Acronyms and "Sophistication"

Fun Fact: If you give something an acronym, it will sound more sophisticated even when it really isn't.

Some examples: DNS for "directed numerical simulations", ROI for "region of interest", and AUC for "area under the curve".

Scientists are very good at this, by the way. :)

The Golden Ratio

Steve Strogatz's latest piece in the New York Times discusses the golden ratio. I didn't like this article as much as many of his other ones, but I suspect that that is an issue of personal subject preference and nothing more.

Congratulations to Dr. Joseph Schaeffer!

It is once again my pleasure to announce the successful thesis defense of one of my good friends. Welcome to the club, Dr. Joe Schaeffer, who unsurprisingly had a very smooth defense of his thesis (which is in the broad area of computational biology)! I'm not putting in more details on the topic just because I'll probably get tons of things wrong if I do, and I would be relying mostly on his paper in SIAM Review that predates tons of stuff in the thesis.

My congratulations might have worked better if I didn't have a bit of a screw up with Joe's phone number, but that is a rather small glitch in the scheme of things.

Update (9/29/12): I'm not sure how I managed to forget to write this, but Joe's PhD is from Caltech and his supervisor is Erik Winfree. So those of you who want to find out more about the work in that lab now have a place to look. :)

Postdoc Opening in My Lab

We have reposted the advertisement for a 3-year (technically, 34-month) postdoctoral position at University of Oxford to study multiplex networks:

https://www.maths.ox.ac.uk/node/19782


This is the same position I circulated a couple of months ago, but we had to take the advertisement down for bureaucratic reasons before. It's back up and applications are due by Friday 26 October, with a start date for as soon as possible thereafter.

The position is in the Mathematical Institute, and the successful candidate will be part of my group.

Please circulate far and wide. :)

The Perfect Valentine's Day Gift

Yup, arranging your partner's funeral ("Surprise!") is the perfect Valentine's Day gift. At least "overwhelmed" seems like an accurate reaction to such a gift.

I suppose I should have held this in until February. :)

"Mason, what do you really think?"

Quote of the day: "Mason, what do you really think?"


Granted, I have gotten numerous variants of this over the years. (Technically, today's quote was probably a slightly variant of this.) And I would venture to guess that anyone who doesn't understand this doesn't know me very well at all.
There is also a particular scene from Buffy that might come to mind.

RIP Herbet Lom (1917-2012)

Herbert Lom died today. He is best known for his role as (Former) Chief Inspector Dreyfuss in the Pink Panther films. My eye has started twitching uncontrollably in his honor.

(Tip of the cap to Steve Van Hooser.)

"Political Moneyball"

Here is a exceptionally cool visualization of political donation networks.

(Tip of the cap to Peter Mucha and someone else who I can't remember.)

Today's Rant: Passive Voice

The subject of today's rant is passive voice

Before going on, let me first acknowledge that passive voice is sometimes necessary. That said, what the fuck? It is used way too often in science. :)

Alright, so now that I've gotten that bit of irony out of the way, what's so bad about it? As far as I can see, there are basically three things wrong with passive voice. I'll illustrate them using an imaginary sentence in a scientific paper that might start with the phrase "An experiment was conducted..." You can fill in something from your favorite discipline to complete the sentence.

(1) It lessens clarity, and that's already a cardinal sin. Who conducted the damn experiment? Was it you? Was it the janitor? Was it done by the authors of the paper you cited a couple of sentences before this one? (D'oh... there goes clarity. Now we don't even know if the experiment was original or not.) Maybe it was done by a bunch of fluffy bunnies?

(2) It dehumanizes science. I suppose I can't make this argument in quite the same compelling manner as I can about clarity, but (seriously) it does do this. You put a human face on science by indicating your ownership of the work, and I think that science (and scientists!) needs all of the humanization it can get. So write it loudly and proudly: "I conducted the fucking experiment!" At least then we know who did the work! (As an exercise, see if you can make an appropriate change at the page proof stage of an article to try to get this exact phrasing in print.)

(3) It's bad writing. In most of its guises, passive voice is just an ugly use of language. Isn't that reason enough to try to minimize how much you use it? (Again, I want to acknowledge that sometimes passive voice really does provide the most parsimonious answer to your phrasing problems, but at least try to find another solution first.)



Here's another question: How in Hell did things get this way? Did a bunch of scientific gods get up one morning and decide that passive voice was somehow the right way to present scholarship? (Because it's really not...) Did the rampant use of passive voice in science just evolve slowly? Anyway, passive voice is bad writing and should be used sparingly. I go through great pains to try to get my students [and other coauthors... :) ] to unlearn such fallacies, and you should do that too. Scientific writing can also be good writing, so let's try doing that, ok?

Corollary: Just as annoying as the unnecessary preponderance of passive voice in science is the use of passive voice to avoid taking responsibility for mistakes. All too many times, I have seen a phrase along the lines of "A mistake was made" coming from the person who made the mistake in question. That's really a bunch of bullshit and a sleazy way to attempt to shirk responsibility. Just admit "I made a mistake." and be done with it---lose the sidestepping bullshit!

This rant was brought to you by the letters A, B, and C, and by the number ε > 0.

Why Your Friends Have More Friends Than You Do

What? You don't believe me? Just read the discussion in Steve Strogatz's latest article in The New York Times. By the way, this idea was one of the modules in our outreach efforts on networks for school kids last spring. That was one of the modules that needed some improvement, and Steve's article gives me some ideas of how to do it.

(Tip of the cap to Mariano Beguerisse Díaz.)

2012 Ig Nobel Prizes

Here are the 2012 Ig Nobel Prizes. For the most part, they're not as funny as usual---though the literature one is brilliant and I have a special fondness for the physics and fluid dynamics prizes.

Some physics stuff in the 2012 prizes---including 2 of them that I nominated (though the ponytail one was in the news so much that the Ig people certainly would have found it anyway; the other is perhaps less clear, though I'm guessing they would have found it). Notice the familiar names in the physics prize. :)

Maybe the synchronizing cows will make it next year...

(Thanks to Damien Storey, who posted on Facebook about the literature prize, for the reminder about these prizes.)

"What Evidence Is There for the Homology of Protein-Protein Interactions?"

Another of my papers has appeared in final form. Here are the details.

Title: What Evidence Is There for the Homology of Protein-Protein Interactions?

Authors: Anna C. F. Lewis, Nick S. Jones, Mason A. Porter, and Charlotte M. Deane

Abstract: The notion that sequence homology implies functional similarity underlies much of computational biology. In the case of protein-protein interactions, an interaction can be inferred between two proteins on the basis that sequence-similar proteins have been observed to interact. The use of transferred interactions is common, but the legitimacy of such inferred interactions is not clear. Here we investigate transferred interactions and whether data incompleteness explains the lack of evidence found for them. Using definitions of homology associated with functional annotation transfer, we estimate that conservation rates of interactions are low even after taking interactome incompleteness into account. For example, at a blastp E-value threshold of 10^{-70}, we estimate the conservation rate to be about 11% between S. cerevisiae and H. sapiens. Our method also produces estimates of interactome sizes (which are similar to those previously proposed). Using our estimates of interaction conservation we estimate the rate at which protein-protein interactions are lost across species. To our knowledge, this is the first such study based on large-scale data. Previous work has suggested that interactions transferred within species are more reliable than interactions transferred across species. By controlling for factors that are specific to within-species interaction prediction, we propose that the transfer of interactions within species might be less reliable than transfers between species. Protein-protein interactions appear to be very rarely conserved unless very high sequence similarity is observed. Consequently, inferred interactions should be used with care.



Update (9/21/12): Nick discusses this paper on his group's blog.

GoldieBlox: The Engineering Toy for Girls

I love Kickstarter because it allows one to back eminently worthwhile projects like GoldieBlox: The Engineering Toy for Girls.

Help fight gender steretypes and also one of the earliest leaks in the science./math/engineering pipeline!

This project is just a big win.

(Tip of the cap to Rae Yip.)

"Taxonomies of Networks from Community Structure"

Well, this paper has certainly taken a while to finally appear in final form. The project started in December 2007 as Stephen Reid's senior thesis project from the winter 2008 term. We put the first version of the just-published paper on the arXiv preprint server in June 2010. Here are more details.

Title: Taxonomies of Networks from Community Structure

Authors: Jukka-Pekka Onnela, Daniel J. Fenn, Stephen Reid, Mason A. Porter, Peter J. Mucha, Mark D. Fricker, and Nick S. Jones

Abstract: The study of networks has become a substantial interdisciplinary endeavor that encompasses myriad disciplines in the natural, social, and information sciences. Here we introduce a framework for constructing taxonomies of networks based on their structural similarities. These networks can arise from any of numerous sources: They can be empirical or synthetic, they can arise from multiple realizations of a single process (either empirical or synthetic), they can represent entirely different systems in different disciplines, etc. Because mesoscopic properties of networks are hypothesized to be important for network function, we base our comparisons on summaries of network community structures. Although we use a specific method for uncovering network communities, much of the introduced framework is independent of that choice. After introducing the framework, we apply it to construct a taxonomy for 746 networks and demonstrate that our approach usefully identifies similar networks.We also construct taxonomies within individual categories of networks, and we thereby expose nontrivial structure. For example, we create taxonomies for similarity networks constructed from both political voting data and financial data. We also construct network taxonomies to compare the social structures of 100 Facebook networks and the growth structures produced by different types of fungi.



And as an extra note, this paper includes the following line: "Moreover, the Louvain and simulated-annealing algorithms are much more popular than spectral algorithms in investigations of community structure [14] (and life is short), so we only compare results using the Louvain and simulated-annealing algorithms for the remainder of this appendix."

Update (9/23/12): Nick Jones has now described this paper on the blog he writes for his research group.

Infinite Loop

Unfortunately, the immigration form I am currently filling out has an infinite loop.

Exploring the World of xkcd

Wow, today's xkcd is awesome! I haven't explored all of it yet --- and maybe I haven't gotten anywhere close to all of it? --- but I'll have to stop now because I urgently need to get some things done. Still, this is awesome! [Maybe today was not the optimal day for this particular one to come out, but that's hardly the worst problem in my life. I'll just have to look at it more later. :) ]

Update: This particular xkcd is not only awesome but also supremely evil, especially for those of us with OCD.

‎"Hi, it's [name] from reception. I've got Jesus here to see you."

The important point is that this was done in complete English deadpan with an English/biblical pronunciation (rather than a Spanish one) of the 'J' and of the vowels.

("Yes. Send him up!")

What To Do About Unlabeled Axes

So.... should I warn the new students about this when they arrive next month?

Mathematics Ability Requires Crosstalk in the Brain

This is a very cool study and, I think, highly amenable to further work that builds on this using methods along the lines of what my collaborators and I have been using to examine learning of motor skills.

But, even more importantly, the name of a center that include's the study's lead author --- "Center for Vital Longevity" --- makes me giggle. :) I guess everything really is bigger in Texas...

(Tip of the cap to MoMath: The Museum of Mathematics and whoever does their Facebook posts.)

My New Favorite Baseball Name

That belongs to Cincinnati Reds shortstop Didi Gregorius (who is Dutch). That name is just amazingly awesome---it's the kind of name that a female porn star should have.

Facebook and Voting

Check out this new paper that was just published in Nature about voter participation and Facebook friendships. It was a collaboration between Facebook Data team, my collaborator James Fowler (who is a political scientist by training), and others at UC San Diego.

This paper is in the process of making waves. For example, here is what the New York Times had to say about it in its article. By the way, the research for this paper was funded in part by a joint grant that James and I have from the James S. McDonnell Foundation, though please note that I was not part of this project. (I did read an early draft of this paper over 1.5 years ago and gave some comments on it, and that is the extent of my involvement.) It is really cool that we get to mention this paper in our report to the funding agency, though!

Survey Says...

This demotivational poster is a thing of beauty.

This reminds me of a survey I once saw in a bank. The bank had huge signs advertising something like an 8.2 satisfaction rating out of 10. I was very bored and my mother was doing her banking (and I guess I had nothing with me to read), so I looked at the bank's survey cards. The three choices for satisfaction were 8, 9, and 10. 8.2/10 alright...

"Singular Sensations"

Steve Strogatz is writing another series of popular articles on mathematics, and here is the first one. It concerns topological singularities. Mmmm... singularities. (And for some of you, note the discussion of "topology" versus "geometry", which I have previously discussed in this blog.)

(Tip of the cap to one of the Cornell-oriented Facebook pages. I don't remember which one anymore, as I spent a couple of hours doing page proofs after copying the link but before actually reading it.)

Fractals in Nature

Here are some nice pictures of fractal-like structures in nature.

(Tip of the cap to Kreso Josić. By the way, in case you were wondering, I make reasonably frequent use of the voluminous html codes for characters for foreign languages available from this web page.)

The "Wedge Entry Problem"

Yup, there is actually a problem called the "wedge entry problem". (And I bet that its solution is not unique...)

The Redshirt in Google Doodle

All I have to say is this: Follow this Google Doodle (with a Star Trek theme) to the end, and see what happens to the redshirt...

Instant "Noooooooo!" Button

In case you're ever distressed, you can click on a Star-Wars-style instant "Noooooooo! button. (Tip of the cap to someone named Cliff Davis. I found this on a Facebook comment on somebody else's status.)

What Happens in Gothenburg Stays in Gothenburg

I am in Heathrow airport and will soon be flying to Gothenburg, Sweden for the 2012 edition of Dynamics Days Europe. I have been to the US wing of this conference several times, but I have never previously been to the European version of it. This is also my first trip to Sweden, and this is my first (and likely last) new country for 2012.

Fun Fact: Gothenburg is the birth place of Ace of Base, so I'll have to find a way to get a gratuitous Ace of Base reference into my talk. (It's also the birthplace of The Knife and quite a few other bands.)

Demotivational Poster of the Day: "Free to a Good Home"

Wow. Is the ad in this demotivational poster real? It's pretty awesome if it is...

(On another note, my 47 blog posts last month are my most in one of the canonical calendar months since my 50 from November 2006. I'm not really sure what happened. :) I expect the numbers will go back to a more normal level soon enough...)

"Synchronized Lying in Cattle in Relation to Time of Day"

A new paper of mine is now available in final form. This is the first sequel to the cow-synchronization paper, and it presents observations that was directly motivated by some of our work on our theory paper. The phrasing in the previous sentence in the previous sentence is important. It's not that our model per se motivated this biological sequel; rather the observations reported in this new paper was motivated by our research into what observations had and had not been reported previously. Our model effectively assumed that space was not an issue, so cows must be in fields rather than pens to use that simplistic model (which still exhibits very complicated dynamics), and we noticed when writing our paper that nearly all previously reported observations are for cows in pens rather than cows in fields. That's the origin of this paper. Here are the details.


Title: Synchronized Lying in Cattle in Relation to Time of Day

Authors: Sophie Stoye, Mason A. Porter, Marian Stamp Dawkins


Abstract: Postural synchrony, in which cattle lie down or stand up at the same time as other members of their herd, occurs both in animals housed indoors when enough resources are available and in those out at pasture, but the mechanisms by which such synchrony is achieved are poorly understood. We report a study of 6 groups of young cattle (Bostaurus) at pasture in which our aim was to study postural synchrony at different times of day and in relation to the postures of neighbouring cattle.

All of the observed groups exhibited a high degree of synchrony in lying/standing, as 70% of animals in a group exhibited the same posture over 93% of the time. Time of day had a significant effect (P ≈ 0.0046): cattle were least synchronized in the middle of the day and most synchronized in the morning and evening. With the increasing use of synchrony of lying as a measure of welfare in cattle, such temporal effects need to be taken into account.

Cattle were more synchronized with the posture of a near neighbour than they were with that of a randomly chosen member of the herd (P ≈ 0.016), suggesting that cattle were actively synchronizing their postures with that of their neighbours. These results indicate that a full understanding of the mechanisms of postural synchronization in cattle herds will need to incorporate both collective (allelomimetic) and concurrent (individual) responses.