Open Science and Access to Medical Research

Jalees Rehman in Scientific American:

RehmanThe idea of open science goes beyond merely providing public access to published scientific articles because it also includes offering access to the original research data. This would permit fellow researchers to help evaluate and analyze the results, so that the broader scientific community as well as the public can weigh in on the interpretation of the scientific findings. This aspect of open science likely does qualify for being a true paradigm shift, because it will require that we think of ourselves as part of research communities and usher in “networked discovery”, as has been described in a recent book by Michael Nielson and discussed by Bora Zivkovic.

There are still many obstacles that need to be addressed before “open science” becomes generally accepted. Academic publishers currently reap significant profits from selling high-priced annual subscriptions to academic institutions, and they would lose this income if scientists started publishing their results in open-access journals that freely provide articles to readers without charging for subscriptions or per-article fees. Furthermore, academic institutions and individual scientists may be concerned about how they would apply for patents, if the discovery process is networked and involves score sof collaborating scientists.

More here.

Thursday Poem

We Did Not Make Ourselves

We did not make ourselves is one thing
I keep singing into my hands
while falling
asleep

for just a second

before I have to get up and turn on all the lights in the house, one
after the other, like opening
an Advent calendar

My brain opening
the chemical miracles in my brain
switching on

I can hear

dogs barking
some trees
last stars

You think you’ll be missed
It won’t last long
I promise

*

I’m not dead but I am
standing very still
in the backyard
staring up at the maple
thirty years ago
a tiny kid waiting on the ground
alone in heaven
in the world
in white sneakers

I’m having a good time humming along to everything I can still
remember back there

How we’re born

Made to look up at everything we didn’t make

We didn’t
make grass, mosquitoes
or breast cancer

We didn’t make yellow jackets

or sunlight

either

*

I didn’t make my brain
but I’m helping
to finish it

Carefully stacking up everything I made next to everything I ruined
in broad daylight in bright
brainlight

This morning I killed a fly
and didn’t lie down
next to the body
as we’re supposed to

We’re supposed to

Soon I’m going to wake up

Dogs
Trees
Stars

There is only this world and this world

What a relief
created

over and over

by Michael Dickman
from The End of the West
Copper Canyon Press, 2009

Nano nod for lab-on-a-chip

From PhysOrg:

ChipYou wouldn't know it from appearances, but a metal cube the size of a toaster, created at the University of Alberta, is capable of performing the same genetic tests as most fully equipped modern laboratories—and in a fraction of the time. At its core is a small plastic chip developed with nanotechnology that holds the key to determining whether a patient is resistant to cancer drugs or has viruses like malaria. The chip can also pinpoint infectious diseases in a herd of cattle.

Talk about thinking outside the box. Dubbed the Domino, the technology—developed by a U of A research team—has the potential to revolutionize point-of-care medicine. The innovation has also earned Aquila Diagnostic Systems, the Edmonton-based nano startup that licensed the technology, a shot at $175,000 as a finalist for the TEC NanoVenturePrize award. “We’re basically replacing millions of dollars of equipment that would be in a conventional, consolidated lab with something that costs pennies to produce and is field portable so you can take it where needed. That’s where this technology shines,” said Jason Acker, an associate professor of laboratory medicine and pathology at the U of A and chief technology officer with Aquila.

More here.

Wednesday, April 25, 2012

Lawrence Krauss and The Anti-philosophy Complex

KraussMassimo Pigliucci in Rationally Speaking:

“Philosophy is a field that, unfortunately, reminds me of that old Woody Allen joke, ‘those that can’t do, teach, and those that can’t teach, teach gym.' And the worst part of philosophy is the philosophy of science; the only people, as far as I can tell, that read work by philosophers of science are other philosophers of science. It has no impact on physics what so ever. … they have every right to feel threatened, because science progresses and philosophy doesn’t.”

Okay, to begin with, it is fair to point out that the only people who read works in theoretical physics are theoretical physicists, so by Krauss’ own reasoning both fields are largely irrelevant to everybody else (they aren’t, of course). Second, once again, the business of philosophy (of science, in particular) is not to solve scientific problems — we’ve got science for that (Julia and I explain what philosophers of science do here). To see how absurd Krauss’ complaint is just think of what it would sound like if he had said that historians of science haven’t solved a single puzzle in theoretical physics. That’s because historians do history, not science. When was the last time a theoretical physicist solved a problem in history, pray?

And then of course there is the old time favorite theme of philosophy not making progress. I have debunked that one too, but the crucial point is that progress in philosophy is not and should not be measured by the standards of science, just like the word “progress” has to be interpreted in any field according to that field’s issues and methods, not according to science’s issues and methods.

The Particle At the End of the Universe

Sean Carroll in Cosmic Variance:

ScreenHunter_06 Apr. 25 19.34I’m currently hard at work writing The Particle At the End of the Universe, a popular-level book on the Large Hadron Collider and the search for the Higgs boson. If all goes well, it should appear in bookstores at the end of this year or beginning of next. (Ideally, it will go on sale the same day they announce the discovery of the Higgs. I’m trying to bribe the right people to make that happen.) The title is somewhat tentative, so it might change at some point.

This will be a somewhat different book than From Eternity to Here. While both are aimed at a general audience, FETH was a rather lengthy tome that made a careful argument in a hopefully novel way. Anyone could read it, but to get the most out of it you have to really sit and think about certain ideas. Particle, on the other hand, aims to be a fun and narratively gripping page-turner — a book that makes you eager to move quickly to the next chapter, rather than taking a few minutes to let the last one sink into your head. A bodice-ripper, if you will. It will be full of stories and fun anecdotes about the human beings who made the LHC happen and have devoted their lives to searching for the Higgs and particles beyond the Standard Model. A book you would be happy to give to your Grandmom in order to convey some of the excitement of modern physics. (Unless your Grandmom is a particle physicist, in which case she might think it’s at too low a level.)

At the same time, of course, I’m going to try to illuminate the central ideas of the Standard Model in as clear a fashion as I can manage. It won’t just be a list of particles; I’ll cover field theory, gauge bosons, and spontaneous symmetry breaking. All in fine bodice-ripping style. (Maybe get Fabio for the cover?)

More here. [Photo: by Jennifer Oulette.]

Narendra Modi’s Ratings

Hartosh Singh Bal in the International Herald Tribune:

ScreenHunter_05 Apr. 25 17.47Narendra Modi, the leading figure of India’s right-wing Bharatiya Janata Party (B.J.P.), didn’t make Time magazine’s list of the 100 most powerful people in the world this year. Midway through the online polling, after Modi’s stock had started to surge, liberals in India organized a counter-campaign. In the end, 256,792 votes were cast for him and 266,684 votes against.

Too bad for Modi: it’s an election year in the state of Gujarat, where he is chief minister, and he is known to be eyeing the country’s prime minister slot. But I, for one, am relieved: finally a defeat for Modi’s formidable PR team, which routinely manages to whitewash his responsibility for fueling sectarian strife and oversells his economic accomplishments, especially to Western journalists.

More here.

Muslim Women in India Seek Gender Equality in Marriage

Lossy-page1-754px-Muslim_Lady_Reclining_

Keeping with today's theme, Nilanjana Roy in the NYT (with accompanying Mughal era image from wikipedia):

For more than a decade, Muslim women’s organizations in India have been fighting for changes in the body of Islamic law that governs marriage, divorce and the property rights of women. But as the All-India Muslim Personal Law Board held its annual convention in Mumbai last week, the battle lines had never been so starkly drawn. Although the Indian Constitution guarantees equal rights to all citizens irrespective of their religion, Muslims are governed by the Muslim Personal Law (Shariat) Application Act of 1937. Attempts to apply a common civil code have often been viewed as interference in the practices of India’s largest religious minority.

The Personal Law Board is one of the country’s more influential Muslim groups. Its chiefly male membership of clerics and scholars has rejected proposals to change Muslim personal law, and is opposing a demand by women’s groups that marriages be legally registered, as is mandatory for non-Muslims.

Zeenat Shaukat Ali, a professor of Islamic Studies at St. Xavier’s College in Mumbai and the author of “Marriage and Divorce in Islam,” is blunt in her assessment of the current situation.

“We are asking for codification of the legal system within the framework of Koranic law,” she said. “The Koran does not support a system that is controlled by the patriarchy, and the government has to treat this matter on a war footing if they truly mean to bring about gender justice.”

The changes that women’s organizations have been discussing for more than a decade — with major meetings held across India over the last three years — include the compulsory registration of marriages with the state, the abolition of the triple talaq on the grounds that violates the Koran and the establishment of a more reliable system of financial support for wives.

“There is no political will to change this law even though we are a secular democratic republic,” said Ms. Ali. “Politicians refuse to move ahead because some males have objected.”

Let’s All Change Our Names To Clothing Measurements

Over at Opinionated:

Samhita [Mukhopadhyay] and Amanda [Marcotte] discuss Mona Eltahawy's powerful and complex piece on misogyny in Muslim nations. In their version of lightening the mood, they also discuss our comical shock troops for ladies who hate ladies, specifically Lila Rose and S.E. Cupp. For this week's #femquery, they take on the question of post-feminism, that slippery beast.

Foreign-Policy-magazine--001UPDATE: Another response in the Guardian by Nesrine Malik:

Reading the article I found myself bristling, yet simultaneously felt guilty for doing so. For who can deny the serious, endemic discrimination from which women in the Middle East suffer? Reading on I tried to convince myself that it was the author's sensational style that was bothering me, and that this shouldn't obscure the message, or that the title and imagery were unfortunate, but the problems they were attempting to illustrate were real.

Yet to my dismay I found, as I read on that instead of unravelling and unpicking the usual stereotypes which pepper the plethora of commentary on Arab women and exposing missing nuances, the author simply reinforced a monolithic view – holding the argument together using rhetoric, personal anecdotes and a rhythmic punctuation with her main theme – that all Arab men hate Arab women. It did not help that with every page scroll, a different iteration of an unbelievably misguided shot of a naked woman, posed and blacked out in paint to expose only her eyes, assaulted one's sensibilities. A lazy effort at controversy, equating women with sex, and jettisoning the whole point of the edition, by ironically, reducing women to the stereotype Eltahawy dismisses as “headscarves and hymens”.

I grew up in Sudan, Egypt, Saudi Arabia, and in personal and professional dealings have had to grapple with most of the problems highlighted in the piece. They are very real. But there is a fine line to tread when writing about the status of Arab or Muslim women. For to do anything but condemn outright, and expose the real suffering we go through feels like shirking a responsibility and wasting an opportunity. And the problem with rejecting generalisations around women's oppression is that it is easy to misunderstand this rejection as a denial of the problem. Who could quibble with highlighting child marriage, female genital mutilation, or legally protected domestic abuse? Only a Stockholm syndrome-suffering apologist for patriarchy and moral relativism. How can one truly call for equivocation when we have a war on women on our hands?

The offences mentioned in the article are undeniable. We should not be distracted by the west's reduction of Muslim women to pawns in culture wars or military campaigns. Nor should we be distracted by ad hominem attacks on Eltahawy herself, or complain at the idea of airing of dirty laundry. But these offences are not just because men hate women. Or, as I fear the article suggests, that Arab men hate Arab women. This is not a disease men are born with, or contract from the Arab atmosphere. Even Eltahawy herself, attributes it to “a toxic mix of religion and culture”. And to this I would add the political oppression and stasis that enabled these structures to become de facto governance, where entrenched tribal allegiances, pre-Islamic mores and social tradition trumped weak political culture. A general retardation that extends not just to women but to every aspect of personal freedom and civic rights.

Smiley and West: Still Fighting for the Poor

From The Root:

If there's any doubt that the economic crisis persists, consider the takeaways from recent headlines: The official unemployment rate remains 8.2 percent. One in six Americans — nearly 52 million people — receives food stamps, even as Republican legislators in Washington and state capitals push austere cuts to social programs.

In a Gallup survey released Monday, two-thirds of Americans say they know someone who has been laid off in the last six months — the highest share in the venerable polling firm's history. But the biggest takeaway is this: The gap between the rich and poor in the United States is not only worsening; it's also greater than those in many other countries. Few people are connecting the dots. Enter The Rich and the Rest of Us: A Poverty Manifesto — a richly insightful, slightly academic book released this month by talk-show host Tavis Smiley and professor Cornel West. The two men have been friends for 25 years. The current book project was born last summer during the duo's 18-city Poverty Tour, which extended from a Native American reservation in Minnesota to Appalachia and Washington, D.C. The tour came just as the Congressional Black Caucus launched a series of job fairs.

More here.

Wednesday Poem

On Chickasaw Road

I.

“You can’t go feed cows without any britches,”
he tells the boy in the diaper
clinging to the fridge for support,
warily walking along the kitchen floor.
Gospel truth: It’s hot outside for February
but a boy can’t just ride a tractor in a diaper
so I grab him a pair of pants
from the laundry pile.

Both mother and grandmother kiss the boy
and I walk out the back door
behind my father-in-law
who wears a plaid shirt worn thin,
holds his grandson in his arms,
holds the door for my two dogs
that smell like wet roots reaching
from the mossy creek bank
where they’ve been playing.

We leave them in the mudroom
so they won’t run the cows
and head out through the gray-green grass
to the open shed where rusted machinery rests
among scattered piles of junk and brittle tangles
of blackberry bramble awaiting the fullness
of the green breath of spring
we can feel on our necks.

My father-in law steps up to take
his seat on the Massey Ferguson,
chipped and flaked as an old turtle’s shell,
faded red as a tail feather shed
by a hawk. I hold my child up
to his grandfather who takes the boy
in his lap, and I watch them ride on
while I walk behind
to open the gate.

Read more »

Futurism Is Still Influential, Despite Its Dark Side

From Smithsonian:

Articulations-Armored-Train-in-Action-520In 2014 the Guggenheim Museum in New York will open the biggest exhibition ever held on the Italian Futurists; the event has been foreshadowed by an article in Smithsonian, accompanied by an online photo gallery of Futurist masterpieces. It’s a good moment to reflect a bit on what Futurism represents, how it happened and how it has transformed the world we live in. Today we think of Futurism as a visual style—a sort of animated Cubism that endows images and objects with a feeling of windblown movement. Remarkably, however, the movement began with a manifesto, and a series of “happenings,” before the artists associated with it had developed a new style.

The movement was first trumpeted in a manifesto by the poet Filippo Marinetti,which was published in the Paris newspaper Le Figaro on February 20, 1909. The intention of the movement, Marinetti explained, was to smash anything old, sentimental or conventional and create a new manly culture based on machines, speed and modernity. Hailing the “beauty of speed,” he argued that museums libraries, academies and “venerated” cities had to be destroyed, since they represented the culture of the past, and were stale and reactionary, as were “morality, feminism and all opportunist and utilitarian cowardice.” In a famous phrase, Marinetti declared that “a roaring motor car which seems to run on machine-gun fire is more beautiful than the Victory of Samothrace” (a reference to the second century Greek sculpture of the goddess Victory). Proud of their ability to irritate the public, the Futurists staged performances in Turin, Naples, Milan and other cities, at which they recited poetry and declaimed their manifestos while the audience responded by showering them with rotten fruit and vegetables and other objects. Developing a Futurists style was clearly a necessary next step. In a later manifesto of April 11, 1910, the Futurists argued that “the construction of pictures is stupidly traditional,” but finding an appropriate visual language for their iconoclastic ideas about modern life was not easy. The early works of the Futurists used the techniques of divisionism, which created patterns with colored dots, and Post-Impressionism, which employed bold, decorative shapes. But they seemed to have quickly sensed that they needed to do something more visually exciting.

More here.

the revolution and space

Arab-men-manger-square-bethlehem-2

In 1991, a Libyan thinker exiled in Geneva, al-Sadiq al-Nayhum, published a book of collected essays in Arabic with the provocative title, “Islam in Captivity: Who Stole the Mosque and Where Did Friday Disappear?”[2] The thesis of the book was not novel. A-Nayhum posited that the failure of modernity to take roots in the Arab world was due in large part to it having grown out of Western history and developed in a Western cultural and epistemological context, which is incompatible with the culture and knowledge nurtured by Islam. Al-Nayhum, predictably, advocated a return to the pure, foundational Islam to rebuild the battered and confused Arab societies.[3] This solution has been proposed by many thinkers before and since, especially after modern Arab states failed to achieve the promised socioeconomic development or military parity with Israel, which had scored a resounding victory against them in 1967.[4] Al-Nayhum, however, differed from other likeminded thinkers in his attention to the role of space in framing, sustaining, and ultimately molding the Islamic political tradition. His focus was of course on the quintessential Islamic space, the mosque, hence its appearance in his title.

more from Nasser Rabbat at Critical Inquiry here.

caligula

Caligula

Caligula occupied the Roman throne for just four years, between 37 and 41 AD. He was the son of the glamorous imperial prince Germanicus (who died in mysterious circumstances in Syria in 19 AD), and spent much of his childhood on military campaigns with his father. Hence his name: although he was born Gaius Caesar Germanicus (and his official title was the Emperor Gaius), the soldiers nicknamed him ‘Caligula’ or ‘Little Boots’, after the mini-military uniform, boots included, in which he used to be dressed – and it stuck. At the death of the elderly Emperor Tiberius, he was eased onto the throne, aged 24, ahead of Tiberius’ natural grandson, who was murdered not long afterwards. The popularity of his father – plus the fact that, through his mother, Agrippina, he was a direct natural descendant of Augustus, the first emperor – provided a convenient veil for what must have been a nasty power struggle, or coup. But another coup soon followed. Four years later Caligula was assassinated, and the throne passed to his uncle Claudius, found, as the story goes, hiding behind a curtain in the palace, so terrified was he in the confusion that followed the murder.

more from Mary Beard at the LRB here.

‘Why Do They Hate Us?’ A Blogger’s Response

RTR2Z846

Mona Kareem in Al-Monitor:

Eltahawy says “they hate us and we need to admit that!” And then she lists more than three pages of recent violations of women’s rights in the Arab world. The issue at stake here is not whether women are discriminated against in the Arab world, as that argument is well established and is only denied by Islamist maniacs. The issue here is: how the hell can those violations prove an argument of “hate?” Eltahawy argues against Arab claims that Jews or Israelis hate us, but she uses the same logic when she puts Arab men under an umbrella of a single emotion: hate.

What should be considered is that we live in patriarchal societies, and the foundations of Middle East-based monotheistic religious texts are established on this patriarchy. Eltahawy’s claim not only degrades Arab culture in general but also patronizes Arab men and women by making the whole struggle for gender equality a conflict between the two sexes based on personal emotions.

Another problem I have with the general speech of “Arab feminism” is the term in itself. I really dislike seeing more than 20 different cultures put under one roof. Eltahawy is not a Pan-Arabist, I am assuming, yet she falls for this very common oriental division imposed by the media and others. Anyone knows how radically divergent the “Arab World” is: the North-African Arab culture is a far different culture from that of the Arabian Gulf.

Tuesday, April 24, 2012

Tom Friedman’s War on Humanity

Belén Fernández in Jacobin:

ScreenHunter_02 Apr. 24 16.36Thomas Friedman, three-time Pulitzer Prize-winning foreign affairs columnist for the New York Times, once offered the following insight into his modus operandi: “I often begin writing columns by interviewing myself.”

Some might see this as an unsurprising revelation in light of Edward Said’s appraisal: “It’s as if … what scholars, poets, historians, fighters, and statesmen have done is not as important or as central as what Friedman himself thinks.”

According to Friedman, the purpose of the auto-interviews is merely to analyze his feelings on certain issues. Given that his feelings tend to undergo drastic inter- and sometimes intra-columnar modifications, one potentially convenient byproduct of such an approach to journalism is the impression that Friedman interviews many more people than he actually does.

For example, while one of Friedman’s alter-egos considered blasphemous the “Saddamist” notion that the Iraq war had anything to do with oil, another was of the opinion that the war was “partly about oil,” and another appeared to be under the impression that it was entirely about oil, assigning the blame for U.S. troop deaths in Fallujah to Hummer proprietors. Despite Friedman’s identification as “a liberal on every issue other than this war,” competing layers of his persona defined said conflict as “the most radical-liberal revolutionary war the U.S. has ever launched” as well as part of a “neocon strategy.”

More here.

How a book about fish nearly sank Isaac Newton’s Principia

Ian Sample in The Guardian:

The-Royal-Society--engrav-007It was a salutary lesson for the Royal Society and made clear that the formidable intelligence of its scientific membership was no guarantee of sound business judgement.

The debacle played out in the 17th century when the country's most prestigious scientific organisation ploughed its money into the lavishly illustrated Historia Piscium, or History of Fishes, by John Ray and Francis Willughby.

Though groundbreaking in 1686, the book flopped and nearly broke the bank, forcing the Royal Society to withdraw from its promise to finance the publication of Newton's Principia, one of the most important works in the history of science.

Today, digital images from Historia Piscium, including a stunning engraving of a flying fish, are made available with more than a thousand others in a new online picture archive launched by the Royal Society.

The images span the society's 350-year history and include highlights from Robert Hooke's 17th century engravings of objects under the microscope; a committee member's doodle of Thomas Huxley from 1882; and the first sighting of a kangaroo, or perhaps a wallaby, by James Cook and the sailors aboard the Endeavour expedition in 1770. Notes accompanying the latter picture state: “it was of a light mouse colour, and in size and shape very much resembling a greyhound.”

More here.

The Ayatollah Under the Bed(sheets)

Karim Sadjadpour in Foreign Policy:

ScreenHunter_01 Apr. 24 16.22In the early years of the Iranian Revolution, an obscure cleric named Ayatollah Gilani became a sensation on state television by contemplating bizarre hypotheticals at the intersection of Islamic law and sexuality. One of his most outlandish scenarios — still mocked by Iranians three decades later — went like this:

Imagine you are a young man sleeping in your bedroom. In the bedroom directly below, your aunt lies asleep. Now imagine that an earthquake happens that collapses your floor, causing you to fall directly on top of her. For the sake of argument, let's assume that you're both nude, and you're erect, and you land with such perfect precision on top of her that you unintentionally achieve intercourse. Is the child of such an encounter halalzadeh (legitimate) or haramzadeh (a bastard)?

Such tales of random ribaldry may sound anomalous in the seemingly austere, asexual Islamic Republic of Iran. But the “Gili Show,” as it came to be known, had quite the following among both the traditional classes, who were titillated by his taboo topics, and the Tehrani elite, who tuned in for comic relief. Gilani helped spawn what is now a virtual cottage industry of clerics and fundamentalists turned amateur sexologists offering incoherent advice on everything from quickies (“The man's goal should be to lighten his load as soon as possible without arousing his woman”) to masturbation (“a grave, grave sin which causes scientific and medical harm”).

More here.

the Knoedler scandal

Cn_image.size.knoedler-gallery

The e-mail that brought the art world’s latest scandal to light came to Knoedler last November 29. It disclosed the results of forensic tests done to a Jackson Pollock painting, Untitled 1950, that the gallery had sold in 2007 for $17 million to Pierre Lagrange, a London hedge-fund multi-millionaire. Done in the painter’s classic drip-and-splash style and signed “J. Pollock,” the modest-size painting (15 inches by 281 1/2 inches) was found to contain yellow paint pigments not commercially available until about 1970. This was discouraging, since the painter’s fateful car crash had occurred on August 11, 1956. Lagrange wasn’t just discouraged. He was furious. Fiftyish, given to long brown locks and blue jeans, he had startled London society in 2011 by leaving his wife and three children, only to take up with a 42-year-old male fashion designer named Roubi L’Roubi. Selling the painting had been part of his effort to divide assets in connection with a divorce settlement that might be one of the largest in British history. Now he was giving Knoedler 48 hours to agree to reimburse him or face a lawsuit. To the art world’s astonishment, the venerable gallery simply pulled its brass doors shut. (Knoedler has said that the closing was a business decision unrelated to the Lagrange suit.)

more from Michael Shnayerson at Vanity Fair here.