May the 4th be with you at the Hayden Orpheum (the right kind of Hayden)

Last Sunday (May the 4th), we went to see the original Star Wars trilogy on the big screen at the Hayden Orhpeum in Cremorne, North Sydney.

It was a lot of fun, as the Orpheum is quite an old cinema and really embraced the whole Star Wars Day thing. The show started with Darth Vader playing music from the Star Wars soundtrack on a Wurlitzer organ and was followed by a competition for the best Star Wars fancy dress before the films themselves.

(The winner was a very cute miniature Boba Fett.)

I must say, it was great watching the old films on the big screen again. They definitely show their age a bit but it was fun watching with an appreciative audience. The good thing about Star Wars fans is that they are perfectly aware that the films are full of cheesy (if charming) moments, and so there was a lot of applause and occasional laughter at some of the hokier lines and innuendo.

Sitting in a classic cinema watching some classic films did make me realise a couple of things, though.

Firstly, modern cinemas are better. They should be, given how much more expensive they are, but seven hours sitting in an old-style cinema seat really made me appreciate modern “stadium style” seating. (Though I’ve never understood why they call it that, given how uncomfortable stadium seats are!)

Secondly, don’t mess with a classic. The most unfortunate thing of the day is that they did not actually screen the original films - instead we got the “Special Edition” versions.

The last time I saw all three films at the cinema was when the Special Editions were released. At that time, the novelty value masked how terrible the changes actually were. This time, it had been quite a few years since I’d last seen the films and the changes - and how bad they were - really stuck out.

At best they were pointless, such as the extra Tatooine CGI sandtroopers on Dewbacks. However, most of the additions actively made the films worse. Slapstick CGI animals and droids in Mos Eisley, during what should have been a tense scene? Bad. CGI addition of “wonderful human being” Jabba the Hutt in Episode IV? Bad. Making Greedo shoot before (or possibly concurrent with) Han Solo? Bad. Bad. Replacing Sebastian Shaw with Hayden Christensen at the end of Return of the Jedi? Bad. Bad. Bad.

In a way, it was actually slightly ironic that we saw the films in the Hayden Orpheum - the Hayden Christensen replacement got the only audience boo of the night. Why, George, why‽‽

The Special Edition nonsense was not a major distraction, though, and I would still recommend the triple bill on a future Star Wars Day. (Although I think I have my fix for a few years!) The final thing it made me realise is that Star Wars is such a cultural phenomenon, enriched by many of the spin-offs (especially those that take the piss), it really is deserving of a day of celebration.

May the Fourth be with you, always.

Loving Helen Arney's animal love

Today was my last undergrad lecture - possibly my last ever at Southampton. It was on "Reproductive Strategies" and so I thought a post relevant to animal reproduction was in order.

Although I missed them the first time around, I came across the Rationalist Association's podcasts a while back, including snippets from "The Nine Days of Godless Christmas" from 2011. The best, in my opinion, is Day 6, which features singer and comedian Helen Arney with a love song inspired by the habits of animals. It's well worth a listen.

You can find the lyrics and buy a high quality version of the track at Helen Arney's website. My favourite part (spolier alert!):

"Let’s make love like Angler Fish, yeah
It’s kind of complicated but it’s worth it
You use your highly developed olfactory sense to swim towards me for several days
And then you bite me
That releases an enzyme that then dissolved your skin & your flesh & your… fins…
Leaving only a pair of genitals attached to the side of my body
For me to use
When it’s convenient."

Funny and educational!

Geek architecture at Cold Spring Harbor Laboratory

As well as the geeky sculptures, the Cold Spring Harbor Laboratory has some good geeky architecture. The tower of the Beckman Laboratory (above) stood out to me as a geneticist, with the four nucleotide abbreviations (g, a, t, c) on its four faces. There was a bit of a missed opportunity with the staircase in the middle, though, which is just a spiral up a central column rather than a double helix (right). Oh well.

As it happens, the conference was too engaging to do much exploration, so I'm not sure if it's a repeating theme across campus. If I get to go back, I will have to find out. Even if there isn't, though, it's a charming place to wander about. Apparently, it used to be a whaling station and many of the labs are in what look like large colonial houses, such as the Luke Building (below).

Geek Sculpture at Cold Spring Harbor Laboratory

A couple of weeks ago, I attended the 2013 "Systems Biology: Networks" meeting at Cold Spring Harbor Laboratory, New York.

Cold Spring Harbor Laboratory has a beautiful little campus on the north shore of Long Island, about an hour or so east of New York city. One of its charms is the many pieces of sculpture dotted around the place, including "The Waltz of the Polypeptides" by Mara G. Haseltine, which we passed each time we travelled between our cabin dorm and the talks or food.

As the plaque states:

"The Waltz of the Polypeptides" is the artist's impression of the birth of a protein. As five ribosomes travel the length of a messenger RNA, a protein is created.

It's quite cute and the large subunit of the ribosome looks like it wants a hug once it's released from the mRNA, as seen to the right of the above photo.

The protein in question is identified as Beta Lymphocyte Stimulator (a.k.a. BLyS a.k.a. B-cell activating factor (BAFF)), officially called tumor necrosis factor (ligand) superfamily, member 13b (TNFSF13B). A separate sculpture of the protein backbone sits on the other side of the path. I like it!

(I stayed on for some holiday after the conference - hence the lack of posts recently - so expect a few more travel posts soon.)

Don't panic!

And if you do, Google can help... (Happy Birthday, Douglas Adams!)

The joys of intext and other Google search tips

Every now and then I revisit my growing pool of half-written blog posts and see if any are worth salvaging. One such post is some useful Google search tips from John Todesco.

His post from last summer, How to solve impossible problems: Daniel Russell’s awesome Google search techniques, was sent to me by a colleague at work. There are lots of useful tips in the article but a few in particular stood out for me, including a couple of things I knew but a couple more that I had wondered about but never got round to looking up for myself (modified from John Todesco's post):

Use quotes to search for phrases.

• Typing “San Antonio Spurs” will show you the websites with the phrase “San Antonio Spurs.” If you don’t use the quotes, Google will search for the terms “San,” “Antonio,” and “Spurs” individually and you might miss pages related to the basketball team.

Use OR but not AND.

• Don’t bother typing AND in your search queries – Google treats it like any other word.
  
• OR in all caps actually works. OR is great for finding synonyms and boilerplate language. Typing “Smith denied” OR “Smith claimed” OR “Smith argued” will find more pertinent websites about the controversy involving Smith.
  

Use minus, not NOT.

• Avoid using NOT if you want to exclude a search term. Instead, type a minus sign in front of the word. So if you’re visiting San Antonio but don’t want to visit the Alamo, type: “San Antonio” -Alamo.That will search for the phrase “San Antonio” on web pages that don’t have the word “Alamo.” There’s no space between Alamo and the hyphen.

Minus does not equal plus.

• Although putting a minus sign in front of a word removes it from a search, adding a plus sign in front of the word does not force Google to include it. It simply stops Google from changing the word into a synonym or correcting the spelling, like putting it in quotes. Typing +Alamo is the same as typing “Alamo”. If you want to force Google to include an exact word or phrase in all your search results, use intext:...

Force Google to include search terms.

• Typing intext:[keyword] might be Google’s least-known search operations, but it’s one of Russell’s favorites. It forces the search term to be in the body of the website. So if you type: intext:”San Antonio” intext:Alamo it forces Google to show results with the phrase “San Antonio” and the word Alamo. You won’t get results that are missing either search term. This also stops Google using an alternative word that it thinks you're searching for.

Find relational search terms.

• What if you’re curious about search terms that are near each other on a website? [keyword] AROUND(n) [keyword] is incredibly handy for finding related terms such as “Jerry Brown” near “Tea Party.” (“n” is the number of words near the search terms.) Typing “Jerry Brown” AROUND(3) “Tea Party” will show you all the websites where the phrase “Jerry Brown” was mentioned within three words of “Tea Party.”

I've not yet used AROUND successfully but intext: and -unwanted has already helped me out a couple of times.

h/t: Alistair Bailey

A fan fixes Star Wars (Machete Order)

Like many of my generation, I am big Star Wars fan. I watched the original films more times than I care to remember and many more times than I care to admit. I probably went through half my teenage years able to recite the entire script to Star Wars (or A New Hope if you must) - including sound effects. I played Star Wars: The Roleplaying Game (the original one) and kicked ass at X-Wing on the PC. I was a Star Wars nerd.

Also like many of my generation, I was less enamoured by the prequels when they came out (although I should have seen the warning signs in the Special Edition trilogy - Han Solo shoots first for crying out loud. Grrrr. (Let it go, Rich, let it go...)) The Phantom Menace in particular was pretty terrible, however much the fan in me tried to be convinced otherwise. I really wanted it to be good. But it sucked. Darth Maul was pretty cool (except his death, which was pretty lame,) but the young Anakin was terrible, Jar-Jar Binks was really terrible, Midi-chlorians were beyond terrible and, perhaps worst of all, the whole script was a shocker. The only good thing about Episode I was the number of fantastically therapeutic spoofs it has spawned, especially at the hands of Robot Chicken (e.g. here and here). Well, that and the poster with the young Anakin and the shadow of Darth Vader.

My own fix to The Menace was to watch the DVD and just fast-forward all the bits I really didn't like, which was basically every time Jar-Jar or Anakin were on screen (except the pod race, which had good sound effects). This, and excising the Midi-chlorian scenes, actually works surprisingly well at turning The Phantom Menace into something quite watchable (and shorter) even if the already weak plot of that particular movie is watered down further still.

Rod Hilton on his blog, Absolutely No Machete Juggling, goes one further and has a plan for fixing the series with The Star Wars Saga: Introducing Machete Order His recommendation:

"Next time you want to introduce someone to Star Wars for the first time, watch the films with them in this order: IV, V, II, III, VI"

As well as re-ordering the films to safeguard some of the plot twists that the prequels ruin mightily, he excises Episode I altogether.

"Episode I is a failure on every possible level. The acting, writing, directing, and special effects are all atrocious, and the movie is just plain boring. Luckily, George Lucas has done everyone a favor by making the content of Episode I completely irrelevant to the rest of the series. Seriously, think about it for a minute. Name as many things as you can that happen in Episode I and actually help flesh out the story in any subsequent episode. I can only think of one thing, which I’ll mention later."

I won't go into the rest of the reasoning here but will instead recommend that you scoot over to Rod's blog. It's an old post (November '11) and quite long but if you are a fan (or were) and you've not come across it before, it's well worth a read. I've not yet tried out Machete Order myself but will be remembering it should I ever need to introduce someone to Star Wars in the future.

I just didn't expect it to be so big

This has been doing the rounds but, in case you've not seen it, there is a full screen version of XKCD's recent epic Click and Drag comic XKCD 1110 in a zoomable version - visualization created by dividuum. It saves a fair amount of clicking and dragging and let's you seek out all the hidden bits in the sky and tunnels (and works especially well on an iPad). I just didn't expect it to be so big
There is also a recent interview with XKCD creator, Randall Munroe, in The Atlantic, which is worth a read.

h/t WEIT.

University of Southampton builds world's first Raspberry Pi supercomputer

It's a bit of a busy time of year, so blogging is on the back burner for a bit (and I'm accumulating half-written posts for later!) but this was just so weird and fun that I had to write a quick post. If you haven't heard of a raspberry pi computer before, you can find out all about them here. Basically, they are a very small, very cheap ($25) "credit-card sized computer that plugs into your TV and a keyboard".



According to the FAQ:

It’s a capable little PC which can be used for many of the things that your desktop PC does, like spreadsheets, word-processing and games. It also plays high-definition video. We want to see it being used by kids all over the world to learn programming.

Well, Prof Simon Cox (and colleagues) of the University of Southampton decided to go one better and used a bunch of them to teach his kid how to build a supercomputer! You can read about it on the Computational Modelling Group website.



What can it do? Well, according to Prof Cox:

“The first test we ran – well obviously we calculated Pi on the Raspberry Pi using MPI, which is a well-known first test for any new supercomputer.”

I suspect it can do a bit more than that: the 64 processor system has 1Tb of memory! Not bad for £2500 (plus switches and, possibly, lego).

Nice one NASA (and Kudos, Curiosity!)

Today, I got up at 6.30 to watch the Mars Rover, Curiosity, come in to land on Mars. Despite it's terrifying landing strategy, Curiosity made it! I've got used to tension and seeing some celebrations over the last few days with the Olympics but watching the NASA control room on NASA TV as they received signals of progress was pretty emotional.

If ever there was something that epitomises why I choose to put my trust in the accomplishments of science and the ingenuity of mankind, this has got to be right up there. To be honest, I'm not sure what blows me away most - the fact that I live in a world where science and technology enables us to remotely land a robot on Mars, or the fact that I was able to sit in my dining room and watch it live on my iPad!

The tension mean that I was a bit slow on the screen grab, but here is a shot from just after they received the first actual picture from Mars - part of Curiosity's wheel. You can see it in the background.

Well done, NASA. Well done, America. Well done, science and engineering geeks!

From the ancient Greeks to the modern Geeks - the #Nerdlympics

This weekend I joined with people from all over the world to witness Olympic history in the making. It was a pleasure to see science and technology celebrated on the world stage and pay a wonderful tribute to the creation of the World Wide Web.

No, I am not talking about the opening ceremony (although I did very much like the cauldron). I am, of course, referring to the #Nerdlympics on Twitter!

I've been on Twitter for a while now and contribute to a couple of trending topics but never got in on one at the beginning and watch it take off before.

Perhaps ironically, I had not really checked my Twitter feed for a while when I logged on last night, Alex Wild (@Myrmecos) had just posted a couple of geeky Olympic event puns with the hashtag #Nerdlympics. ("Star Trek and Field" was one of the early ones.) Never one to resist a good pun (as readers of The Cabbages of Doom could testify!), I tweeted "PCRchery" back (an event to be held in the velodrome with the rest of the thermal cycling). There were then a trickle of tweets, including some of my own contributions:

☺"Modem pentathlon"
☺"Circadian Rhythym Gymnastics" and
☺"Geeko-Roman Wrestling".

A couple of my favourites were tweeted at this time, including:

☺"Periodic table tennis" (@Myrmecos),
☺"Kreb's Cycling" (also @Myrmecos),
☺"Higgs Field Hockey" (@paulcoxon) and
☺<table>Tennis</table> (@gr33ndata).

Then, it suddenly took off and tweets were flying in, causing Alex to tweet:

The good news is, I've finally created my first successful hashtag. The bad news is, it's #Nerdlympics

As I replied at the time - I don't see the bad news here! Top work, Alex - you gave many nerds (including me) an entertaining evening.

It was quite interesting to see the different approaches taken. I was definitely of the "pun" class but there was a clear set of proposed events from an actual Nerdlympic competition. (Alex himself posted both types, e.g. "Synchronized Centrifuging".) At this point it became hard to keep up but here are a few more of my favourites (in no particular order):

☺@artologica: Tenure Track and Field,
☺@SuzeMarsupial: Basketball Galactica
☺@RalphCipolla: Heavy Water Polo
‏☺@skepticCanary: Petri Discus.
☺@CarolMorton: Beach bucky ball
☺@eric_andersen: Angry Birdminton
☺@abdelrahmanG: Spammer throw
‏☺@scientelle: Logarithmic Gymnastics
☺@marvel_matt: TATA-Boxing
☺@JamieBeach: Floppy Discus Throw
☺@JoeyMcMorrow1: Molecular weight lifting

Well done, all! It made me proud to be a nerd.

I am sure that there were some other classics that I have missed. To get a few more, try searching Twitter for #Nerdlympics - the early posts are all events but then later posts start referring to summaries of the event (recursive trending?) - or check out the Storify summaries by Bug Girl and Tarek Amr.

What If? (XKCD+)

For those who haven't already seen it, the outstanding XKCD comic now has a weekly "What If?" section,

"answering your hypothetical questions with Physics, every Tuesday"

or, as the main site puts it:

"abusing science to answer hypothetical questions".

I prefer this second description as the second question answered ("What if everyone who took the SAT guessed on every multiple-choice question? How many perfect scores would there be?") does not seem to have much to do with Physics. The inaugarul entry, however, "What would happen if you tried to hit a baseball pitched at 90% the speed of light?", has a definite Physics theme and is highly entertaining, complete with great XKCD illustrations. (The footnote at the end is also most excellent but I won't spoil the punchline here!)

The Glossariser 1.0 is here

A while ago, I made a molecular evolution glossary page in case it was of use to anyone. Being a geek and a programmer, rather than actually making the webpage myself, I made a program to make the webpage for me. From a plain text set of terms and definitions, this program will construct a formatted web page, including hyperlinks between terms (if so desired).

As I now need to make another glossary for MapTime, I thought I would throw together a quick cgi script to make the code available online, and the Glossariser was born.



It's rather crude at present and, in particular, contains no documentation - trial and error only, I'm afraid! Input is, again, raw text with a number of delimiter options. (It only splits on the first occurrence of the chosen delimiter, so periods can be used quite happily.) There are currently a limited selection of output styles available. Unless "tabs" is chosen, terms will be split up according to their first letter and output alphabetically:



The "Header" or "bold" style refers to the formatting for the letters A-Z. The "table" output is similar but has each letter in a row of a table. The tabs style was a bit experimental and doesn't really work that well, so I won't bother to explain it here. (Feel free to try it!)

If you just want a standalone HTML page, you can (hopefully) just save the output directly. Otherwise, you will either want to copy and paste the text into a Word document or, to use in Blogger or other existing framework, just "view source" and copy the bits you need. (That's how I made the molecular evolution glossary.)

I have some plans for improvements - there are a few bugs to iron out and I would like to add URLs etc. - but, as with most things, they will probably wait until I, or someone else, really wants them in place. So, if it is useful but doesn't quite do what you want, let me know and I might be able to update it. There's also no reason that its use should be limited to a glossary. Any list of names/keywords and associated short paragraphs will do - perhaps I should make the alphabetical arrangement optional in this case?

The Glossariser is available at: http://bioware.soton.ac.uk/glossariser.html.

(If it ever saves you an evening of writing HTML and you want to say thanks, buy The Cabbages of Doom for just 99p! ☺ (You can't blame a guy for trying!))

Cakes! (And nematode cookies!)

Today, we had a charity cake sale at work. Mmmmm! Chocolate cupcakes with a peanut butter frosting are highly recommended! Being a bunch of science geeks, there were even some baked DNA gels and C. elegans worms!

It was all in aid of Cancer Research UK and if you want to support the idea of cookie nematodes from afar, you can sponsor the "Girls of B85" for the upcoming 5k Race for Life Southampton.
I am happy to report that the C. elegans were very tasty!

Just 24 to go until a big round-number milestone

I love geeks! Happy cartoon 1111101000, xkcd!

Learn while you wash

Having recently(ish) moved into a new flat, we have been lucky enough receive a couple of house-warming gifts. This has to take first prize... a Periodic Table shower curtain! Who knew such things existed?! Fantastic!

And the geeks shall inherit the earth... :o)