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For the purposes of this article, we’ll focus on the fundamental difference between two major types of life-forms: those that have a cell wall but few or no internal subdivisions, and those that possess cells containing a nucleus, mitochondria, chloroplasts and other smaller substructures, or organelles.

Even before quorum sensing was discovered in V. fischeri, scientists had noted many examples of coordinated action, such as “swarming,” in which a colony of bacteria moves as a unit across a surface, and the development of “fruiting bodies,” in which bacteria glom together to form inert spores as a means of surviving severe environmental conditions.

Bacteria can live solitary lives, of course, but they prefer to aggregate in biofilms, also known as “slime cities.” Biofilms usually form on a surface, whether it’s the inner lining of the intestines or inside water pipes or on your teeth. In these close-knit colonies, bacteria coordinate group production of a slimy translucent coating and fibers called “curli” and “pili” that attach the colony to something else. Biofilms can harbor multiple types of bacteria as well as fungi and protists (microscopic eukaryotes). A complex vascular system for transporting nutrients and chemical signals through a biofilm may also develop. As Tim Friend described in his book The Third Domain, explorers diving to the wreck of the Titanic found these features in “rusticles” — draped colonies of microbes — feeding on the iron in the Titanic‘s hull and skeleton, more than 2 miles under the surface.

in practice, the medical notion of friendly microbes has yet to extend much past the idea that eating yogurt is good for you. For most doctors and medical microbiologists, microbes are enemies in a permanent war. Medicine certainly has good reason to view microbes as dangerous, since the germ theory of disease and the subsequent development of antibiotics are two of medical science’s greatest accomplishments.

When threatened, bacteria become defensive, often producing toxins that make the host even sicker. They also tend to speed up their acquisition of and purging of genes when under external selection pressure, of which antibiotics are an obvious and powerful example.

Gut bacteria play a role in obesity, which affects about a third of American adults.

Research in animals supports the idea that gut bacteria play a role in weight regulation.

bacteria produce some of the same types of neurotransmitters that regulate the function of the human brain.

it’s been known for a while that sick people get depressed and anxious. This seems so obvious as to be a no-brainer, but research suggests that some of the fear and fatigue associated with infections stems from immune responses affecting the brain.

As it turns out, however, very few bacteria can be grown in the relatively austere conditions of laboratories. In fact, only about 0.1 percent of all bacteria are currently culturable. Many bacteria don’t do well in monoculture, preferring to live in mixed communities of microorganisms. Those living in extreme temperatures and pressures require very specialized equipment to grow in a typical lab.

In fact, they wrote, the genes that enable these processes today “may have been distributed across a common global gene pool, before cellular differentiation and vertical genetic transmission evolved as we know it today.”

The grand story of human exceptionalism — the idea that humans are separate from and superior to everything else in the biosphere — has taken a terminal blow from the new knowledge about bacteria. Whether humanity decides to sanctify them in some way or merely admire them and learn what they’re really doing, there’s no going back.

First, he campaigned intensely against the Bush policy in Iraq, arguing that it was the wrong war in the wrong place.

Second, he argued that the important war was in Afghanistan, where he pledged to switch his attention to face the real challenge of al Qaeda.

Third, he argued against Bush administration policy on detention, military tribunals and torture, in his view symbolized by the U.S. detention facility at Guantanamo Bay Naval Base.

In a fourth element, he argued that Bush had alienated the world by his unilateralism

The European view — or more precisely, the French and German view — was that allies should have a significant degree of control over what Americans do.

Thus, in spite of the Nobel Peace Prize in the early days of the romance, the bloom wore off as the Europeans discovered that Obama was simply another U.S. president. More precisely, they learned that instead of being able to act according to his or her own wishes, circumstances constrain occupants of the U.S. presidency into acting like any other president would.

Campaign rhetoric notwithstanding, Obama’s position on Iraq consisted of slightly changing Bush’s withdrawal timetable. In Afghanistan, his strategy was to increase troop levels beyond what Bush would consider. Toward Iran, his policy has been the same as Bush’s: sanctions with a hint of something later.

The idea that nations weren’t designed to trust or like one another, but rather pursued their interests with impersonal force, was alien to him. And so he thought he could explain the United States to the Muslims without changing U.S. policy and win the day.

It is not that anyone expected his rhetoric to live up to its promise, since no politician can pull that off, but that they see Obama as someone who thought rhetoric would change things. In that sense, he is seen as naive and, worse, as indecisive and unimaginative.

The questions I have heard most often on many different issues are simple: What is the American position, what is the American interest, what will the Americans do? (As an American, I frequently find my hosts appointing me to be the representative of the United States.)

What his meaning is? And what he proposes by all these curious researches?

When he awakes from his dream, he will be the first to join in the laugh against himself, and to confess, that all his objections are mere amusement, and can have no other tendency than to show the whimsical condition of mankind, who must act and reason and believe;

Pursing doubt to its ultimate end, Santayana challenges self-consciousness, discourse, logic, change, memory and time. In doing so, he goes well beyond Descartes’ doubts to discover the ultimate certainty, the perusal of a passing datum, a mere instance of awareness.

Knowledge does not arise until intelligence arrives on the scene and connects these instances of awareness into larger, meaningful wholes, which can then be interpreted as symbols of a posited, external reality existing in time and space.

this animal faith is by no means an entirely groundless or “arbitrary” inclination, but one which is tested and corroborated during every moment when intelligence holds dominion over our lives.

Critical to Santayana’s view is the notion that some views are biologically inevitable, so that philosophers who deny them are not being altogether sincere.

the nature of truth is correspondence, the test of truth is pragmatic

in relation to these issues, often equivocates between rationalistic speculation (e.g., the Objectivist axioms) and an extreme empiricism (e.g., basing all knowledge on the “evidence” of the senses)

Maybe sometimes it’s the questions that are biased, not the answers,” he said, flashing a friendly smile.

That question has been central to Ioannidis’s career. He’s what’s known as a meta-researcher, and he’s become one of the world’s foremost experts on the credibility of medical research.

He charges that as much as 90 percent of the published medical information that doctors rely on is flawed.

“I take all the researchers who visit me here, and almost every single one of them asks the tree the same question,” Ioannidis tells me, as we contemplate the tree the day after the team’s meeting. “‘Will my research grant be approved?’” He chuckles, but Ioannidis (pronounced yo-NEE-dees) tends to laugh not so much in mirth as to soften the sting of his attack. And sure enough, he goes on to suggest that an obsession with winning funding has gone a long way toward weakening the reliability of medical research.

“I assumed that everything we physicians did was basically right, but now I was going to help verify it,” he says. “All we’d have to do was systematically review the evidence, trust what it told us, and then everything would be perfect.” It didn’t turn out that way. In poring over medical journals, he was struck by how many findings of all types were refuted by later findings. Of course, medical-science “never minds” are hardly secret. And they sometimes make headlines, as when in recent years large studies or growing consensuses of researchers concluded that mammograms, colonoscopies, and PSA tests are far less useful cancer-detection tools than we had been told; or when widely prescribed antidepressants such as Prozac, Zoloft, and Paxil were revealed to be no more effective than a placebo for most cases of depression; or when we learned that staying out of the sun entirely can actually increase cancer risks; or when we were told that the advice to drink lots of water during intense exercise was potentially fatal; or when, last April, we were informed that taking fish oil, exercising, and doing puzzles doesn’t really help fend off Alzheimer’s disease, as long claimed. Peer-reviewed studies have come to opposite conclusions on whether using cell phones can cause brain cancer, whether sleeping more than eight hours a night is healthful or dangerous, whether taking aspirin every day is more likely to save your life or cut it short, and whether routine angioplasty works better than pills to unclog heart arteries.

“I realized even our gold-standard research had a lot of problems,” he says.

This array suggested a bigger, underlying dysfunction, and Ioannidis thought he knew what it was. “The studies were biased,” he says. “Sometimes they were overtly biased. Sometimes it was difficult to see the bias, but it was there.” Researchers headed into their studies wanting certain results—and, lo and behold, they were getting them. We think of the scientific process as being objective, rigorous, and even ruthless in separating out what is true from what we merely wish to be true, but in fact it’s easy to manipulate results, even unintentionally or unconsciously. “At every step in the process, there is room to distort results, a way to make a stronger claim or to select what is going to be concluded,” says Ioannidis. “There is an intellectual conflict of interest that pressures researchers to find whatever it is that is most likely to get them funded.”

He chose to publish one paper, fittingly, in the online journal PLoS Medicine, which is committed to running any methodologically sound article without regard to how “interesting” the results may be. In the paper, Ioannidis laid out a detailed mathematical proof that, assuming modest levels of researcher bias, typically imperfect research techniques, and the well-known tendency to focus on exciting rather than highly plausible theories, researchers will come up with wrong findings most of the time.

The article spelled out his belief that researchers were frequently manipulating data analyses, chasing career-advancing findings rather than good science, and even using the peer-review process—in which journals ask researchers to help decide which studies to publish—to suppress opposing views.

Ioannidis was putting his contentions to the test not against run-of-the-mill research, or even merely well-accepted research, but against the absolute tip of the research pyramid. Of the 49 articles, 45 claimed to have uncovered effective interventions. Thirty-four of these claims had been retested, and 14 of these, or 41 percent, had been convincingly shown to be wrong or significantly exaggerated. If between a third and a half of the most acclaimed research in medicine was proving untrustworthy, the scope and impact of the problem were undeniable. That article was published in the Journal of the American Medical Association.

When a five-year study of 10,000 people finds that those who take more vitamin X are less likely to get cancer Y, you’d think you have pretty good reason to take more vitamin X, and physicians routinely pass these recommendations on to patients. But these studies often sharply conflict with one another. Studies have gone back and forth on the cancer-preventing powers of vitamins A, D, and E; on the heart-health benefits of eating fat and carbs; and even on the question of whether being overweight is more likely to extend or shorten your life. How should we choose among these dueling, high-profile nutritional findings? Ioannidis suggests a simple approach: ignore them all.

the odds are that in any large database of many nutritional and health factors, there will be a few apparent connections that are in fact merely flukes, not real health effects—it’s a bit like combing through long, random strings of letters and claiming there’s an important message in any words that happen to turn up.

nd these problems are aside from ubiquitous measurement errors (for example, people habitually misreport their diets in studies), routine misanalysis (researchers rely on complex software capable of juggling results in ways they don’t always understand), and the less common, but serious, problem of outright fraud (which has been revealed, in confidential surveys, to be much more widespread than scientists like to acknowledge).

And so it goes for all medical studies, he says. Indeed, nutritional studies aren’t the worst. Drug studies have the added corruptive force of financial conflict of interest. The exciting links between genes and various diseases and traits that are relentlessly hyped in the press for heralding miraculous around-the-corner treatments for everything from colon cancer to schizophrenia have in the past proved so vulnerable to error and distortion, Ioannidis has found, that in some cases you’d have done about as well by throwing darts at a chart of the genome.

Though scientists and science journalists are constantly talking up the value of the peer-review process, researchers admit among themselves that biased, erroneous, and even blatantly fraudulent studies easily slip through it.

Of those 45 super-cited studies that Ioannidis focused on, 11 had never been retested. Perhaps worse, Ioannidis found that even when a research error is outed, it typically persists for years or even decades. He looked at three prominent health studies from the 1980s and 1990s that were each later soundly refuted, and discovered that researchers continued to cite the original results as correct more often than as flawed—in one case for at least 12 years after the results were discredited.

Medical research is not especially plagued with wrongness. Other meta-research experts have confirmed that similar issues distort research in all fields of science, from physics to economics (where the highly regarded economists J. Bradford DeLong and Kevin Lang once showed how a remarkably consistent paucity of strong evidence in published economics studies made it unlikely that any of them were right).

Ioannidis initially thought the community might come out fighting. Instead, it seemed relieved, as if it had been guiltily waiting for someone to blow the whistle, and eager to hear more. David Gorski, a surgeon and researcher at Detroit’s Barbara Ann Karmanos Cancer Institute, noted in his prominent medical blog that when he presented Ioannidis’s paper on highly cited research at a professional meeting, “not a single one of my surgical colleagues was the least bit surprised or disturbed by its findings.” Ioannidis offers a theory for the relatively calm reception. “I think that people didn’t feel I was only trying to provoke them, because I showed that it was a community problem, instead of pointing fingers at individual examples of bad research,” he says. In a sense, he gave scientists an opportunity to cluck about the wrongness without having to acknowledge that they themselves succumb to it—it was something everyone else did.

The irony of his having achieved this sort of success by accusing the medical-research community of chasing after success is not lost on him, and he notes that it ought to raise the question of whether he himself might be pumping up his findings.

Tatsioni doesn’t so much fear that someone will carve out the man’s healthy appendix. Rather, she’s concerned that, like many patients, he’ll end up with prescriptions for multiple drugs that will do little to help him, and may well harm him. “Usually what happens is that the doctor will ask for a suite of biochemical tests—liver fat, pancreas function, and so on,” she tells me. “The tests could turn up something, but they’re probably irrelevant. Just having a good talk with the patient and getting a close history is much more likely to tell me what’s wrong.” Of course, the doctors have all been trained to order these tests, she notes, and doing so is a lot quicker than a long bedside chat. They’re also trained to ply the patient with whatever drugs might help whack any errant test numbers back into line.

patients often don’t even like it when they’re taken off their drugs, she explains; they find their prescriptions reassuring.

Already feeling that they’re fighting to keep patients from turning to alternative medical treatments such as homeopathy, or misdiagnosing themselves on the Internet, or simply neglecting medical treatment altogether, many researchers and physicians aren’t eager to provide even more reason to be skeptical of what doctors do—not to mention how public disenchantment with medicine could affect research funding.

being wrong in science is fine, and even necessary

Mr. Rushdie started using a computer only when the Ayatollah Khomeini’s 1989 fatwa drove him underground. “My writing has got tighter and more concise because I no longer have to perform the mechanical act of re-typing endlessly,” he explained during an interview while in hiding. “And all the time that was taken up by that mechanical act is freed to think.”

At the Emory exhibition, visitors can log onto a computer and see the screen that Mr. Rushdie saw, search his file folders as he did, and find out what applications he used. (Mac Stickies were a favorite.) They can call up an early draft of Mr. Rushdie’s 1999 novel, “The Ground Beneath Her Feet,” and edit a sentence or post an editorial comment.

To the Emory team, simulating the author’s electronic universe is equivalent to making a reproduction of the desk, chair, fountain pen and paper that, say, Charles Dickens used, and then allowing visitors to sit and scribble notes on a copy of an early version of “Bleak House.”

The heart of the lab is the Forensic Recovery of Evidence Device, nicknamed FRED, which enables archivists to dig out data, bit by bit, from current and antiquated floppies, CDs, DVDs, hard drives, computer tapes and flash memories, while protecting the files from corruption.

Back in the 1990s, Allen interviewed me at length about a feature story he was doing (it was later published in the WP) on how people of different ages react to that old Warner Brothers cartoon about Roadrunner and Wile E. Coyote.  In a talk he was giving at a local college, he discovered by accident that all of the (Xer) students sympathized with the coyote, not the roadrunner.  He was flabbergasted, because for as long as he could remember, he and his peers had always rooted for the roadrunner.

Back before the digital revolution, access to information was an issue. The size of the library mattered. One reason to go to college was to get access.

By emphasizing mass and sameness and rankings, colleges have changed their mission.

The more applicants they reject, the higher they rank in US News and other rankings. And thus the rush to game the rankings continues, which is a sign that the marketers in question (the colleges) are getting desperate for more than their fair share.

The data I'm seeing shows that a degree (from one of those famous schools, with or without a football team) doesn't translate into significantly better career opportunities

We now have much better technologies, and a much better understanding of the Martian environment, but we still haven’t had a life-detection experiment since Viking!

all our biological molecules have a certain “handedness,” a left- or right-handed orientation to their structures. So if the molecules in the organisms from Mars have a different handedness than the molecules from Earth life, that would be pretty good proof.

The biggest thing is that we don’t yet understand the origin of life on Earth. Rather, we understand the persistence of life in habitable environments on this planet. There are tons of potential habitable environments elsewhere in our own solar system, and we know that life originated on Earth and spread nearly everywhere.

it takes much more subtle forms, and we’re all guilty of it from time to time.

the enjoyment of a good conversation is becoming more of a rarity these days. In our time of cell phones, text messaging, and emails, we’re having less face-to-face interactions, and thus when we do meet up with people in the flesh, our social skills can be a bit rusty.

A good conversation is an interesting thing; it can’t be a solely individual endeavor—it has to be a group effort.

During a conversation, each person makes initiatives. These initiatives can either be attention-giving or attention-getting. Conversational narcissists concentrate more on the latter because they are focused on gratifying their own needs. Attention-getting initiatives can take two forms: active and passive.

The shift-response if often very subtle. People put in a nice transition to disguise it by prefacing their response with something like, “That’s interesting,” “Really? “I can see that,” right before they make a comment about themselves.

it’s fine to share things about yourself, as long as you loop the conversation back to the person who initiated the topic.

Background acknowledgments

Supportive assertions

Supportive questions

Once someone introduces a topic, your job is to draw out the narrative from them by giving them encouragement in the form of background acknowledgments and supportive assertions, and moving their narrative along by asking supportive questions.

Arousal comes from deep inside the brain, in those primal regions of the autonomic nervous system where ingoing and outgoing signals are monitored and the glass over the big fight-or-flight button waits to be smashed.

Misattribution of arousal falls under the self-perception theory.

Arousal can fill up the spaces in your brain when you least expect it. It could be a rousing movie trailer or a plea for mercy from a distant person reaching out over YouTube. Like a coterie of prairie dogs standing alert as if living periscopes, your ancestors were built to pay attention when it mattered, but with cognition comes pattern recognition and all the silly ways you misinterpret your inputs.

The research into arousal says you are bad at explaining yourself to yourself, but it sheds light on why so many successful dates include roller-coasters, horror films and conversations over coffee.

There is a reason playful wrestling can lead to passionate kissing, why a great friend can turn a heaving cry into a belly laugh. There is a reason why great struggle brings you closer to friends, family and lovers. There is a reason why Rice Krispies commercials show moms teaching children how to make treats in crisp black-and-white while Israel Kamakawiwo’ole sings Somewhere Over the Rainbow. When you want to know why you feel the way you do but are denied the correct answer, you don’t stop searching. You settle on something – the person beside you, the product in front of you, the drug in your brain. You don’t always know the right answer, but when you are flirting over a latte don’t point it out.

At last count, there were 245 millionaires in congress, including 66 in the Senate.

All weekend I was thinking about this “jealousy” question, and I just kept coming back to all the different ways the game is rigged. People aren't jealous and they don’t want privileges. They just want a level playing field, and they want Wall Street to give up its cheat codes, things like:

Ordinary people have to borrow their money at market rates. Lloyd Blankfein and Jamie Dimon get billions of dollars for free, from the Federal Reserve.

Or the banks borrow billions at zero and lend mortgages to us at four percent, or credit cards at twenty or twenty-five percent. This is essentially an official government license to be rich, handed out at the expense of prudent ordinary citizens, who now no longer receive much interest on their CDs or other saved income.

This is equivalent to a trust fund teenager who trashes six consecutive off-campus apartments and gets rewarded by having Daddy co-sign his next lease. The banks needed programs like TLGP because without them, the market rightly would have started charging more to lend to these idiots. Apparently, though, we can’t trust the free market when it comes to Bank of America, Goldman, Sachs, Citigroup, etc.

Defenders of the banks like to talk a lot about how we shouldn't feel sorry for people who've been foreclosed upon, because it's they're own fault for borrowing more than they can pay back

Time after time, when big banks screw up and make irresponsible bets that blow up in their faces, they've scored bailouts.

When was the last time the government stepped into help you "avoid losses you might otherwise suffer?" But that's the reality we live in. When Joe Homeowner bought too much house, essentially betting that home prices would go up, and losing his bet when they dropped, he was an irresponsible putz who shouldn’t whine about being put on the street.

I've already gone off on this more than once, but it bears repeating. Bankers on Wall Street pay lower tax rates than most car mechanics.

Bank of America last year paid not a single dollar in taxes -- in fact, it received a "tax credit" of $1 billion.

Thank God our government decided to pledge $50 billion of your tax dollars to a rescue of General Motors! You just paid for one of the world's biggest tax breaks.

One thing we can still be proud of is that America hasn't yet managed to achieve the highest incarceration rate in history -- that honor still goes to the Soviets in the Stalin/Gulag era. But we do still have about 2.3 million people in jail in America.

Virtually all 2.3 million of those prisoners come from "the 99%." Here is the number of bankers who have gone to jail for crimes related to the financial crisis: 0.

That means that every single time a bank kicked someone out of his home, a local police department got a cut. Local sheriff's offices also get cuts of almost all credit card judgments, and other bank settlements. If you're wondering how it is that so many regional police departments have the money for fancy new vehicles and SWAT teams and other accoutrements, this is one of your answers.

The point being: if you miss a few home payments, you have a very high likelihood of colliding with a police officer in the near future. But if you defraud a pair of European banks out of a billion dollars  -- that's a billion, with a b -- you will never be arrested, never see a policeman, never see the inside of a jail cell.