nutrition science fad? Fat is bad for you! Eliminate fat and you’ll be healthy. No, wait! Cholesterol! Now trans fats! Oh look, someone said chocolate is good, rejoice!

Science takes time to work. It doesn’t really prove anything. It collects a body of evidence and makes predictions about the natural world. Hopping on a new result – before it has been confirmed by repeated experiments, before it has been absorbed into the body of evidence and incorporated into existing results – does nothing useful. In fact, it is capable of harming the reputation of science (even though science itself isn’t at fault). When an article jumps the gun, or exaggerates a result, the public sees the science as being misleading, rather than the reporting.

This particular example is especially frustrating to me because it is an extreme example of this problem. The multiverse/parallel universes theory has not been proven. By a long shot. And to say otherwise is utterly irresponsible.

*I know, I know, it’s Fox News. Are they really a reliable source of anything? Still.

Posted by: Jamie | March 24, 2010

Finding Ada in Physics

Today, March 24th, is Ada Lovelace Day. Rather than attempt to explain it myself, let me just quote from the website:

Ada Lovelace Day is an international day of blogging to celebrate the achievements of women in technology and science.

The first Ada Lovelace Day was held on 24th march 2009 and was a huge success. It attracted nearly 2000 signatories to the pledge and 2000 more people who signed up on Facebook. Over 1200 people added their post URL to the Ada Lovelace Day 2009 mash-up. The day itself was covered by BBC News Channel,, Radio 5 Live, The Guardian, The Telegraph, The Metro, Computer Weekly, and VNUnet, as well as hundreds of blogs worldwide.

If you’re unfamiliar with Ada Lovelace, well, she’s 100% awesome:

Augusta Ada King, Countess of Lovelace was born on 10th December 1815, the only child of Lord Byron and his wife, Annabella. Born Augusta Ada Byron, but now known simply as Ada Lovelace, she wrote the world’s first computer programmes for the Analytical Engine, a general-purpose machine that Charles Babbage had invented.

Ada had been taught mathematics from a very young age by her mother and met Babbage in 1833. Ten years later she translated Luigi Menabrea’s memoir on Babbage’s Analytical Engine, appending notes that included a method for calculating Bernoulli numbers with the machine – the first computer programme. The calculations were never carried out, as the machine was never built. She also wrote the very first description of a computer and of software.

Understanding that computers could do a lot more than just crunch numbers, Ada suggested that the Analytical Engine “might compose elaborate and scientific pieces of music of any degree of complexity or extent.” She never had the chance to fully explore the possibilities of either Babbage’s inventions or her own understanding of computing. She died, aged only 36, on 27th November 1852, of cancer and bloodletting by her physicians.

Women have made great strides in representation in the sciences since Lovelace’s time. In many science fields, women comprise 50% or more of the population. In physics, however, the inclusion of women has risen very slowly – such that as of this time only 20% of physicists are women, overall. If one separates the demographics into levels of education, each higher level has subsequently fewer women. Ethnic minorities face still greater under-representation.

It is for this reason that when I think of physicists who are women and to whom I look as a role model, the first name that comes into my mind is that of Dr. Patricia Rankin. Professor Rankin established herself as a particle physicist, eventually coming to work on questions of matter/antimatter asymmetry in the universe at the University of Colorado at Boulder. As extraordinarily interesting as I find that research, it is not the reason why I want to bring her to your attention.

Currently, Dr. Rankin serves as a Faculty Director in the Provost’s office at UC Boulder and is the PI on a project called LEAP. I’ll quote from her faculty page (I have made a few grammatical edits):

[Her] current focus is on a program to increase the number of women in leadership positions in the sciences and engineering. This project is supported for five years by the NSF – more details can be found at the LEAP web site. LEAP is focused on working with all faculty members – irrespective of their gender or discipline – to improve their professional skill set. Workshops funded through LEAP have sessions on topics such as time management collaborative leadership and conflict management. Research studies cover topics such as networking, salary equity and demographic inertia studies.

I first met Dr. Rankin at the 1st Annual Midwest Conference for Undergraduate Women in Physics, in 2008 at the University of Michigan, Ann Arbor. She gave a presentation which summarized for us the overwhelming data indicating that women and minorities face real, though generally unintentional, biases based on their gender and/or skin color in attempting to navigate through their chosen profession. I felt as if I’d been struck by lightning. Here was an explanation for the confusion poking at the back of my mind. Here, an explanation for why so many of my friends had opportunities simply fall into their laps. Opportunities that I had to seek out and cultivate. I was energized. Dr. Rankin offered an explanation, a sense of no longer being alone and at fault, and – best of all – she offered solutions. Rankin has worked with the physics department at UC Boulder to make impressive strides in improving the department’s inclusiveness. And she isn’t stopping there. Dr. Rankin is actively seeking to improve the situation for women in physics. Here is her vision for the LEAP program, in her own words:

LEAP began in January 2002, after receiving $3.5 million in funding from the NSF as one of the first projects funded through the ADVANCE initiative. This funding was matched by a further $900,000 from the University of Colorado, Boulder.

We work with the premise that models of effective institutional change emphasize the need to work at multiple levels of the organization on multiple aspects of the problem. LEAP therefore has programs aimed at individuals and at the department level, as well as activities promoting changes in policies at the highest levels.

The goal of the leadership workshops is to give faculty the skills they need to thrive within the institution. In the process, we believe that faculty will develop an understanding of how the institution works and of how it can be changed. The primary goal of the coaching program is to improve the support structure for junior faculty and to help them achieve success at the institution. These are key LEAP program elements.

The leadership workshops and the coaching program, while focused on individuals, are producing a growing community of people who are realizing that they share a vision of a better CU. The goal is to develop an institutional environment at CU within which different styles and different approaches are not only accommodated but encouraged. While LEAP cannot eliminate problems associated with “two-career couples”, raising a family while pursuing a tenure track appointment, or moving from an instructor position to the tenure track, it can provide a framework within which to hold discussions on these important issues. It can also help empower faculty to work to create solutions within the system.

As the program matures, it is broadening its reach and growing in influence. LEAP is working to formulate specific policy changes and promoting the adoption of practices that promote LEAP’s core goal of changing the environment at CU. These include working on the implementation of a professional code of conduct for faculty, making chairs training compulsory, addressing changes in recruitment practices, and encouraging the centralization of faculty development programs.

It is our hope that LEAP will have a permanent impact on the institution and beyond by producing a set of best practices for any institute to follow in fostering an inclusive environment.

In addition to her presentation at the Midwest UWiP conference, the physics department here at the University of Louisville invited her to come speak at our weekly colloquium. I was fortunate enough to attend a luncheon with her and various department chairs, where she offered advice on, for example, how to address a department’s willingness to accommodate a two-career couple without breaking hiring laws or scaring off potential hires who think they will be discriminated against for wanting to start a family. Her presentation covered the evidence for unconscious bias and was attended by administrative-level faculty from across the campus.

Dr. Rankin’s UWiP presentation was the first inkling that I ever had that I could do physics and activism at the same time – a notion that has subsequently been the driving force behind my career plan. Whether she knows it or not, I will eternally be grateful to her for showing me that I can be an agent for change, and a physicist, and be successful.

Thank you, Dr. Rankin, for being an amazing physicist, an amazing woman, and for believing fervently that there should be nothing odd about being both of those simultaneously.

Posted by: Jamie | March 8, 2010

Wikis Win

In my last post, I discussed a major issue I was having with the ATLAS TWiki in terms of clarity for someone unfamiliar with the computer side of the research.

Today I was again trying to work through the instructions on the site and ran into a problem. The instructions told me to make a script and make it executable. That instruction was followed by some code that I recognized as being the commands for running the analysis program – obviously not the commands to make a script! So I was stumped. How does one make a script, and what does the analysis program have to do with it? Fortunately, one of our computer-y types was in the lab, and I asked for his help.

Since the TWiki is, in fact, a wiki, I decided to register to be able to edit it. Anyone with a CERN login is able to sign up. I changed the instructions to be clear enough that pre-help Jamie could have followed the directions.


First prepare a small job script, suh as myjob, and make it executable (chmod +x myjob):

source ~/cmthome/ -tag=15.3.0
cd ~/testarea/15.3.0/PhysicsAnalysis/AnalysisCommon/UserAnalysis/run

Now you can submit it to the batch system via:

> bsub -q 1nh myjob


First prepare a small job script, such as myjob, by creating a text document which contains the following:

source ~/cmthome/ -tag=15.3.0
cd ~/testarea/15.3.0/PhysicsAnalysis/AnalysisCommon/UserAnalysis/run

Make it executable:

> chmod +x myjob

Now you can submit it to the batch system via:

> bsub -q 1nh myjob

Make sure you run the bsub command in the same directory as your script.

Maybe this is a trivial change, and would seem like a condescending level of explanation to someone with more computer experience. But had the instructions read like this initially, I would not have needed to interrupt someone else’s work to continue with my own. So. Wikis win! =P

Posted by: Jamie | March 1, 2010

Procedures vs. Understanding

My advisor has recently begun to work with the ATLAS project. My first year of courses are almost over, and so I’m beginning the “Getting Started” process with ATLAS, as well. I am extremely impressed that ATLAS has its own wiki, which gives instructions to collaborators on how to get their account set up, how to start working with the analysis program, etc. If I’d had something like this when I was trying to finish up my research with Fermilab, I’d have been golden.

Being able to follow a procedure to get everything set up is great, don’t get me wrong. But I’m running into a problem. I followed the procedure for modifying their HelloWorld program. And it didn’t work. That particular page didn’t come with troubleshooting instructions. With the help of my advisor, we got it working (as is so often the case with computers, we can’t see anything that I did wrong the first time). But, see, what if I were the advisor? Or what if my advisor weren’t so willingly helpful? What if I didn’t have Linux-knowledgeable lab-mates?*

The ATLAS wiki has appendices with basic Linux commands. That’s nice. They’re really basic commands. They don’t explain how they integrate with what you’re trying to do in the instructions. More importantly, I think, they don’t tell you how not to use the commands. Let me try an example to see if I can’t be more concise.

Go to your testarea and check out the AthExHelloWorld package:

> cd testarea/15.3.0
> cmt co -r AthExHelloWorld-01-02-00 Control/AthenaExamples/AthExHelloWorld

Navigate to the src directory

> cd Control/AthenaExamples/AthExHelloWorld/src

and edit the C++ file HelloAlg.cxx for instance by adding this to the initialize() method:

ATH_MSG_INFO ("Hello ATLAS User");

and save the file.

Now build this package:

> cd ../cmt
> cmt config
> gmake

Go back to the UserAnalysis package and rerun Athena:

> cd ../../../../PhysicsAnalysis/AnalysisCommon/UserAnalysis/run

You should now see this somewhere in the output:

HelloWorld INFO Hello ATLAS User

Okay, so if I do everything exactly as printed in that procedure, where is the likely culprit when my output doesn’t contain the indicated line? What did gmake…make? Where I can find a visual diagram of the folder (directory, whatever) hierarchy?

So, I was thinking it would be really handy if the wiki incorporated some sort of mouseover functionality. If I mouseover the word gmake in this procedure, it could tell me what file is being executed. Even better, there could be a note about what happens if I accidentally use the gmake command in the wrong directory. (Does anything bad happen? How badly can I manage to break this setup just through my own lack of familiarity with the system?)

I don’t deny that becoming familiar with the operating system and jargon of this research community is vital, and is often best done through a hands-on approach. But I think including resources directly where they’re relevant, instead of just generically tacked on at the end of a website, is going to make that process a lot more efficient. And, frankly, there are enough people working on this project who are intimately familiar with the intricacies of Linux and Athena for whom it would be relatively simple, if time-consuming, to add these little helper notes.

Maybe I’m being lazy. But you know what? I’m an experimental physicist. I want to get my hands dirty and do research. I think it’s reasonable of me to ask that I not need a computer science degree (or equivalent tinkering time) in order to do that research.

*While experiences will vary, my experience with getting help from non-faculty people** who “get” Linux has thus far been overwhelmingly negative. It has been my experience that the go-to Linux person in a group has spent so long using the system that the syntax, steps, and functions are intuitive for them, and they haven’t yet developed the ability to properly explain to a newbie what needs to be done. More often than not they will simply steal the mouse or keyboard from you, because it is – correctly – faster for them to just fix it themselves. I understand the feeling. I’ve tried to help my grandparents troubleshoot minor problems in Windows. I have used some form of Windows OS for literally as long as I can remember. So I get it, and explaining it is hard. But I also try to keep in mind that if they don’t do it themselves, they’re not going to remember what they did, and so they’re not going to be able to modify what they did to adapt to new problems in the future. Thank you, Linux fankids for being a valuable resource. But screw you for being impatient.

**I say non-faculty people because faculty, in general, have spent a lot more time teaching or explaining to subordinates and in my experience have much more highly-developed methods for passing on the needed information without coddling.

Posted by: Jamie | February 26, 2010


Riding the bus home today, I was sitting near a mom and her three kids. The kids were quite obviously bored out of their wee minds. I found myself wishing I had some of the swag I got from the Sigma Pi Sigma Congress. One of the booths there had some nifty activity books for kids (maybe the AAPT?). Of course, then I’d have to always be carrying around activity books and crayons, but still. I’d have been able to promote science to bored bus-kids! ^_^

In other news, at the urging of my proto-advisor, I have a draft in progress about actual real “science” I’ve been doing. Stay tuned! :)

Posted by: Jamie | January 28, 2010

Lofty Ideals

Thanks to a recent speaker here at my uni, I have a new favorite quote.

Dr. Robert Wilson (Fermilab’s first director), when testifying before the Congressional Joint Committee on Atomic Energy, was asked by Senator John Pastore how a multimillion-dollar particle accelerator improved the security of the country. (This was in 1969 but that question sure sounds familiar.) Wilson replied that it had nothing at all to do with security. When Pastore pressed him further, Wilson responded (emphasis mine):

It has only to do with the respect with which we regard one another, the dignity of men, our love of culture. It has to do with: Are we good painters, good sculptors, great poets? I mean all the things we really venerate in our country and are patriotic about. It has nothing to do directly with defending our country except to make it worth defending.

Posted by: Jamie | January 25, 2010


Logo depicting laser beams and the words, "LaserFest: Celebrating 50 years of laser innovation."Preferred to Oktoberfest by 3 out of 4* scientists! No, really! I mean, I love me some booze, but if someone offered me the choice between a laser pointer (it would have to be green, though) or a beer, I would definitely take the laser. I might have to think about it really hard if they offered me a dirty martini, but a nice green laser pointer is still an essential component of my Scientist’s Arsenal that I have yet to acquire.

ANYWAY. LaserFest! It is happening! You might find yourself asking, “Why, dear god, why?” The answer to that is that it is now 2010 and, therefore, 50 years since the LASER (it’s an acronym but we seem to have given up on capitalizing it) was invented. In that time, laser innovations have become an integral part of the science and technology that surrounds us, serving functions both mundane (like the bar code scanners at grocery stores) and arcane (like using lasers to cool atoms down to near-absolute zero temperatures).

If you are so inclined, you can find a LaserFest event near you. The anniversary celebration will be going on all year. I checked the map and it doesn’t look like there’s anything planned for the US Midwest, yet. I will see if I can remedy that. In the meantime, check out the website for some cool info on why lasers are awesome.

Hat-tip to Uncertain Principles.

*Also, 38.7% of all statistics are made up on the spot.

Posted by: Jamie | January 16, 2010


Okay, so I have done about fifteen minutes worth of “research” with Google and as far as I can tell there is no existing justification for qualifying and/or preliminary exams (I mean, of course, aside from, “Well, that’s how we’ve always done it,” or, “I had to take quals, so these kids should take quals, otherwise they’re not real Ph.D.s”).

Here are my thoughts.

1) If you were accepted into the program and offered money and all that, presumably they think you’re good enough to succeed, and trust that the grades you received from your undergraduate institution are meaningful. If not, why did they accept you?

2) If you passed all your graduate coursework with the minimum or better grades required for your program, presumably your institution believes those grades mean something. If not, why do they care what grade you get in the classes?

3) Given the circumstances in 1) and 2), there is absolutely no logical reason for a department to administer either preliminary or qualifying examinations, as their existence essentially renders moot any previous assessments of your work.

Therefore, I declare that we must put a stop to this heinous practice immediately, as it is contributing to the declining value of letter grades everywhere! It is also contributing to the declining value of my Saturday mornings, which, depending on your perspective, might be considered even more heinous.

I think the University of Texas at Austin’s Department of Physics has got it right. Instead of quals, you take “core classes” (I think there are four) that cover the main topics in the field (Mechanics, E&M, Quantum, and probably Thermo or something like that) in addition to more elective-type courses. The classes are harder than usual and you have to get a particular grade in them. But if you pass them properly, then it is assumed that you both a) had sufficient preparation from your undergraduate studies and b) are sufficiently prepared to continue with your research and your career as a physicist, as per the standards of that university. Unlike other universities, these core classes are not separate from your standard coursework – thus eliminating the ridiculous redundancy that is your average qualifier.

Excuse me now, I have to go put away this soapbox.

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