Will There Be a Mass Editorial Resignation at Scientific Reports?

Will There Be a Mass Editorial Resignation at Scientific Reports?

There might be.

(And a "Way to go!" and a "Huzzah!" to my colleagues from the complex-systems community for taking this action!)

An Addendum to 'Critical Truths About Power Laws'

Here is a brief addendum to the opinion paper "Critical Truths About Power Laws that I coauthored with Michael Stumpf in 2012. I wanted to post this addendum on the arXiv, but the arXiv admins wouldn't let me post it and removed my submission. I am attempting to 'set the record straight' (or at least my perspective on it) on a specific point.

Title: An Addendum to 'Critical Truths About Power Laws'

Author: Mason A. Porter



Main Text of the Article: In Ref. [3], my coauthor Michael Stumpf and I wrote that "The power law reported for allometric scaling stands out as genuinely good" and reinforced this comment in the paper's figure. We also wrote that "... few people would dispute the reality of such a relationship." I have since learned that the "power law" in allometric scaling is in fact the subject of intense debate. Please see the discussions in Refs. [1, 2] (and in references therein) for details.



You can click on the addendum to see which references I cite.

Statistics? We Don't Need No Stinkin' Statistics!

The paper described in this blog entry is "awesome". Indeed, it has the best 'Results' section ever.

The 'Results' section in the original published version of the paper started out with the following sentence: In this study, we have used (insert statistical method here) to compile unique DNA methylation signatures from normal human heart, lung, and kidney using the Illumina Infinium 27 K methylations arraysand [sic] compared those to gene expression by RNA sequencing.

D'oh!

(Tip of the cap to Krešo Josić.)

Experimental Results Related to DNLS Equations

The final version of this paper is actually over a year old, but it was just published as a book chapter in a monograph written by one of my collaborators (Panos Kevrekidis). Panos wrote the first sections of the book, and then he invited a number of people to contribute individual chapters on more specific topics. He asked me to write a paper based on experiments relevant to discrete nonlinear Schrodinger (DNLS) equations because of the fact that I work closely with experimentalists on a number of topics. Hence, this paper is a review article that covers a theorist's view on experimental results. (Note that I purposely ran the paper by several experimental colleagues in relevant fields to ensure that I didn't say anything stupid.)

The title of the published version of the chapter (which you probably won't be able to download for free, which is why I included the link to the version on my website) has "DNLS" because the acronym has already been well-established by that point in the context of the book.

Keep your eyes on this spot for a number of additional papers. I have a bunch of stuff that's about to come out. Also, I have a comment to make related to the first-mover scientific advantage, but I'll leave that for a different blog entry because it relates to my networks research rather than nonlinear waves research.

Fermi, Pasta, Ulam, and the Birth of Experimental Mathematics

The May-June 2009 issue of the magazine American Scientist will include the article, Fermi, Pasta, Ulam and the Birth of Experimental Mathematics, which I coauthored with Norm Zabusky, Bambi Hu, and David Campbell. (I added an extra comma in the title of the blog entry, as I prefer that style. I was not allowed to use it in the article because of the magazine's official style policy.

This article is basically "FPU for Dummies", as it attempts to discuss the Fermi-Pasta-Ulam problem (and the massive amount of exciting work it has spawned; this includes multiple subdisciplines of math and physics!) without using mathematical equations. This is really hard for a subject like this...

Mathematical Models of Bipolar Disorder

I've blogged about this paper multiple times before---including discussions of a very snarky letter-to-the-editor that my colleague and I wrote.

The paper itself has now been assigned its official journal volume, number, and page numbers. You can find the article here.


Title: Mathematical Models of Bipolar Disorder

Authors: Darryl Daugherty, Tairi Roque-Urrea, John Urrea-Roque, Jessica Troyer, Stephen Wirkus, and Mason A. Porter

Abstract: We use limit cycle oscillators to model bipolar II disorder, which is characterized by alternating hypomanic and depressive episodes and afflicts about 1% of the United States adult population. We consider two non-linear oscillator models of a single bipolar patient. In both frameworks, we begin with an untreated individual and examine the mathematical
effects and resulting biological consequences of treatment. We also briefly consider the dynamics of interacting bipolar II individuals using weakly-coupled, weakly-damped harmonic oscillators. We discuss how the proposed models can be used as a framework for refined models that incorporate additional biological data. We conclude with a discussion of possible generalizations of our work, as there are several biologically-motivated extensions that can be readily incorporated into the series of models presented here.

Community Structure in the U.S. House of Representatives

My winning entry in the 2006 Nonlinear Science Gallery of Images was published today in Chaos. This appeared in poster form at the 2006 APS March Meeting. My coauthors are A. J. Friend (an undergraduate at Georgia Tech), Peter Mucha, and Mark Newman.

The Nonlinear Science Gallery, in its third year, was inspired by the Gallery of Fluid Mechanics, which has been around for quite a while. In each of the last two years, the stuff in the gallery constituted the most downloaded papers in Chaos, so besides the value of the short article itself (which is basically an extended abstract, so I'm not going to describe it here), this should do wonders for the exposure of this research project. (The project is already reasonably well-known, but every little bit helps.)

My collaborators and I are currently working on doing some revisions of our archival paper before we resubmit it. We are also working on a follow-up paper that uses the work of one of my SURF students as a basis. (Right now, he's doing a couple extra calculations to quantify his findings. A 0th draft of this paper currently exists, but I'm not sure when we're going to have something ready to submit for publication.)

Modulational Instability in a Layered Kerr Medium: Theory and Experiment

My second PRL was just published a couple days ago.

My coauthors are experimentalists Martin Centurion, Ye Pu, and Demetri Psaltis from Caltech and theorists Panos Kevrekidis from University of Massachusetts at Amherst (one of my primary collaborators), and Dimitri Frantzeskakis of the University of Athens. (I was the main theorist on the paper and the second author overall.)

Here is the abstract:

We present the first experimental investigation of modulational instability in a layered Kerr medium. The particularly interesting and appealing feature of our configuration, consisting of alternating glass-air layers, is the piecewise-constant nature of the material properties, which allows a theoretical linear stability analysis leading to a Kronig-Penney equation whose forbidden bands correspond to the modulationally unstable regimes. We find very good quantitative agreement between theoretical, numerical, and experimental diagnostics of the modulational instability. Because of the periodicity in the evolution variable arising from the layered medium, there are multiple instability regions rather than just one as in a uniform medium.


On November 13th, we submitted an archival follow-up to this paper to an applied math journal. I don't expect we'll hear from them for a while, but I have 4 other papers currently in press, and a couple should actually show up in their final form soon. (I've done the proofs for three of these. One of them is available online but hasn't been assigned to an official print issue and probably won't be for a little while. The 4th of these, for which we don't yet have the page proofs, will have an interesting blog entry when it finally comes out.) There's a 5th paper that just got virtually accepted ("more or less"): the referees just asked for a very small number of cosmetic changes and wrote lots of various positive statements about the science. However, this isn't an official acceptance, so I can't count it as in press.

We are currently looking at following up the above research with studies of multi-bump solitons in layered Kerr media. (We also may put the glass slides at an angle because then one gets a linear-profile spatial inhomogeneity in the nonlinearity coefficient, which can lead to some cool dynamic effects.) The experiments are just starting, and we'll see if we find something interesting. (The experiments in which we hoped to look at dislocation dynamics didn't work.)

I have a newer project that is joint with an experimentalist. I'm still trying to get the code to work to simulate the system. This is the one where you have a chain of beads that one then strikes to examine wave propagation. (This is very much like the Newton's cradle classroom demonstration and, in fact, there is even one direct analog of it that definitely works but still needs a theoretical explanation for the mechanism.) This one is currently at the level of trying to get the code to work by comparing the output with that from previous code that was used in other papers.