Archive for July, 2008

HowTo: resubmit!

July 22, 2008

Though I have not resubmitted a rejected paper to another journal (not that mine haven’t been rejected; we just chose to rewrite the manuscript and submit them to the same journal), sometimes one may have to; and, FSP has some suggestions on how to go about doing it:

Executive summary: Don’t send reviews and other information about rejected manuscripts along with your resubmission if you really don’t want to, but realize that sending this information might actually help your resubmission, not harm it, especially if you provide a calm and sincere explanation of the relationship of submission #1 to submission #2.

Along the way, FSP also tells something which, young researchers should be aware of:

There is no shame in revealing that the manuscript has previously been rejected.

Take a look!

Materials miscellanea: AFM characterization of human hair

July 22, 2008

Here is an interesting paper published in the latest issue of Acta Materialia (thanks to Phani for the email alert):

Effect of ethnicity and treatments on in situ tensile response and morphological changes of human hair characterized by atomic force microscopy

Indira P. Seshadri and Bharat Bhushan

Abstract

Human hair fibers experience tensile forces during grooming and styling processes. The tensile response of hair is hence of considerable interest to the cosmetics industry. In this study, in situ tensile characterization studies have been carried out in an atomic force microscope (AFM) on different hair under different conditions. A custom-built AFM sample stage allows hair fibers to be loaded in tension. A technique to locate and image the same control area at different strains has been developed to study the changes in morphology that occur with deformation. Virgin Caucasian, Asian and African hair were studied to understand the differences between different ethnic hair types. Also, the tensile response and morphological changes of virgin, chemically damaged and conditioner-treated Caucasian hair after soaking were compared against the corresponding dry tensile response. Finally, virgin, damaged and treated Caucasian hair fibers were subjected to fatigue cycling to simulate combing/detangling, and their tensile response studied.

Those of you who have access to the journal, have fun; in case you haven’t, here is Indira Seshadri’s thesis on the topic (pdf)!

On reading fiction!

July 22, 2008

Louis Bayard reviews James Wood’s How Fiction Works for Salon:

Of course, literary figures as great as E.M. Forster and Virginia Woolf and F.R. Leavis and Roland Barthes have already tried to explain fiction to us, and it may seem churlish to wonder — after so many fine minds have labored so long at it — if fiction really needs to be explained. Surely, if it’s doing its job, it need only be experienced. If it can’t be experienced without tearing off its gown to expose the skivvies beneath, then it’s even more of a minority art form than we feared. What, finally, is better for the soul: reading Tolstoy or reading how to read Tolstoy?

In fact, there is at least one good reason to read “How Fiction Works”: Wood writes like an angel, with all the austerity and voluptuousness that implies. More to the point, he is one of the very few critics alive who can engage fiction on its own terms. Muriel Spark’s novels are “fiercely composed and devoutly starved.” Flaubert’s sentences are “laid as slowly and agonizingly as a fuse.” A character in Michelangelo Antonioni’s film “L’Eclisse” “slips through our changing perceptions, like a boat moving through canal locks.” Wood has the ear and the brain to wrestle with his masters and even, when he’s feeling his oats, surpass them, as he does in a cunning parody of Graham Greene: “Wentworth, he noticed, was giving off a slight odor. It was the smell of sin.”

The sin, of course, is Greene’s: too imitable, too ordinary. Many canonical authors are, in fact, denied entry to Wood’s pantheon, but as longtime readers know, the ones who do make it are treated with sacramental care. “Novelists should thank Flaubert the way poets thank spring; it all begins again with him.” Don’t forget to thank Chekhov and Tolstoy, too. And Woolf and Austen. James, Stendhal, Dickens, Joyce, Proust, Conrad. Among latter-day authors, the late Saul Bellow still sits at the head of the table: “a writer who makes even the fleet-footed … seem like monopodes.” Ian McEwen has a chair near the fire, Philip Roth is by the door (he made an ugly scene last year), but if you’re scanning the seating plan for Updike or Pynchon, for DeLillo or Jonathan Franzen or Salman Rushdie or Zadie Smith — if you’re wondering where good ol’ Henry Fielding has gotten to — well, that’s a story for another time.

An interesting piece; take a look!

The best education money can’t buy!

July 21, 2008

That is, if you have an endowment to the tune of $1.1 billion; from this NYTimes report:

Berea College, founded 150 years ago to educate freed slaves and “poor white mountaineers,” accepts only applicants from low-income families, and it charges no tuition.

“You can literally come to Berea with nothing but what you can carry, and graduate debt free,” said Joseph P. Bagnoli Jr., the associate provost for enrollment management. “We call it the best education money can’t buy.”

Actually, what buys that education is Berea’s $1.1 billion endowment, which puts the college among the nation’s wealthiest. But unlike most well-endowed colleges, Berea has no football team, coed dorms, hot tubs or climbing walls. Instead, it has a no-frills budget, with food from the college farm, handmade furniture from the college crafts workshops, and 10-hour-a-week campus jobs for every student.

Take a look!

What has Sacks been listening to, recently?

July 20, 2008

Via Jenny at Light Reading, I learn about this post of Gregory Cowles in which Sacks tells about his recent music listening (rather, playing) habits:

I still do not have a computer, but having resisted an iPod as long as I could, I have now succumbed. On my iPod at the moment I have nothing but Bach, but I have all of Bach — incredibly, the entire 157-CD set fits on this tiny thing without difficulty. I have been in a very Bach mood for the last few months, having started piano lessons again after a gap of more than 60 years. I have been concentrating on the 48 preludes and fugues; I am practicing a few of these.

Pablo Casals, at 93, told an interviewer that he played one of the 48 every morning, and had done so for the previous 85 years. Asked if he had not grown tired of them by this time, he said, no, he discovered fresh beauties in them each time he played one.

One of my own birthday resolutions, then, is to start every morning with one of the preludes or fugues. Much as I delight in listening to Bach, there is no pleasure like actually playing, or trying to play, music — even if it is completely beyond one. One discovers new details and delights that may not be apparent with simple listening. And I am heartened to find that one can learn new pieces and acquire new skills, even well into one’s eighth decade.

Take a look!

On reading Ulysses

July 20, 2008

Elizabeth Bachner tells why Ulysses is not only not so hard but also satisfying everytime you read it:

I get why everybody makes a fuss about Ulysses, what with all of its maddening and spectacular qualities, and with James Joyce’s shameless (and, to me, satisfying) arrogance about his own work. But I’ve never really gotten why people find this funny, dirty novel so hard to read.

I’ve picked up — and put down — The Corrections, Jonathan Strange and Mr. Norell, various books by Paul Auster, Middlesex (even though I loved The Virgin Suicides), The Shipping News, Tipping the Velvet, Memoirs of a Geisha, She’s Come Undone and Cold Mountain. I couldn’t get into them, even by cheating and flipping through to sections later in the book that might be more interesting. They seemed like slogs. They may well be great books. Everyone says so. I just can’t get into them or through them. So it’s not like I’m a reader with epic stamina. It’s not an issue of length, either, although it always seems less horrible to slog through a book you’re not that into when it’s nice and slim. Maybe reading Ulysses is like meditating? (Meaning, if it’s easy, you’re doing it wrong.) I don’t understand every reference in Ulysses, but then, I don’t understand every reference in most novels I’ve enjoyed reading. Certainly Ulysses is a novel the way New York (more than Dublin) is a city — it’s different every time you visit it.

Take a look!

WhenTo: edit!

July 20, 2008

Jonah Lehrer quotes Zadie Smith:

Zadie Smith, writing in The Believer, offers future novelists some advice:

When you finish your novel, if money is not a desperate priority, if you do not need to sell it at once or be published that very second – put it in a drawer. For as long as you can manage. A year or more is ideal – but even three months will do. Step away from the vehicle. The secret to editing your work is simple: you need to become its reader instead of its writer. I can’t tell you how many times I’ve sat backstage with a line of novelists at some festival, all of us with red pens in hand, frantically editing our published novels into fit form so that we might go on stage and read from them. It’s an unfortunate thing, but it turns out that the perfect state of mind to edit your novel is two years after it’s published, ten minutes before you go on stage at a literary festival. At that moment every redundant phrase, each show-off, pointless metaphor, all of the pieces of dead wood, stupidity, vanity, and tedium are distressingly obvious to you.

Though the entire piece of Smith might be worth reading, it is behind pay wall, unfortunately!

The parable of Alice’s rattle!

July 20, 2008

Sean at Cosmic Variance writes on Crackergate:

We should hold our friends to a much higher standards than we hold our adversaries. There is no way in which PZ is comparable to the folks sending him death threats. I completely agree with him on the substantive question — it’s just a cracker. It doesn’t turn into anyone’s body, and there’s nothing different about a “consecrated” wafer than an unconsecrated one — the laws of physics have something to say about that.

But I thought his original post was severely misguided. It’s not a matter of freedom of speech — PZ has every right to post whatever opinions he wants on his blog, and I admire him immensely for his passionate advocacy for the cause of godlessness. But just because you can do something doesn’t mean you should. And there’s a huge difference between arguing passionately that God doesn’t exist, and taking joy in doing things that disturb religious people.

Let me explain this position by way of a parable, which I understand is the preferred device in these situations. Alice and Bob have been friends for a long time. Several years ago, Alice gave birth to a son, who was unfortunately critically ill from the start; after being in intensive care for a few months, he ultimately passed away. Alice’s most prized possession is a tiny baby rattle, which was her son’s only toy for the short time he was alive.

Bob, however, happens to be an expert on rattles. (A childhood hobby — let’s not dig into that.) And he knows for a fact that this rattle can’t be the one that Alice’s son had — this particular model wasn’t even produced until two years after the baby was born. Who knows what mistake happened, but Bob is completely certain that Alice is factually incorrect about the provenance of this rattle.

And Bob, being devoted to the truth above all other things, tries his best to convince Alice that she is mistaken about the rattle. But she won’t be swayed; to her, the rattle is a sentimental token of her attachment to her son, and it means the world to her. Frankly, she is being completely irrational about this.

So, striking a brave blow for truth, Bob steals the rattle when Alice isn’t looking. And then he smashes it into many little pieces, and flushes them all down the toilet.

Surprisingly to Bob, Alice is not impressed with this gesture. Neither, in fact, are many of his friends among the rattle-collecting cognoscenti; rather than appreciating his respect for the truth, they seem to think he was just being “an asshole.”

I think there is some similarity here. It’s an unfortunate feature of a certain strand of contemporary atheism that it doesn’t treat religious believers as fellow humans with whom we disagree, but as tards who function primarily as objects of ridicule. And ridicule has its place. But sometimes it’s gratuitous. Sure, there are stupid/crazy religious people; there are also stupid/crazy atheists, and black people, and white people, and gays, and straights, and Republicans, and Democrats, and Sixers fans, and Celtics fans, and so on. Focusing on stupidest among those with whom you disagree is a sign of weakness, not of strength.

It seems to me that the default stance of a proud secular humanist should be to respect other people as human beings, even if we definitively and unambiguously think they are wrong. There will always be a lunatic fringe (and it may be a big one) that is impervious to reason, and there some good old-fashioned mockery is perfectly called for. But I don’t see the point in going out of one’s way to insult and offend wide swaths of people for no particular purpose, and to do so joyfully and with laughter in your heart.

A must read post!

HowTo: read scientific papers!

July 19, 2008

One of the very early lessons for me when I became a grad student (which also gave me quite a jolt at that time), is that the way you read the scientific papers is quite different from reading other technical documents — say, a text book or monograph.

Initially, I could not figure out how my advisor could read any paper so fast and get the gist so precise; and, sometimes make pronouncements about the soundness or silliness of some of the reported results based on my reports — without even looking at the paper; it looked like magic till I started paying close attention, and realised that his flipping the papers this way and that, and reading a few sentences here and there, and looking at this figure and that, is not all that random as it seemed; he looked at the title, then abstract, then conclusions, then the introduction, and the figures in between; he sometimes looked at some sentences and the references listed in them; occasionally, he read a paragraph or two from the core of the paper — formulation, results and discussion; and,  that was sufficient for him to make up his mind as to the worthiness of pursuing the paper; still, I do not remember a single case in which his judgement was off the mark.

Of course, there is a very large repository of information at the back of one’s mind on which one relies when reading a technical paper; that is what helps greatly in reaching conclusions fast; however, even with the availability of such information, it is the order which plays a crucial role in making the decisions faster.

Via Coturnix, I saw a blogpost at Blogrivet, which gives almost similar order for reading papers:

Scientific papers are broken into sections that are best read out of order. The headings for each section may vary from publication to publication, but the general concept is the same. Here I’ve identified each of those sections in the order that you should read them.

1. Abstract (…) 2. Charts and graphs (…) 3. Conclusion (…) 4. Introduction (…) 5. Discussion (…)

Bill, the author of the post (and the blog, Blogrivet) goes on to give detailed instructions for each section by taking an example paper from PLOS as a case study. A wonderful post! Have fun!

Copolymerization, information, second law and Maxwell’s demon

July 19, 2008

In the latest issue of PNAS, David Andrieux and Pierre Gaspard write about the nonequilibirum process involved in the copolymerization process in a paper titled Nonequilibrium generation of information in copolymerization process:

We consider general fluctuating copolymerization processes, with or without underlying templates. The dissipation associated with these nonequilibrium processes turns out to be closely related to the information generated. This shows in particular how information acquisition results from the interplay between stored patterns and dynamical evolution in nonequilibrium environments. In addition, we apply these results to the process of DNA replication.

The commentary of Christopher Jarzynski on the paper titled The thermodynamics of writing a random polymer also reads extremely well, and puts the work in perspective:

The notion that information has physical, and in particular, thermodynamic, content can be traced to the paradox of Maxwell’s demon, a sly creature who observes the microscopic motions of gas particles on both sides of a partition. By controlling a trap door the demon segregates fast particles from slow ones to create a temperature difference across the partition, seemingly without expending any work. Generations of physicists have scratched their heads over this apparent violation of the second law of thermodynamics. The resolution that has eventually emerged acknowledges that a real-life Maxwell’s demon—say, a nanoscale machine designed for the task—collects information as it operates, and work must be expended to erase this information, otherwise the demon’s memory banks fill up. The minimum work required is k B T ln 2 per bit of information, precisely what is needed to rescue the second law from the paradox. In this issue of PNAS, Andrieux and Gaspard analyze the flip side of the thermodynamic cost of information erasure; namely, the cost of information acquisition. The setting of their analysis is not a demon and a gas, but rather a process essential to living organisms: copolymerization, in which a chain-like molecule grows by the addition of chemically distinct units (monomers). The most celebrated example is the replication of DNA, by which genetic information is copied at the molecular level, ultimately to pass down the generations of a family tree.

A very interesting piece; take a look!