Life as a Physicist

After the GLAST launch the other week I’ve looking at things space and astro when I surf the web (honestly - I don’t do it much! Especially at work! Especially while waiting for an ATLAS build!). I stumbled on this pod-cast on writing software for spacecraft.

It was a fascinating listen. Hans-Joachim Popp is the head of computing (CIO) at Deutsches Zentrum für Luft- und Raumfahrt, a company that makes software for German spacecraft. Some of the things that he said were jaw dropping in the context of the ATLAS software (and DZERO software). For example, averaged over the whole project about 0.6 lines of code are written per hour. They have code reviews, where the developer stands in a room and has to defend every single line of code. Their test code is a x12 longer than the actual code they write. They scan all of their code with a static analysis tool to look for “dumb” bugs.

Apparently the programming environment is similar for devices that run in intensive care units in hospitals. Comforting, I suppose. Modern critical airplane software has dueling versions of the code written (much like the space shuttle). In the case of the A380, apparently, one is written in C and the other in Ada* (other than this podcast this slide show was the only reference I could find).

Of course, the standard modern day project is only 20,000 lines of code. Voyager, which has been up there for 30 years now, has only 4 KB of memory for programming - so only 4000 assembly language instructions. He also mentioned that the ability to update the code in Voyager has been crucial to keeping the missing going this long.

I wonder how much of this formal methodology was followed for the GLAST LAT software? The trigger, for example? I remember Toby talking about how it was impossible to change because of all the paperwork and reviews involved in changing a single line of code.

One thing I’ll miss about returning to Seattle is I’ll loose this commute. Yeah, backwards. I’d rather be without the commute. But one advantage is I get to listen to all these podcasts (normally I listen to news and politics from the USA).

* I was in love with the idea of Ada when it first came out. I never wrote any code in it, but I thought that was the coolest programming language when it came out. Heck - it has multi-threading built in. Was over designed to catch errors early. Now, I’d hate it as being too restrictive.

** Imagine if all of this code was written at 0.6 lines per hour!?

Lots of things in life are acquired tastes. For example, I’ve been told beer is not something you are born liking. Other things you don’t have to be taught — like ice cream. Under that latter classification I would have included sun, the beach, and the ocean.

Apparently not.

Last weekend, with Paula out of town and my sister visiting, we decided to take Julia to the beach for the first time this year. She has been in the surf before, actually, but she was so young she probably doesn’t remember (she loved it). This time, as soon as we were at the edge of the sand my sister and I removed our shoes. She didn’t look happy. Then she got really unhappy when we removed hers and realized we expected her to walk on the sand barefoot. We finally had to put her shoes back on. And she was also quite vocally angry that we didn’t have out shoes on. She kept grabbing them and trying to get us to put them on. In the end we had to carry her across the sand.

Looking at the water made her cry. Finally, seeing all the other kids around her having a fantastic time, she allowed herself to be put down. But wanted to immediately walk away from the water and only with tightly gripping my hand (much tighter than she normally does).

Yes. We have a weird kid. But hey, look at the parents. We should count ourselves lucky, I guess.

There is an incredible article over on Wired right now, The End of Theory: The Data Deluge Makes the Scientific Method Obsolete. The article’s premise is that we now have so much data on hand that you don’t need to look at why things happen, just that they do happen. The author, Anderson, uses Google advertising as an example:

Google’s founding philosophy is that we don’t know why this page is better than that one: If the statistics of incoming links say it is, that’s good enough. No semantic or causal analysis is required.

Anderson then wants to extend it to science:

In short, the more we learn about biology, the further we find ourselves from a model that can explain it. There is now a better way. Petabytes [of data] allow us to say: “Correlation is enough.” We can stop looking for models. We can analyze the data without hypotheses about what it might show. We can throw the numbers into the biggest computing clusters the world has ever seen and let statistical algorithms find patterns where science cannot.

His basic thesis is that when you have so much data you can map out every connection, every correlation, then the  data becomes the model. No need to derive or understand what is actually happening — you have so much data that you can already make all the predictions that a model would let you do in the first place. In short — you no longer need to develop a theory or hypothesis - just map the data!

This definitely works for some things. For example, we have measured that aspirin works by basic data-mining. We know it helps reduce heart risk because of the many trials where that was measured. Imagine if everyone’s detailed medical history was available for data mining. What other hidden gems are there? Probably lots!

In particle physics we use this technique all the time to analyze our data. But I have several basic problems with the thesis that this can replace science.

First, in order for this to work you need to have millions and millions and millions of data points. You need, basically, ever single outcome possible, with all possible other factors. Huge amounts of data. That does not apply to all branches of science. Take medicine — testing a new drug compound means there is no data availible — you definitely don’t want to unleash it on millions of people to see what is going on. It might be much better to use the data mining tools to find something else that sort of does what you want, then isolate the compound. At that point you might know the agent, and the group of people it affects, and now you can study what is actually happening. Given that, you can now create something new and more powerful. Take the retro-virial drugs developed for AIDS. I don’t see how their development could have come out from anything other than understanding how AIDS works.

The second problem with this approach is you will never discover anything new. The problem with new things is there is no data on them!

Third is more subjective. I just can’t imagine living in a world where I’m told “well, that is the way it happens, so we just do it like that.” But WHY!? I couldn’t do it.

Anderson is right — we are entering a new age where the ability to mine these large amounts of data are going to open up whole new levels of understanding. Discoveries will be made using this technique alone. I predict Woody Allen was right — we will discover that chocolate milkshakes are a health food — and tools like this will discover those sorts of things. This is a new tool, and it will open up all sorts of doors for us. But the end of the scientific method? No — because that implies an end of discovery. And end of new things.

Update: Ars does a better job than I do (of course):

Correlations are a way of catching a scientist’s attention, but the models and mechanisms that explain them are how we make the predictions that not only advance science, but generate practical applications. One only needs to look at a promising field that lacks a strong theoretical foundation—high-temperature superconductivity springs to mind—to see how badly the lack of a theory can impact progress

Lately I’ve been getting science funding updates from an organization calling itself ASTRA (www.aboutastra.org and www.usinnovation.org). What do people know of this organization? Is it on the up-and-up? While the data on it seems focused at science, in the email all links are redirected through “http://x.jtrk12.net/” — which seems a bit suspicious - claims “this domain is used as part of a tracking mechanism in an e-mail marketing application”. Which means they are tracking to see if you clicked on their links in the email. Which makes me take a dim view. Anyone know?

My brother-in-law sent me this YouTube video by Johnny Lee showing off a poor-mans head tracking using Wii controllers and game. It is stunning. Watch it. He goes through a fairly careful description of how it works (and his web pages have descriptions of how it works).

So, when can we hook this up to the ATLAS event display?

I’ve not said much (or here) about the lawsuit that seeks to halt the turn-on of the LHC because it may produce a mini-blackhole or other object that devours our earth and the universe. In response to the press when the original suit was filed, CERN sponsored a safety review, which was recently released.

Ars has a great summary of the report:

The report’s conclusion is that, if the LHC were capable of destroying the earth, nature would have beaten us to the punch.

Read the report. It takes 96 pages to arrive at that pithy sentence. Or read the Ars bit which is a good summary. They end with:

Overall, it’s hard to read this report and not wind up viewing the apocalyptic fears as simply being poorly thought through. It was striking how clearly the worries over the LHC have parallels to the fears over biotechnology, which came up during our recent interview with Carl Zimmer. There too, billions of years of natural experiments and decades’ worth of scientific experiment should be informing our view of safety; for at least some segment of the public, that’s not happening.

This dataflow diagram showed up the other day (warning: VERY LARGE JPEG) in an ATLAS e-news article. It shows how we go from raw data in ATLAS to fully reconstructed objects. It is part of an article describing our reconstruction software performance.

On the left side of the diagram signals digitally recorded enter. We also have information about where in space those signal occurred, and, of course, in what detector (calorimeter, muon system, tracking, etc.). As the data moves from the left to the right it is slowly assembled into objects like charged particle tracks, muon candidates, electron candidate, etc. One thing to keep in mind is we never know with 100% certainty what we are looking at. We might be 99% sure we are looking at an electron, for example, but never 100%. Heck — when we start we don’t even know if those signals that appear in the detector are real: they could be noise! These uncertainties must be tracked along with the objects as they move from the left to the right. It takes of order 15 seconds to get from one side of that diagram to the other on a modern processor (we write data to tape at about 200 Hz).

I don’t know what the oldest bit of software is in ATLAS. We, of course, have all the software in a cvs repository. But this is the product of over 10 years of work (this is just the software, remember, not the hardware which has been going on even longer).

Lets hope that it works!

Agile programmers we are not!

Check this out:

At least parts of the non-password protected parts of the D0 web site have been copied and put onto the web. We don’t know why, but there are several nefarious possibilities. None of them good. At least some of the password protected links are redirected to (apparent) porn sites.

So if the URL in your browser’s address box is not http://www-d0.fnal.gov/… contact d0web-support@fnal.gov with a description of how you got there. The first report was via Google. So be aware.

That came across our DZERO news. I’d not heard of this technique before. I suppose they look for web sites that are pretty high in the search engine ranking and then spoof them in hopes that they can suck a few people in with links. I’ve heard of them doing it to popular bloggers before — but a particle physics experiment? I guess we have made the big-time!

Just booked my first flight after I arrive back in North America on August 31st. I’m going to miss Marseille.

I was mentioning how my internet connection is failing. A friend of mine has recently moved and decided to go cold-turkey (names not mentioned to protect the sane). My jaw dropped. I can’t imaging living without it. He claims he is getting to bed earlier, reading books again, going out, etc. Hmmm, maybe there is something to this.

I wonder if there is any coincidence between this and him securing a permanent position?