Carl Zimmer in The New York Times:

For a century, doctors have waged war against bacteria, using antibiotics as their weapons. But that relationship is changing as scientists become more familiar with the 100 trillion microbes that call us home — collectively known as the microbiome. “I would like to lose the language of warfare,” said Julie Segre, a senior investigator at the National Human Genome Research Institute. “It does a disservice to all the bacteria that have co-evolved with us and are maintaining the health of our bodies.” This new approach to health is known as medical ecology. Rather than conducting indiscriminate slaughter, Dr. Segre and like-minded scientists want to be microbial wildlife managers.

No one wants to abandon antibiotics outright. But by nurturing the invisible ecosystem in and on our bodies, doctors may be able to find other ways to fight infectious diseases, and with less harmful side effects. Tending the microbiome may also help in the treatment of disorders that may not seem to have anything to do with bacteria, including obesity and diabetes. “I cannot wait for this to become a big area of science,” said Michael A. Fischbach, a microbiologist at the University of California, San Francisco, and an author of a medical ecology manifesto published this month in the journal Science Translational Medicine. Judging from a flood of recent findings about our inner ecosystem, that appears to be happening. Last week, Dr. Segre and about 200 other scientists published the most ambitious survey of the human microbiome yet. Known as the Human Microbiome Project, it is based on examinations of 242 healthy people tracked over two years. The scientists sequenced the genetic material of bacteria recovered from 15 or more sites on their subjects’ bodies, recovering more than five million genes.

More here.

Uri Friedman at Foreign Policy:

On the campaign trail, Mitt Romney contrasts his vision of American greatness with what he claims is Barack Obama's proclivity for apologizing for it. The “president doesn't have the same feelings about American exceptionalism that we do,” Romney has charged. All countries have their own brand of chest-thumping nationalism, but almost none is as patently universal — even messianic — as this belief in America's special character and role in the world. While the mission may be centuries old, the phrase only recently entered the political lexicon, after it was first uttered by none other than Joseph Stalin. Today the term is experiencing a resurgence in an age of anxiety about American decline.

More here.

An interview from The Economist with Satoshi Kanazawa on intelligence and evolution:

What, if any, evolutionary advantage does intelligence give us?

Actually, less intelligent people are better at doing most things. In the ancestral environment general intelligence was helpful only for solving a handful of evolutionarily novel problems.

You mean our ancestors did not really have to reason?

Evolution equipped humans with solutions for a whole range of problems of survival and reproduction. All they had to do was to behave in the ways in which evolution had designed them to behave—eat food that tastes good, have sex with the most attractive mates. However, for a few evolutionarily novel problems, evolution equipped us with general intelligence so that our ancestors could reason in order to solve them. These evolutionarily novel problems were few and far between. Basically, dealing with any type of major natural disaster that is very infrequent in occurrence would require general intelligence.

More here.

Over at Columbia University Press, Gary Francione, author of Animals as Persons: Essays on the Abolition of Animal Exploitation, The Animal Rights Debate: Abolition or Regulation?, and several other titles, and Michael Marder, author of the forthcoming Plant-Thinking: A Philosophy of Vegetal Life debate the ethics of eating plant life:

Michael Marder: As I have pointed out, contemporary research in botany gives us ample reasons to believe that plants are aware of their environment in a nonconscious way—for instance, thanks to the roots that are capable of altering their growth pattern in moving toward resource-rich soil or away from nearby roots of other members of the same species. To ignore such evidence in favor of a stereotypical view of plants as thing-like is counterproductive, both for ethics and for our understanding of what they are.

When we, humans, use ourselves as a measuring stick against which everything else in world is evaluated, then an anthropomorphic image of sentience and intelligence comes to govern our ethics. True: the life of plants resembles our living patterns to a lesser extent than the life of animals. But to use this as a cornerstone of ethics and a justification for rejecting the moral claim plants have on us is a case of extreme speciesism.

Gary Francione: Speciesism occurs when the interests of a being are accorded less or no weight solely on the basis of species. To say that a being has interests is to say that the being has some sort of mind—any sort of mind—that prefers, desires, or wants. It is to say that there is someone who prefers, desires, or wants. You cannot act with speciesism with respect to a being that has no interests, such as a plant.

Your entire argument rests on your confusing a reaction with a response. If you put an electrical current through a wire that is attached to a bell, the bell will ring. The bell reacts; it does not respond. It is as absurd to say that a bell has a “nonconscious response” as it is to say a plant does.

Over at Philosophy Bites:

Recent research in neuroscience following on from the pioneering work of Benjamin Libet seems to point to the disconcerting conclusion that free will is an illusion. Adina Roskies of Dartmouth College is not convinced that this conclusion follows. In this episode of the Philosophy Bites podcast she explains to David Edmonds why the conclusion that free will is an illusion is far stronger than the evidence warrants.

Listen to Adina Roskies on Neuroscience and Free Will

Early in the spring of 1950, Ray Bradbury, a budding author working at a coin-operated typewriter in the UCLA library, managed — in 49 hours, at 20 cents an hour — to write the first draft of a prophetic novel that is still very much with us, half a century later. Originally, he called it The Fire Man. We know it now by the far more poetic and memorable title he coined before the finished book went to press in 1953: Fahrenheit 451. His tale’s premise is ironic, given that he was writing it in a library. His hero, Montag, is a fireman of the future — a municipal worker whose job is to burn books. Reading is a rebellious and even dangerous activity in the late 20th and early 21st centuries, as Bradbury envisioned them. (And here we are.) Reading leads to asking questions, and questions lead to thinking for oneself: a great crime in his nightmarish yet plausible future America. Books are torched like witches. The story hinges on Montag’s gradual conversion, as he discovers, by inexorable degrees, the life-giving power of what he is burning. He grows curious; he steals a book and smuggles it home, though to do so is to risk prison.

more from F.X. Feeney at the LA Review of Books here.

Jeremy Waldron over at the NYT's Opinionator:

The issue of hate speech legislation is, in my view, a difficult one. There are good arguments on both sides and, among the respondents, the critics have flagged a number of important issues.

Of course some of the critics are just dismissive: “Is Waldron’s book … a joke?” asked Ron Hansing of Columbus, Mo. “God help us from this kind of thinking!” And Robert Cicero of Tuckahoe, N.Y., wrote: “Shame on the whole lot of you” for even discussing this; the discussion, he said, “is yet one more assault on the US Constitution.” Or as Paz from New Jersey put it, “What part of ‘shall not be infringed’ do you fail to understand?”

But even those who love the First Amendment should be interested in at least understanding the things that can be said on the other side, if only to reinforce their sense of what’s distinctive about this country’s commitments. A large proportion of the other advanced democracies in the world combine a commitment to free speech with rules prohibiting hate speech. Isn’t it worth considering how they do this? And why? No one is burning the constitution here. We’re just trying to think about it.

Democracies like Britain, France, Germany, Denmark, Canada and New Zealand all prohibit hate speech of various kinds. They do so for what they think are good reasons. It is worth thinking about those reasons. Are they good reasons that (from an American First Amendment perspective) are just not strong enough to stand up against our overwhelmingly powerful commitment to free speech? Or are they simply bad reasons?

I think some of the things people cite in favor of hate speech regulation are bad reasons — like trying to protect people from being offended and annoyed. I agree with Stanley Fish about that. But some of the reasons are about dignity, not offense — I spend a lot of time in the book thinking aloud about that distinction — and these reasons are worth taking seriously, even if ultimately we think they are trumped by the value of free speech.

The civilians who had war brought to them: could there be a better encapsulation of the twentieth century’s trajectory of armed conflicts? “That statement shows a real clarity on Gellhorn’s part,” says Jon Lee Anderson, a reporter for The New Yorker who has covered wars in Central America, Iraq, and Syria. Statistics confirm Gellhorn’s insight: the Marxist historian Eric Hobsbawm, for instance, has estimated that in World War I, soldiers constituted 95 percent of casualties; in contemporary conflicts, most of which are intra-national, unarmed civilians account for 80 to 90 percent of casualties. In many of today’s wars, civilians are the deliberate—indeed, the primary—targets: think, for instance, of the Lord’s Resistance Army, the Ugandan group that enslaves children; of the militias in the Democratic Republic of Congo, who are systemic practitioners of mass rape and vaginal mutilation; of the Taliban’s bombings of schools and marketplaces; of Al Qaeda’s attacks on Iraqi mosques; of Al Shabaab’s assaults on medical students, teachers, and soccer fans; of the recent wars in Darfur, Colombia, Chechnya, Liberia, and Sierra Leone. Political theorist John Keane has dubbed these conflicts “uncivil wars” whose perpetrators practice “violence according to no rules except those of destructiveness itself—of people, property, the infrastructure, places of historical importance, even nature itself . . . Some of today’s conflicts seem to lack any logic or structure except that of murder on an unlimited scale.” Mary Kaldor of the London School of Economics has written that these new wars replace “the politics of ideas” with “the politics of identity” and cannot, therefore, be understood in conventional political terms.

more from Susie Linfield at Guernica here.

Fiona Apple has always been in the process of breaking up, usually preëmptively—before you can ask, she will provide a list of reasons not to love her. On a brief tour this spring, she opened each night with the rollicking “Fast As You Can,” from 1999, which is her signature guarantee of interpersonal mayhem: “Oh, darling, it’s so sweet, you think you know how crazy, how crazy I am. You say you don’t spook easy, you won’t go, but I know, and I pray that you will.” Much has been made of her comments at the 1997 MTV Video Music Awards that the music world is “bullshit,” and of several instances of her leaving the stage mid-performance. These moments have become to Apple as bat-biting has been to Ozzy Osbourne—dramatic anecdotes that play well. But those stories have been replaced with a calmer narrative; by her own account, she’s spent much of the past few years doing little more than walking her dog, visiting the club Largo, near her house in Los Angeles, and working on small projects like filming hummingbirds. The stories do say something about obsession and control, and are indicative of how exacting an artist she is. After four albums in sixteen years, Apple has racked up maybe five bad songs, total. “Idler Wheel” is less crammed with detail than her last record, “Extraordinary Machine,” but it has the same effect: once heard, a song lodges in the mind, melodies take root, and words loop of their own accord. It is an astonishing album.

more from Sasha Frere-Jones at The New Yorker here.

Hello,

The editors of 3QD have made their decision. The twenty semifinalists have been winnowed down to six, and three wildcard entries added. Thanks again to all the participants.

Once again, Carla Goller has provided a “trophy” logo that our finalists may choose to display on their own blogs. And if you like our site, please do add us to your blogroll!

So, here it is, the final list that I am sending to Sean Carroll, who will select the 1st, 2nd, and 3rd prize winners: (in alphabetical order by blog name here)

1. Boing Boing: What Fukushima can teach us about coal pollution
2. Empirical Zeal: The crayola-fication of the world: How we gave colors names, and it messed with our brains
3. Quantum Diaries: Helicity, Chirality, Mass, and the Higgs
4. Scientific American Guest Blog: Trayvon Martin’s Psychological Killer: Why We See Guns That Aren’t There
5. The Mermaid's Tale: Forget bipedalism. What about babyism?
6. The Primate Diaries: Freedom to Riot: On the Evolution of Collective Violence
7. The Trenches of Discovery: The War of the Immune Worlds
8. Three-toed Sloth: In Soviet Union, Optimization Problem Solves You
9. viXra log: Higgs Boson Live Blog: Analysis of the CERN announcement

We'll announce the three winners on or around June 25, 2012.

Good luck!

Abbas

P.S. The editors of 3QD will not be making any comments on our deliberations, or the process by which we made our decision, other than to simply say that we picked what we thought were the best posts out of the semifinalists, and added three others which we also liked.

Sughra Raza. Untitled. Maine, June 2012.

Digital photograph.

Hello,

The voting round of our science prize (details here) is over. A total of 2,615 votes were cast for the 107 nominees (click here for full list of nominees). Thanks to the nominators and the voters for participating.

Carla Goller has designed a “trophy” logo that our top twenty vote-getters may choose to display on their own blogs. So here they are, in descending order from the most voted-for:

1. Astronomy Picture of the Day: Red Aurora Over Australia
2. Scientific American Guest Blog: The educational value of creative disobedience
3. Above the Market: We Suck at Math
4. Empirical Zeal: The crayola-fication of the world: How we gave colors names, and it messed with our brains
5. Amy Shira Teitel: Was NASA’s First Launch Delay its Most Significant?
6. Why We Reason: Does Pinker’s “Better Angels” Undermine Religious Morality?
7. Scientific American Guest Blog: Trayvon Martin’s Psychological Killer: Why We See Guns That Aren’t There
8. Science Sushi: Time – and brain chemistry – heal all wounds
9. viXra log: Higgs Boson Live Blog: Analysis of the CERN announcement
10. The Mermaid's Tale: Forget bipedalism. What about babyism?
11. World Science Festival: E.O. Wilson’s Controversial Rethink of Altruism
12. Gaines, On Brains: Seeing into the future? The neuroscience of déjà vu
13. The Primate Diaries: Freedom to Riot: On the Evolution of Collective Violence
14. The Scorpion and the Frog: Snakes Deceive to Get a Little Snuggle
15. The Spectrum of Riemannium: Time of Flight
16. Inkfish: Life Advice: Think More about Death
17. Boundary Vision: Do scientific explanations have to ruin wonder? Stargazing and more with songwriter Jim Fitzpatrick
18. Cedar's Digest: Purple Doesn’t Exist: Some thoughts on Male Privilege and Science Online
19. Cosmology Science Blog: Cosmic Microwave Angular Resolution Surprise
20. The Trenches of Discovery: The War of the Immune Worlds

The editors of 3 Quarks Daily will now pick the top six entries from these, and after possibly adding up to three “wildcard” entries, will send that list of finalists to Sean Carroll for final judging. We will post the shortlist of finalists here in the next day or two.

Good luck!

Abbas

Daniel Cole in The Guardian:

Elinor Ostrom, who has died of pancreatic cancer aged 78, was the first and only woman to win the Nobel prize for economics. She received the award, shared with Oliver E Williamson, in 2009 for her analyses of how individuals and communities can often manage common resources – ranging from irrigation and fisheries to information systems – as well or better than markets, companies or the state. Earlier this year, she appeared on Time magazine's list of the 100 most influential people in the world.

Lin, as she was known to friends, family and colleagues – of whom I was one – was born in Los Angeles and attended Beverly Hills high school. After completing her doctorate in political science at the University of California, Los Angeles, in 1965 – a time when it was still rare for women to hold advanced degrees, let alone tenured positions, in the social sciences – she moved, with her husband, the political theorist Vincent Ostrom, to Bloomington, Indiana, where Lin was initially hired as a visiting assistant professor at Indiana University. The couple remained at the university for the rest of their long and productive careers. Her work was for a long time considered far outside the mainstream of American political science.

More here.

More here.

A little old, but worth a read from The Guardian:

It is the convention of awards-ceremony etiquette for the winner to perform a convincing impression of bashful disbelief. The man I meet just hours before he was awarded the Guardian First Book award last Thursday has just stepped off a flight from New York, however, only an hour ago, and his bearing doesn't say “What, little old me? Wow!” so much as “So what time is it here anyway?” In fact, he conveys that precise blend of exhaustion, distraction and authority instantly recognisable from any hospital ward in the world. This should come as no surprise, for he is a senior oncologist – assistant professor of medicine at Columbia University, and staff cancer physician at Columbia University Medical Centre. And yet, until we met it had seemed scarcely possible that the author of The Emperor of All Maladies could really be an actual doctor and not a writer, so exquisitely is his book crafted and paced.

Published a year ago, the Emperor of All Maladies has won the Pulitzer prize for non-fiction, been shortlisted for the National Book Critics Circle award, and named one of the Top 10 Books of the Year by the New York Times, Time magazine and Oprah Winfrey; the sort of success that soars beyond the wildest heights of literary ambition into the stratosphere of fantasy. Yet when Siddhartha Mukherjee talks about his book, it is with a striking air of disinterested detachment. At first I put it down to jet lag. Then I think, no, of course, the poor man must just be so accustomed by now to the carousel of plaudits and prizes and media demands, he has reached the glaze of autopilot. Soon, though, I realise that is not it either. Mukherjee's impression of reluctant ownership of his own success is, I suspect, down to a profound sense of personal insignificance in the face of his subject's enormity. Mukherjee decided to write a history of cancer when a terminally ill patient asked him a simple question: could he explain exactly “what it is I'm battling?” But as Mukherjee immersed himself in research, the disease quickly began to assume the characteristics of a personality, and so cancer's historian became its biographer. He takes us from the earliest records of cancer in 2,500BC, through medieval theories of black bile and bloodletting, on to the surgical butchery of 19th-century mastectomies, performed with no anaesthetic or penicillin but reckless confidence, before reaching the rollercoaster of 20th-century medical politics, which swung between indifference, euphoria and despair, each wild lurch owing more to socio-economic fashion than to anything resembling solid science.

More here.

From Smithsonian:

Having children changes a man. All of us know examples of that. I’m pretty sure, for instance, that the only time I ever saw my father sing was to his kids. It wasn’t always pretty, but it was pure Dad. But is there something about fatherhood that actually changes the male brain? Studies suggest that it does, including one published a few years ago which found that new sets of neurons formed in brains of mouse dads that stayed around the nest after their pups were born. Still, there’s much yet to be learned about the effects of being a father. And so scientists continue to explore the eternal question: “What’s with this guy?” Here are 10 recent studies deconstructing dad:

1.The upside to an old old man: So what if they’re only good for one throw in a game of catch. Old fathers can do something for their kids that young dads can’t–pass on genes that give them a better shot at a long life. A study published earlier this week in the Proceedings of the National Academy of Sciences says children of older fathers–men who wait until their late 30s to have children–inherit longer telomeres, caps at the end of the chromosomes that protect them from degeneration. And that seems to to promote slower aging and likely a longer lifespan for those kids.

2. See what I do for you?: Most dads know they’re going have to make a few sacrifices for their kids, but lose testosterone? Who knew? A recent study of 600 men in the Philippines found that testosterone levels dropped considerably after they fathered children. Scientists were quick to counter the notion that raising kids makes someone a less manly man and instead concluded that men’s bodies helped them evolve hormonal systems that make it easier to commit to their families. And the men who spent the most time taking care of their kids had the lowest testosterone levels, suggesting that biology helps them shift into parent mode.

More here.

Do Not Go Gentle Into That Good Night

Do not go gentle into that good night,
Old age should burn and rage at close of day;
Rage, rage against the dying of the light.

Though wise men at their end know dark is right,
Because their words had forked no lightning they
Do not go gentle into that good night.

Good men, the last wave by, crying how bright
Their frail deeds might have danced in a green bay,
Rage, rage against the dying of the light.

Wild men who caught and sang the sun in flight,
And learn, too late, they grieved it on its way,
Do not go gentle into that good night.

Grave men, near death, who see with blinding sight
Blind eyes could blaze like meteors and be gay,
Rage, rage against the dying of the light.

And you, my father, there on the sad height,
Curse, bless me now with your fierce tears, I pray.
Do not go gentle into that good night.
Rage, rage against the dying of the light.

by Dylan Thomas