Tuesday, June 29, 2010

"Psychic Octopus" picks Germany over Argentina

The "psychic octopus" (who lives in Germany but was born in the UK) has now picked Germany over Argentina. If the octopus's winning streak keeps up, the family is not going to be happy.

The octopus apparently took 45 minutes to make its decision this time, whereas it chose Germany over England in seconds. And then, sure enough, England got trounced.

We shall see what happens this time.

Monday, June 28, 2010

This hits way, way, way too close to the truth.

Here is a recent strip (6/25) from Ph.D Comics. It hits way, way, way too close to the truth.

(Tip of the cap to Justin Howell.)

Sunday, June 27, 2010

Jamie Moyer is awesome!

I have been watching the baseball game between the Phillies and the Blue Jays, and I have been doing this for one very specific reason: to watch Jamie Moyer give up career homerun #506 to set a new all-time record. Well, he just gave up this homerun to Vernon Wells and has now allowed the most homeruns of any pitcher who has ever played Major League Baseball. The (currently-in-progress) box score for the game is at this website.

Back in 1986, I didn't exactly think that he'd still be pitching now. Moyer is an amazing baseball player, a late-bloomer (he wasn't immediately successful in the Major Leagues), and a freak. (Moyer is 47 years old, and I wonder if he might still be pitching at age 50.)

Oh, and by the way: Moyer also pitched his 4000th career inning in this game.


Via some googling (because one of my articles is cited on one of the pages), I accidently found SklogWiki, a wiki dedicated to thermodynamics and statistical mechanics.

At the moment, it doesn't seem to be in particularly great shape. Scholarpedia seems to be in much better shape. (I really need to revise my soliton article and let the referees know that I have addressed their comments. That will have to occur after I return from Shanghai...)

Saturday, June 26, 2010

Garden Party

I had a garden party today.

The weather, the games, the banter, the desserts, and (most importantly!) the company were all wonderful. This is really the best way to spend a summer's day. (Well, I was actually extremely productive with my work until 5pm, and then the party started at 5pm---so both lots of work and lots of play today!)

For those of you back home, I hope that someday you'll be able to meet my friends in Oxford, but in the meantime you can see this photoblog picture that I took at the party.

I love my friends.

Friday, June 25, 2010

Separated at Birth: UK Prime Minister David Cameron and Star Trek's Brent Spiner

How could I not notice this before?

The UK's new Prime Minister, David Cameron (as pictured in this article), looks very much like Brent Spiner (as he looked 20 years ago), who played Data in Star Trek: The Next Generation. Here is a picture of Spiner as Data (with makeup). And here is an even younger Spiner (without makeup).

I don't normally care about UK politics at all, but this resemblance is just way too awesome. How did I not notice this before? Separated at birth!

OK, back to work now...

Update: I came up with this on my own, but evidently I am not the first person to have noticed this. It's still awesome, though...

Remember Erick Carreira?

Well, I do. As you can see, he can be extremely classy.

I had him for Chem 41b (second term of organic chemistry). His lectures were very good and he did bring hydrocarbons to class for us to sniff (though I just got dizzy), but he can apparently cross the line. It's fine to be hard-core, and I remember how he was very annoyed when somebody got a 98 on one exam (and it was a hard exam; the rest of us did much worse---he should have been happy that there was somebody who had mastered the material to that extent), but there are also lines that one shouldn't cross. I myself am a demanding supervisor (I think that is very important), but I think that I am also a reasonable one. Neither the request nor the tone of that letter are even remotely reasonable.

Also, some of you might remember that there was a certain professor who went ballistic and crashed through Caltech's giant black plastic maze during my junior year. My memory is hazy now, but I'm pretty sure that was Carreira.

Update: It is important that I add the following note that I just got from Julius Su: "To be fair, I heard Carreira knew he'd gone too far with that letter soon after writing it, has been embarrassed by its wide circulation since, and that he and Guido patched up quickly and remain good friends to this day." This is very good to hear.

(Tip of the cap to Stephen Shepherd.)

Thursday, June 24, 2010

Sometimes, I can't help myself.

At Somerville's SCR leavers party, one of our physics fellows (who is from Poland) was talking about Chopin wanting his heart removed after his death (well, it's actually a bit more complicated than this) to be returned to Poland. Naturally, my immediate reaction---which I couldn't hold in---was to bring up the song "I Left My Heart in San Francisco." Did I mention that I'm awesome?

Wednesday, June 23, 2010

The Wacky World of Sports

First, we have spontaneous concert-disrupting soccer matches breaking out and now this? At least we can still count on Jamie Moyer...

(Tip of the cap to Zifnab.)

Tuesday, June 22, 2010

Monday, June 21, 2010

Noodly Appendages in Nature

I so, so, so approve of this article title in the journal Nature.

Long live the FSM!

Dubious Origins of the Word "Seminal"

In retrospect, I really should have realized a long time ago that the origin of the word "seminal" is dubious.

A couple of weeks ago, I saw a letter in APS News commenting on why the word "seminal" shouldn't be used in formal publications, and I can definitely understand the point that the author is making. I don't agree with the conclusion---the word "seminal" is hardly alone in this respect---but it's at the very minimum worth pausing and thinking about it.

And, in case you haven't figured it out yet, seminal originally meant to be of seed or semen rather than full of possibilities (and 'foundational', which seems to be the current predominant meaning).

Sowing the seeds of science, indeed. (Yes, that song by Tears for Fears was indeed seminal---in at least three senses of the word, and I would arguably include a fourth if you want to include the music video.)

Sunday, June 20, 2010


I think that this poster is hilarious!

Of course, it helps that I have seen a huge number of Aflac commercials (and in-game quizzes) while watching baseball games.

Saturday, June 19, 2010

Maybe they'll hire me eventually?

I meant to blog about this a while ago, but I forgot the name of the guy in question and then I forgot about the story entirely...

Anyway, for several years, the Dodgers apparently hired Russian physicist-healer Vladimir Shpunt to send positive vibes to the team in order to boost wins. Now that's rocket science!

You know, I've been sending the Dodgers positive vibes for over three decades, and I've been doing it for free! And I even have physics cred.

"Internet Remarks Doom Pierogi"

Best. Article title. Ever.

I like to call this "pierogi-gate".

Simpler times?

Um, wow... I was trying to figure out the year that the advertisement depicted in this demotivational poster came out. Surely this wouldn't have gotten through nowadays? The product of a simpler time, I suppose.

"Discrete Breathers in One-Dimensional Diatomic Granular Crystals"

A new paper by my collaborators and me has just appeared in Physical Review Letters. This is my 4th paper in PRL. The concerns discrete breathers in granular crystal, and it includes theory, numerical simulations, and (especially!) experiments. In fact, this paper gives the first experimental demonstration of intrinsic localized modes (these are the discrete breathers) in granular crystals, which is a rather exciting result. I believe that Caltech is going to be issuing a press release, so I'll pass along that and any ensuing press coverage later.

Title: Discrete Breathers in One-Dimensional Diatomic Granular Crystals

Authors: N. Boechler, G. Theocharis, S. Job, P. G. Kevrekidis, Mason A. Porter, and C. Daraio

Abstract: We report the experimental observation of modulational instability and discrete breathers in a one-dimensional diatomic granular crystal composed of compressed elastic beads that interact via Hertzian contact. We first characterize their effective linear spectrum both theoretically and experimentally. We then illustrate theoretically and numerically the modulational instability of the lower edge of the optical band. This leads to the dynamical formation of long-lived breather structures, whose families of solutions we compute throughout the linear spectral gap. Finally, we experimentally observe the manifestation of the modulational instability and the resulting generation of localized breathing modes with quantitative characteristics that agree with our numerical results.

Thursday, June 17, 2010

"Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks"

My first paper on biological networks has just been officially published.

Title: Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks

Authors: Sumeet Agarwal, Charlotte M. Deane, Mason A. Porter, Nick S. Jones

Abstract: The idea of ‘‘date’’ and ‘‘party’’ hubs has been influential in the study of protein–protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. Here, we show that the reported importance of date hubs
to network connectivity can in fact be attributed to a tiny subset of them. Crucially, these few, extremely central, hubs do not display particularly low expression correlation, undermining the idea of a link between this quantity and hub function. The date/party distinction was originally motivated by an approximately bimodal distribution of hub co-expression; we
show that this feature is not always robust to methodological changes. Additionally, topological properties of hubs do not in general correlate with co-expression. However, we find significant correlations between interaction centrality and the functional similarity of the interacting proteins. We suggest that thinking in terms of a date/party dichotomy for hubs in protein interaction networks is not meaningful, and it might be more useful to conceive of roles for protein-protein interactions rather than for individual proteins.

As you can see from the discussion in this paper, the idea of "date" versus "party" hubs has been controversial ever since it was introduced in 2004. We started this project as agnostics regarding whether or not such a sharp distinction exists. We used a different perspective from what was previously in the literature, and we ended up concluding after lots of work that this kind of sharp distinction does not really exist (despite claims to the contrary).

Some Like It Hot

Apparently, baseball players become more aggressive as temperature increases. The heat is on...

(Tip of the cap to Justin Howell.)

Congratulations to Somerville's new mathematics graduates!

Congratulations to Somerville's new mathematics graduates! (Now your choice is to either go to grad school or make money and give some back to us. Such is life.)

Tuesday, June 15, 2010

Monday, June 14, 2010

Mentorship Fecundity

A new paper in Nature uses data from the Mathematical Genealogy Project to explore "mentorship fecundity".

Title: The role of mentorship in protege performance

Authors: R. Dean Malmgren, Julio M. Ottino, and Luis A. N. Amaral

Abstract: The role of mentorship on protege performance is a matter of importance to academic, business, and governmental organizations. While the benefits of mentorship for proteges, mentors and their organizations are apparent, the extent to which proteges mimic their mentors' career choices and acquire their mentorship skills is unclear. Here, we investigate one aspect of mentor emulation by studying mentorship fecundity---the number of proteges a mentor trains---with data from the Mathematics Genealogy Project, which tracks the mentorship record of thousands of mathematicians over several centuries. We demonstrate that fecundity among academic mathematicians is correlated with other measures of academic success. We also find that the average fecundity of mentors remains stable over 60 years of recorded mentorship. We further uncover three significant correlations in mentorship fecundity. First, mentors with small mentorship fecundity train proteges that go on to have a 37% larger than expected mentorship fecundity. Second, in the first third of their career, mentors with large fecundity train proteges that go on to have a 29% larger than expected fecundity. Finally, in the last third of their career, mentors with large fecundity train proteges that go on to have a 31% smaller than expected fecundity.

I haven't read the paper, but the results remind me of regression towards the mean. However, the authors have used randomly shuffled networks to try to account for such things, so maybe it really is more than that?

Sunday, June 13, 2010

Retired Muppets

The blog "Mental Floss" lists 9 muppets who were kicked off Sesame Street. Obviously we all know Kermit the Frog, but I actually remember Don Music well. (A few of the other ones who were kicked off are also familiar.)

Saturday, June 12, 2010

Congratulations to Caltech's Class of 2010

Congratulations to the class of 2010 at Caltech! The new Bachelors of Science alums include four of my former undergraduate research students, and in fact these are the last of my former Caltech undergraduate mentees to graduate. (They are Ye Pei, Olga Mandelshtam, Sherry Chen, and Tatjana Wiese.)

Commencement was yesterday, so I should actually have written this blog entry then.

Friday, June 11, 2010

A Picture Worth 1000 Words

Sometimes, a picture truly is worth a thousand words---like this one, for instance.

(Tip of the cap to Deb Eason.)

Last Expo Standing

The Daily Something wonders who will be the last Expo standing. My prediction is Jon Rauch.

(Tip of the cap to Rob Neyer.)

Wednesday, June 09, 2010

Quantum Chaos in Nature

Doug Stone has a News and Views article about quantum chaos in the June 10, 2010 issue of Nature.

In case you don't have full-article access to Nature, you can find the abstract here (it's the second article).

Nuns and Dementia

This NPR article about the 'Nun Study' of dementia and Alzheimer's disease is extremely cool. The part that's especially fascinating is the discovery of the biographies that the "nuns" (technically not nuns, as stated in the article... not that I would know) wrote when they first entered the order at 18 and the use of the 'complexity' of the text in those articles to see if it correlated with development of the signs of dementia (as measured in their brains after they died). A very strong correlation was observed between increasingly complex writing---see the article for a rough statement of how this was measured (it was basically how densely ideas were packed, on average, into 10-word segments)---and the onset of features in the brain associated with Alzheimer's Disease and dementia.

By the way, I love the 'causation versus correlation' comment at the end of the article. :)

Now I'm very curious to see my writing analyzed in this way... Of course, one can train oneself to write in different ways---e.g., I strongly prefer simple, clear sentences for scientific exposition (clarity >> elegance). We'll see how much dementia I develop... ;)

Agatha Christie was also mentioned extensively in the article, but the Nun Study is cooler.

(Tip of the cap to Rachel Gray.)

Update (6/10/10): I checked: The idea density of my writing is actually pretty damned high. (Also, I took a look at the .ppt presentations of one of these people to get a better idea of how it's calculated, and short nuanced ideas---sub-sentences but not necessarily full sentences---are the type that score the highest, and in fact my writing style goes very strongly and specifically in that direction.) I put in 4 writing samples from recent stuff that I have done (2 examiner reports, one document containing 3 articles I just wrote for a newsletter---in a format reminiscent of my blogging style, and one research statement), and I ranged from 5.03 - 5.48. (The word numbers in the documents ranged roughly from 500 - 2000.) Unsurprisingly, the newsletter articles---the least technical of the four documents by leaps and bounds---scored the lowest. A really neat thing to do---though indubitably this has been done before---would be to take a cohort of children and examine how their writing density changes as they age.

Baseball-Cricket Origins Exhibition in London Museum

This CNN article was written in relation to the premier of an exhibition about the dual origins and baseball and cricket in London's Marylebone Cricket Club (MCC) Museum. I am so there (at some point... I have until December)!

You might recall that I blogged about the news that baseball is a "British sport" a couple of years ago.

Intriguing Blog: Strange Maps

The blog Strange Maps looks pretty cool. I'm not planning on adding it to the blog roll, but I did want to point it out. Naturally, many of the maps make me think along network lines. :)

(Tip of the cap to Alexander Morisse.)

Monday, June 07, 2010

"The Brothers Bloom"

I have only one word to describe this movie: Wow.

This film was amazingly good---one of the best that I've seen for a long time.

The Misinformation Effect

Here is a neat blog post, from a blog called You Are Not So Smart, about The Misinformation Effect. Neat stuff!

(Tip of the cap to Rob Neyer.)

Sunday, June 06, 2010

Six Degrees of Black Sabbath

Six degrees of Black Sabbath is actually rather old, but I haven't seen this particular web page before. (This web page allows one to construct a path between any two artists, and---as you can see from my link---the path length between Loreena McKennitt and Depeche Mode is surprisingly short.)

Now back to marking exams... (though I'll be rewarding myself tonight with a Crowded House concert!!!)

(Tip of the cap to Mariano Beguerisse Díaz.)

Friday, June 04, 2010

RIP Vladimir Arnold (1937-2010)

I was looking at the website for the American Mathematical Society, and I noticed (to my surprise) a brief obituary for Vladimir Arnold, a very prominent mathematician who died yesterday.

Arnold was one of the mathematical giants of the 20th century, and he was particularly important in the subject of dynamical systems (which is the mathematical subfield of my birth and which is still one of my primary scientific interests). You can take a look at his wikipedia entry for some of his many important mathematical accomplishments. Let me only mention KAM theory (the 'A' is for Arnold), which gives important insights into mixed regular ('integrable') and chaotic dynamics in Hamiltonian systems.

Update (6/05/10): I didn't write much detail in my blog entry, but here's a blog entry that has some more details. The wikipedia entry and the links therein also contain discussions of the relevant mathematics.

Tales from the ArXiv: Unfortunate Author Name Department

Check out this recently-posted paper (which was actually published in 2008):

Title: Peristaltic Transport of a Physiological Fluid in an Asymmetric Porous Channel in the Presence of an External Magnetic Field

Authors: J.C. Misra, S. Maiti, G.C. Shit

Abstract: The paper deals with a theoretical investigation of the peristaltic transport of a physiological fluid in a porous asymmetric channel under the action of a magnetic field. The stream function, pressure gradient and axial velocity are studied by using appropriate analytical and numerical techniques. Effects of different physical parameters such as permeability, phase difference, wave amplitude and magnetic parameter on the velocity, pumping characteristics, streamline pattern and trapping are investigated with particular emphasis. The computational results are presented in graphical form. The results are found to be in perfect agreement with those of a previous study carried out for a non-porous channel in the absence of a magnetic field.

Sometimes, one's last name can become unfortunate when multiple cultures are involved...

Thursday, June 03, 2010

Tales from the ArXiv: arXiv vs snarXiv

OK, arXiv vs snarXiv is officially the best website ever. Wow, this is awesome!

(Tip of the cap to Anna Lewis. My PhD students send me the best things!)

Update: Wow, this is my 7th post of the day. This might actually be a record...

Can one patent a community detection method?

One can patent a community detection method? What?

Will somebody please explain this to me?

Update: The patent apparently belongs to Huberman and Wu (familiar names, and now I know what community detection method it's based on). You can find the details here. In the 6 years since the patent was filed and when it was rewarded (in January 2010), the method has become completely out of date. Still, WTF?

Standing on the Shoulders of Freaks

Henry Phillips said it best: "We're standing on the shoulders of freaks."

Indeed, this unsurprising statement is being reported in a recent study.

Money quote: reative people, like those with psychotic illnesses, tend to see the world differently to most. It's like looking at a shattered mirror. They see the world in a fractured way.

Well, duh.

And I should also mention the fact that this article hits a bit too close to home...

(Tip of the cap to Meredith Alden.)

The Perfect Game That Wasn't

Wow, a blown call by an umpire cost Armando Galarraga of the Detroit Tigers a perfect game last night. (The umpire admitted after seeing replays that he blew the call.) This would have been the third perfect game of the 2010 season, which is already the first season with 2 perfect games. Well, the record books might indicate that there have been 2 perfect games this year, but unofficially there have now been three. Wow.

Among other things, I bet that this will help hasten the expansion of instant replay in baseball. This story isn't over.

Wednesday, June 02, 2010

Cake of the Day

This cookie cake is even better than the one I once special-ordered.

This demotivational poster is also pretty damn funny.

Ken Griffey Jr. has retired

Ken Griffey Jr. has announced his retirement, effective immediately. He's going to baseball's Hall of Fame, but he's a shell of his former self and it was past time that he retire. See you in Cooperstown!

Lego Printer

This printer made out of Lego is seriously awesome.

(Tip of the cap to Puck Rombach.)

Tuesday, June 01, 2010

The Geometry of Music

There is a new article in Time Magazine about Dmitri Tymoczko's the geometry of music, as illustrated by his articles in Science on music theory. (I vaguely remember blogging about that article last year.) If you take a look at his web site, you can look at interesting videos that show links between music and geometry.

I definitely remember hearing about at least one of the Science articles when it came out, but to say that this stuff borrows stuff from string theory is quite a stretch. (It's like say that one thing borrows from something else because one uses calculus for both of them. In this case, one uses geometry for both things.)

Tymoczko is giving a plenary talk at the 2010 SIAM Annual Meeting, and I would definitely have loved to go to that seminar.

(Tip of the cap to SIAM's Facebook team, who posted a link to the Time article.)