InsectNation

Science TV is too nice

Sun, 14 Apr 2013 00:00:00 GMT

Well well well, another blog post, eh? So soon: it’s only been… erm, two years. Oh. Well I never promised to be prolific. This one’s come about because I grumbled briefly on Twitter about the nature of (British) pop-science TV and immediately hit the restrictions of that medium. Twitter is a wonderful way to share neat things that you find online, and to make pithy soundbites & jokes (and for describing what you’re eating, the form of public transport that you happen to be on, listing film names with comic vegetable name substitutions…), but for exploring a non-trivial issue 140 characters is, to put it mildly, a limitation. I have difficulty fitting one of my normal sentences into 140 characters. So of course I came across as a whining idiot, prompting the reply “Yeah, we really should do more about how shit it all is. You don’t see that tone ANYWHERE” from Dara O’Briain. Well, not remotely what I meant, but who can blame him? So here’s an attempt at a more coherent and nuanced version that hopefully doesn’t make me come across as an anti-science, axe-grinding git. But perhaps as a slightly grumpy science nerd, which is fair enough.

Academic journals aren't helping us to do science anymore

Sun, 13 Feb 2011 00:00:00 GMT

Having recently concluded a long-ongoing saga to get the first ATLAS underlying event study both through the experiment’s internal review procedures and then into the perverse format demanded by the academic journal, Physics Review D, to which we submitted it, it seems an apt time to offer a few comments on the state of the sacred academic publishing and peer review process.

It's a bug, not a feature, René

Mon, 27 Dec 2010 17:28:02 GMT

I’ve had my attention drawn to this reply to a ROOT bug report, which I think highlights a serious problem with how the ROOT project interacts with the LHC experiments. In short, someone contacted the ROOTtalk mailing list to inform them that ROOT’s calculation of weighted means is incorrect if there are negative weights involved. There is a well-defined procedure for calculating weighted means, and in fact it’s dead simple. There’s no reason to not get it right. This is a bug report, about a significant numerical error in just about the simplest statistical quantity that anyone might want to calculate: any statistical analysis tool worth bothering with would provide a bug fix as fast as possible. So how did ROOT respond?

Well, the response from René Brun, the ROOT project leader, is that ROOT have “no plans to change this algorithm”. This is absurd: the LHC experiments depend on ROOT to provide them with accurate statistical results. Errors in ROOT mean mistakes in the LHC physics programme: this is not a feature request that can be turned down because it doesn’t fit with ROOT’s plans, it’s a bug which needs to be fixed. That ROOT’s management appears to see no reason to get simple calculations correct, and that errors this simple still exist after nearly 20 years of development, is an indictment of ROOT’s relationship with the LHC programme… and of how CERN and the experiments have dropped the ball in making ROOT a useful tool targetted to LHC physics. I’ve often heard comments that ROOT is all about empire-building and CERN politics rather than about good science – I’d rather not believe that, but examples such as this make it hard to draw a more appealing conclusion. The nicest thing I can say is that René apparently hasn’t understood that this is a bug. If I were feeling more conspiracy-minded I’d interpret it as saying that he doesn’t care if ROOT is right, as long as it’s used. And it is certainly used – ROOT has a virtual monopoly over LHC physics data analysis, without delivering the sort of quality that such a position demands.

Back to life

Fri, 24 Dec 2010 18:55:57 GMT

I’ve never been the most active blogger, but 2 years between posts seems a little excessive, even to me! I wish I could explain the cornucopia of reasons for this, but I’ll just point a couple of accusatory fingers at the extraordinary busyness of life (in the intervening time I moved to Edinburgh, the LHC restarted, and my working life has generally been batshit insane) and general frustration at my server setup. You may also be frustrated with the slowness of this server: turns out that running a mail server and a Rails application on a 256 MB virtual server puts me deep into the swap memory zone and site performance accordingly drops into the region marked “painful”. I’d have loved to fix this 2 years ago, but a) I’ve written enough web apps in the past to not want to make another half-assed one, and b) did I mention work being batshit insane? Anyhoo, someone asked me at a recent meeting when I was going to start blogging again, and after the initial shock of discovering that I have some sort of niche audience I decided that I should start venting my spleen in more substantial ways than the 140 chars offered by Twitter.

A bit of recent server upgrading means that this site is not quite as slow as it has been – I’m enormously impressed by the service from Slicehost, by the way – and I’m going to try and replace Radiant with something a little more fun, speedy, and memory-efficient in this little pre-2011 gap. Suggestions of CMSes/blog engines with user comments, picture galleries, code highlighting support, etc. and support for static content (such as this site’s Cambridge night climbing content) would be much appreciated. Oh, and because I’m a picky person and have not found Ruby/Rails to be a terribly pleasant development experience, being based on Python would also be a big bonus!

Removing Beamer nav widgets

Wed, 21 Jan 2009 17:24:06 GMT

Here’s a handy tip for all the people I see giving talks made with the super-genius LaTeX Beamer package, all of whose slides have a row of never-used navigation widgets (back, forward, start, end, next frame…) getting in the way of the slide content. It’s dead easy to remove them, and then (if you’re like me) you can finally sleep at night. Just put this in your Beamer document preamble:

\mode<presentation> {
  \setbeamertemplate{navigation symbols}{}
}

Voila — no more silly nav crap! You will now be the envy of obsessive-compulsive, LaTeX fiend scientists everywhere you go!

A week in the land of contradictions

Sat, 22 Nov 2008 01:08:27 GMT

It’s the end of another busy week. Work life has been busy to the point of insanity recently, burrowing its way into every available bit of spare time… if you consider every weekend since mid October to be spare time rather than “essential time”, that is. I’m actually inclined to the latter view: while happy to declare that my work is captivating and inspiring, some downtime is definitely needed. In the last month I’ve been to two week-long conferences in Italy, snatched a week back in Durham and then spent the last week in Chicago. After one more week in Durham, in which to pay some attention to demonstrating and marking Frank’s excellent new computational physics course, I’m off on my travels again, this time to CERN for a week. And then it’s Christmas and skiing; January is looking a bit crazy, and I’m trying not to think about that. Fortunately Jo has been a star and given me some (unearned) slack, but this schedule isn’t really fair on either of us: I think I’ll be imposing a more restricted travel schedule in the New Year and hopefully sending some collaborators out to do the salesman thing instead ;)

Anyway, reflections on the past week: I have to say, I’ve really enjoyed Fermilab. Most people seem to bitch about the “boring site”, the strip malls of West Chicago, the weather and anything else that springs to mind, but I must be a bit funny in the head because I like it all. Okay, not the strip malls — a bit of restriction on the suburban planning process would have been welcome — but here’s a list of hat I’ve been up to, other than giving talks and coding up experimental analyses in Rivet:

Burying the hatchet

Mon, 17 Nov 2008 14:03:55 GMT

“Ah, the famous Andy Buckley. Or perhaps infamous, no?”. When a dapper French gent at a statistics conference addresses you this way, I guess it’s normal to feel a bit perturbed, particularly when you’ve devoted a serious chunk of time in the last few years to publicly demonizing their work. Really, I suppose it’s maybe a minor miracle that Rene Brun and I haven’t crossed paths before now — although I guess this is largely to do with me being keen to avoid a fight.

XML: restraining the knee-jerk reflex

Mon, 10 Nov 2008 21:57:36 GMT

XML is a useful technology, sometimes: that’s about as positive as I can be about it these days. While there was a period when I got quite excited about the idea of a standard syntax for, well, everything, time tempers such enthusiasm. See, 90% of the time, XML is just too damn cumbersome. When what you want to say is

Param1 = 3

or something of that complexity, then having to write

<param name="Param1" value="3"/>

is just a bit hefty. Anyone who’s ever tried using Ant or Maven will surely sympathise with the idea that XML is a pain in the arse way to write make-files. And XSL transforms? Phew, glad I’m not going back into that arse-end of software engineering gone mad. It’s also a pain in the arse to read XMLified data in C++ or Fortran. Hell, even Python and Java make you jump through SAX or DOM-shaped hoops in their lowest common denominator implementations! Frankly, XML is a serious candidate for “no silver bullet”-type debunking: merely wrapping everything in angle brackets actually solves nothing, even if it looks totally SOAP-AJAX-Web 2.0, dude. Much of the time, something simpler is quite enough.

The God Delusion

Sun, 09 Nov 2008 23:17:16 GMT

I’ve recently finished reading Richard Dawkins’ The God Delusion. I was pretty determined to not read it when it first came out since a) I object to specifically indulging in writing that I know I’ll agree with — I suspect that searching out compliant opinions leads to foam-mouthed Daily Mail reader behaviour and obstinate old man disease, and b) Herr Dawkins has been on a bit of an ego/PR trip in recent years, in an area which he’s not really all that qualified to talk about. But then, as he points out in the book, it’s not like religious “authorities” are really qualified to say anything meaningful about well… anything, so when Jo got a copy, I decided to steal it and finish it before her ;)

Bundling LaTeX for arXiv submission

Fri, 26 Sep 2008 16:12:11 GMT

I always have trouble submitting papers to the arXiv, on account of my tendancy to use a whole bunch of style files etc. that aren’t in the standard arXiv collection. They aren’t usually in my document source directory, either, but are spread around my system in various texmf trees. Accordingly, getting papers to upload is a pain (and if you try to upload just a PDF, arXiv detects that the PDF was made with TeX and refuses to accept it! Dang, foiled!)

So here’s the method that seems to work for me.

Get the snapshot package, and use it in your document with the usual \usepackage{snapshot}
Run latex etc. on your document until it’s happy (note, I use pdflatex pretty much exclusively these days, but arXiv will use good o’ DVI-producing latex, so that’s what you need to use when producing your submission)
If your document was called mydoc.tex, you will now have a dependencies file, mydoc.dep. This can be used to bundle your source files for submission. To do this, get bundledoc.
Run bundledoc on the deps file — you may need to provide an explicit config file. Here’s my command: bundledoc --config=$HOME/local/texmf/tex/latex/bundledoc/tetex.cfg mydoc.dep
You now have a tarball or zip archive, depending on whether you used the TeTeX/TeX Live or MikTeX config file. This should be okay for uploading to arXiv. Happy bundling.