My Erdos Number is 4

Related to my previous post, I now have an Erdős number of 4. Another thing I’ve always wanted! Here are the details and an explanation of Erdős numbers for those who aren’t familiar with them.

I’ve posted previously about the mathematician Paul Erdős. Among other things, Erdős was insanely prolific and published 1,475 papers with 511 collaborators. Since one of his many areas of interest was graphs, it’s not surprising that a collaboration graph of his co-authors, and their co-authors, and so on…should be of interest. Courtesy of Wikipedia:

The Erdős number…describes the “collaborative distance” between a person and mathematician Paul Erdős, as measured by authorship of mathematical papers. It was created by friends as a humorous tribute to the enormous output of Erdős, one of the most prolific modern writers of mathematical papers, and has become well-known in scientific circles as a tongue-in-cheek measurement of mathematical prominence.

The Erdős collaboration graph is too huge to visualize, sadly, but the Erdős Number Project site has some interesting facts about the graph. Unfortunately, I think this information is skewed because it is based only on papers published in mathematical journals, while the high degree of interdisciplinary collaboration means that many people outside of mathematics have finite Erdős numbers. Anyway, according to this information, about 83,642 other people have Erdős number 4 (probably a gross underestimate.)

My relationship to Erdős comes from the fact that one of my co-authors, Michael Brudno, was a collaborator with at least two authors with Erdős number 2: Serafim Batzoglou and Lior Pachter. Each of those authors is a co-author with Daniel J. Kleitman, who not only has Erdős number 1, but has the lowest known Erdős-Bacon number: 3.

It’s conceivable that through one of Mike Brudno’s other collaborators, his number could in fact be 2, making mine 3, but confirming or disconfirming that would be too laborious. I’m more than satisfied with 4, which is slightly lower than the mean–especially considering that I never dreamed I’d have an Erdős number at all!

Savant: Genome Browser for High-Throughput Sequencing Data

I forgot to mention I now have a peer-reviewed publication! I don’t have a “bucket list” as such, but this is something I’ve always wanted. Not being an academic has made that unlikely, but because of my job in a research lab, it’s finally happened. Yay! Here are the details:

Savant: genome browser for high-throughput sequencing data
Marc Fiume, Vanessa Williams, Andrew Brook, Michael Brudno
Bioinformatics 2010; 26:1938-1944, August 15, 2010
doi: 10.1093/bioinformatics/btq332.

Read the abstract or the full paper (PDF). It has pretty pictures ;)

Cryptanalysis and genomics

For some reason it occurred to me that these two things should go together (while reading about Schroedinger’s brilliant notion about “the stuff of the gene” being some kind of aperiodic crystal). Anyway, while searching for stuff on this topic, I came across this great bit: Craig Venter’s synthetic bacterium contains coded “watermarks” in its DNA. One of these watermarks actually contains a Webpage, complete with a link. Others include quotations by James Joyce and Richard Feynman.

It sounds like science fiction, doesn’t it? Seriously cool–and slightly creepy. Imagine this kind of thing being introduced into humans via gene therapy!

I also found this paper on using cryptanalytic techniques to predict introns and exons. Sadly, that was all I could find. Perhaps it is not a fruitful avenue of research. Or perhaps it is just new and/or obscure. Time will tell.

First days with an iPad

I’m one of those seemingly few people who thought they had a real purpose for an iPad. I have a laptop and various old computers at home, but hate hauling my laptop around the apartment just to check email or look up something on wikipedia. So I splurged and bought one, which arrived Friday.

While it has it’s flaws, it’s quickly becoming indispensable!

A word to the wise, though: stay away from the app store. I’ve already spent an insane amount on stuff I really do not need. Those micro charges add up fast!

Platonic Solids: Generative Architecture by Subdivision

We’ve all heard of generative graphics, how about generative architecture? The computational experiment Platonic Solids by Michael Hansmeyer is something you can get lost in for a good while. Especially since he’s added a 3-D anaglyph presentation. I hope you kept a pair of red-cyan 3D glasses in your junk drawer like I did!

Here’s what the project’s all about, in the artist’s words.

Gruple moved to Codehaus

As promised, Gruple has moved from Googlecode to Codehaus. You find it’s new home here: http://gruple.codehaus.org.

All the documentation has been ported. There are new mailing lists. The source is now in a Git repository. And the 1.1.1 distribution is available from the distro site. Everything is (or should be) linked to from the main page.

Thanks to everyone who commented or helped.

Gruple 1.1.1 with Transactions released

I had almost given up on Gruple because I had no idea if anyone was using it. But it turns out I need it so badly myself that I got a second-wind and implemented transactions. I released v.1.1 yesterday and then realized with horror that it had serious bugs. After a frantic morning, I’ve got Gruple v.1.1.1 out and I believe (pray) those bugs are addressed.

That is not to say that I’m completely confident there are no bugs in Gruple as it stands! I have noticed occasional bad behaviour, the sure sign of a concurrency time-bomb somewhere. I’ll keep doing my best to track it down, starting with adding concurrent unit tests with the help of GroboUtils. If you use Gruple and have any problems please do let me know.

Finally, Gruple will be moving to Codehaus fairly soon (it’s approved, but there is work to do.) This will give it greater exposure. I’ll be switching to a git repo, because that just seems to be the thing to do (and I hate SVN with a passion anyway.)

Now if only I could get someone at Terracotta and SpringSource to work on supporting Groovy in the Terracotta product, I’d be laughing. And so would you.

Tuple Spaces for Large-scale Parallel Event-Based Systems

I just mean to point out this great post by Mauricio Arango on “Coordination in parallel event-based systems”. He mentions message passing, actors, message queues, pub/sub and tuple spaces, but seems to conclude that we’ll be seeing more tuple space usage in the future.

New Direction: Computational Biology

After an absurdly long job search, I’ve finally found myself a comfortable place in a computational biology lab. I’ve been here a bit more than a month and thought I should mention something about what I’m doing.

I’m working for Dr. Michael Brudno in the Computational Biology Lab at the University of Toronto. At the moment, I’m developing an application for visualization and analysis of biological sequence and annotation data with a graduate student named Marc Fiume. (We just chose a name for our project today: SAVANT. I like it.) I’m also sitting in on a graduate seminar on analysis of high throughput sequencing data and attending the occasional presentation on related research at The Centre for Applied Genomics. I’ll be spending one day a week at Sick Kids hospital, in order to interact with biologists and bioinformaticians who are among the target users of SAVANT.

I’m having a great time.

This is all a huge change from the enterprise web development that is more or less what I’ve been doing since 1996. A huge change that I really needed. Sometimes you just need to start over, you know? It was getting to the point where I honestly couldn’t picture myself actually taking any of the jobs I was applying for. I couldn’t face the same-old, same-old any longer.

I’m not sure where this is all going to lead, but I’m kind of hoping to make a career in this relatively young field. I believe that my many years of experience in commercial software engineering will be useful here. I think I can have fun and make a difference. The territory is huge; the problem space practically inexhaustible. I can’t imagine getting bored any time soon. Heading off in a new direction feels exactly right. So work-wise right now, it’s all good. :)

A “New Space Opera” Reading List

Many of my friends and acquaintances read SF, but there are a lot of sub-genres and I’ve noticed recently that many people either don’t know of “New Space Opera” or have just discovered it and want help finding more. Since I read as much of it as I can get my hands on, I figured I’d make a short, annotated, reading list to give those so-inclined a leg up.

First, the inevitable question: what is “Space Opera?” As far as I can make out, “Space Opera” was originally a derogatory term for the type of “cowboys in space” stories popular in the pulps once upon a time. Of course, low-brow or not, Space Opera is both very common and highly entertaining in television and film: “Star Trek” being the most obvious—in all its incarnations—as well as “Stargate” (likewise in 3 different series), “Firefly”, “Babylon 5″, and others you either know of if you’re a fan, or don’t need to know about if you’re not.

So what’s “New Space Opera?” This seems to be a much more controversial and slippery concept. For my part, I think of it as an updated, more high-brow version of Space Opera. It’s still primarily about adventure in space, but space isn’t just the setting anymore. The usual concerns of humanity far away from here and now—wild new technologies, bizarre and hostile environments, cultural evolution and upheaval—that you find in other types of SF are also found in New Space Opera. Since the late eighties, writers like Iain M. Banks, Alastair Reynolds, Peter F. Hamilton, Neal Asher, and others threw out the laws of physics as regards FTL travel (in “real” or “hard” SF you obviously cannot go faster than light) and then decided to see what kinds of ripping good yarns they could tell while sticking to most of the other rules of the SF genre. Usually, the canvas must be big: inter-stellar or even inter-galactic wars (including the cold kind); smuggling, piracy, espionage and terrorism; the rise and fall of empires; vast spans of space and time—that kind of thing.

So without further ado, here’s my short list of “New Space Opera” for anyone who wants to give it a go. This is by no means an exhaustive list (that would be impossible), nor is it necessarily a list of “the best” New Space Opera. It’s just my idea of some good places to start. Enjoy!

  1. Iain M. Banks. Not to be confused with Iain Banks, who is the same person writing non-genre fiction. To the best of my knowledge Banks was among the very first (if not the first) to kick of this new kind of space adventure. His first space opera Consider Phlebas is a classic, but my personal favourites are the later Use of Weapons and Feersum Endjinn. Both Consider Phlebas and Use of Weapons are so-called “Culture” novels (involving a human civilization Banks calls simpy “The Culture”), while Feersum Endjinn is set in a universe of its own. Banks’s more recent work is still worth reading, but it seems to me to be running out of steam.
  2. Alastair Reynolds. Reynolds has to be the undisputed master of vastness. His stories take place over such enormous spans of space and time that they sometimes feel a little bleak. Nevertheless, it’s brilliant and imaginative stuff. His debut series of novels Revelation Space, Redemption Ark, and Absolution Gap are must-reads. But if you’ve only got the time or taste for a singleton, I’d recommend the recent House of Suns
  3. Peter F. Hamilton. Hamilton tends to write long books with lots of characters. It’s the many points of view that bring the stories to life and make them so much fun. Probably the best place to start is with the two-volume “Commonwealth Saga”: Pandora’s Star and Judas Unchained. He has what promises to be an even better series in the works, but as it’s unfinished, I wouldn’t start there (ok, it’s The Dreaming Void and The Temporal Void…so far.)
  4. Neal Asher. Asher took a little while to grow on me. I think he grew as a writer, too, which certainly helped. His first novel Gridlinked was well-reviewed and is probably worth reading because it’s the first “Agent Cormac” novel, but I didn’t think much of it at the time. An ultra-violent high-tech secret agent yarn. **yawn** But things definitely got better after that. Asher has a marvellously creepy bio-aesthetic that’s unlike any other writer I can think of. Asher’s “Polity” owes much to Banks’s “Culture”, in that it’s a utopian society ruled by (allegedly) benevolent AIs often embodied in warships (?!) But that’s about all they have in common. My favourites are probably the Agent Cormac novels, which are, in order: Gridlinked, The Line of Polity, Brass Man, Polity Agent, and Line War.
  5. Charles Stross. Stross does more than just Space Opera, but he’s written a couple of decent ones: Iron Sunrise, Singularity Sky, and by stretching the definition of Space Opera a bit, you could probably include Accelerando
    —which is worth a read anyway, because it’s the only attempt I know of to write up to and through the “Vingean singularity”. Deserves a prize for bravery, that.
  6. John Scalzi. This series is a must-read: Old Man’s War, The Ghost Brigades, The Last Colony and Zoe’s Tale. The last is a bit of a do-over of The Last Colony, but even though I was originally doubtful, it turned out to be well-worth the read.
  7. David Weber. This is probably the most controversial entry on my list. Weber writes military SF (and fantasy), and he’s very prolific. Military SF is sort of a sub-genre of Space Opera (itself already a sub-genre). Still, it’s got all the right elements: lots of big space ships getting blown to smithereens. Honor Harrington, the heroine of an apparently endless series of novels, owes probably everything but her gender and her Queen to Horatio Hornblower. Nevertheless, the first 4 books in the series, On Basilisk Station, The Honor of the Queen, The Short Victorious War, and Field of Dishonor are highly entertaining.
  8. Gardner Dozois and Jonathon Strahan (Eds.) If you’re an SF fan, you’ve probably noticed the ever shrinking shelf-space for SF in bookstores. The “Science Fiction & Fantasy” section is typically 99% fantasy and most of the SF is video-game and television tie-ins. The industry seems to be in some kind of (hopefully non-fatal) tail-spin, so the real writing and publishing effort is going into (or should I say: returning to) short fiction. The New Space Opera and The New Space Opera 2 are two excellent anthologies of short fiction, some of it by the aforementioned authors, and many more besides. I can’t wait for the next instalment!

Note that all of the authors mentioned above (well, most of them, anyway) have written many more books than those I have listed. Those are just my suggestions for places to start. After that, Amazon’s search feature is your friend. Enjoy!