Boris Indrikov's art

Boris Indrikov's art: "


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Do bacteria control your brain?

Do bacteria control your brain?: "

A new study has found evidence suggesting that you are not what you eat, so much as you are what's living in your gut. In mice, at least, the presence of normal gut bacteria has a significant impact on how an individual mouse behaves, and how its brain develops.

this new study is the first to extensively evaluate the influence of gut bacteria on the biochemistry and development of the brain. The scientists raised mice lacking normal gut microflora, then compared their behavior, brain chemistry and brain development to mice having normal gut bacteria. The microbe-free animals were more active and, in specific behavioral tests, were less anxious than microbe-colonized mice.

In one test of anxiety, animals were given the choice of staying in the relative safety of a dark box, or of venturing into a lighted box. Bacteria-free animals spent significantly more time in the light box than their bacterially colonized littermates. Similarly, in another test of anxiety, animals were given the choice of venturing out on an elevated and unprotected bar to explore their environment, or remain in the relative safety of a similar bar protected by enclosing walls. Once again, the microbe-free animals proved themselves bolder than their colonized kin ...

Consistent with these behavioral findings, two genes implicated in anxiety -- nerve growth factor-inducible clone A (NGF1-A) and brain-derived neurotrophic factor (BDNF) -- were found to be down-regulated in multiple brain regions in the germ-free animals ...

When Pettersson's team performed a comprehensive gene expression analysis of five different brain regions, they found nearly 40 genes that were affected by the presence of gut bacteria. Not only were these primitive microbes able to influence signaling between nerve cells while sequestered far away in the gut, they had the astonishing ability to influence whether brain cells turn on or off specific genes.

Personally, I'd like to see more analysis on what these findings mean. The Scientific American story quoted above makes it sound like normal gut bacteria are, on the whole, kind of cramping the brain's style. Given the evidence that exists about healthy gut bacteria's importance to maintaining other aspects of physical health, I'm curious whether this study implies that we humans have accepted a bit of a trade off. We get gut bacteria that help us digest food and train our immune systems—but we loose some control over how our brains function, possibly to our detriment, but possibly not, depending on the circumstances.

Oh, and, before the rest of you get a chance, I'm going to jump in here and make the obvious comment: 'I, for one, welcome our new E. coli overlords.'

Scientific American: The Neuroscience of the Gut

Via Matt Feltz

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Carved-away goose-egg

Carved-away goose-egg: "
Instructables user Bbstudio has been doing some extraordinary egg carving for the Eggbot Easter challenge. This carved-away goose egg is probably the most physically impressive, though there's a lot more aesthetically pleasing (if less improbable) designs in his portfolio.

BBStudio

(via Neatorama)

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DOG vs. BUBBLES

DOG vs. BUBBLES: "

Hysterical bubbles! (original) [Video LInk]


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Meet Science: What is "peer review"?

Meet Science: What is "peer review"?: "

When the science you learned in school and the science you read in the newspaper don't quite match up, the Meet Science series is here to help, providing quick run-downs of oft-referenced concepts, controversies, and tools that aren't always well-explained by the media.

'According to a peer-reviewed journal article published this week ...'

How often have you read that phrase? How often have I written that phrase? If we tried
to count, there would probably be some powers of 10 involved. It's clear from the context that 'peer-reviewed journal articles' are the hard currency of science. But the context is less obliging on the whys
and wherefores.

Who are these 'peers' that do the reviewing? What, precisely, do they review? Does a peer-reviewed paper always deserve respect, and how much trust should we place in the process of peer
review, itself? If you don't have a degree in the sciences, and you aren't particularly well-versed in self-taught
science Inside Baseball, there's really no reason why you should know the answers to all
those questions. You can't be an expert in everything, and this isn't something that's explicitly taught
in most high schools or basic level college science courses. And yet, I and the rest of the science media
continue to reference 'peer review' like all our readers know exactly what we're talking about.

I think it's high time to rectify that mistake. Ladies and gentlemen, meet peer review:

What does the phrase 'peer-reviewed journal article' really mean?

This part you've probably already figured out. Journal articles are like book reports, usually written
to document the methodology and results of a single scientific experiment, or to provide evidence
supporting a single theory. Another common type of paper that I talk about a lot are "meta analyses"
or "reviews"—big-picture reports that compare the results of lots of individual experiments,
usually done by compiling all the previously published papers about a very specific topic. No single
journal article is meant to be the definitive last word on anything. Instead, we're supposed to improve
our understanding of the world by looking at what the balance of evidence, from many experiments
and many articles, tell us. That's why I think reviews are often more useful, for laypeople. A single
experiment may be interesting, but it doesn't always tell you as much about how the world works as a
review can.

Both individual reports and reviews are published in scientific journals. You can think of these
as older, fancier, more heavily edited versions of 'zines. The same scientists who read the journals
write the content that goes in the journals. There are hundreds of journals. Some publish lots of
different types of papers on a very broad range of topics—"Science" and "Nature", for
instance—while others are much, much more specific. "Acute Pain", say. Or "Sleep Medicine
Reviews". Usually, you have to pay a journal a fee per page to be published. And you—or the
institution you work for—has to buy a subscription to the journal, or pay steep prices to read
individual papers.

Peer review really just means that other scientists have been involved in helping the editors of these
journals decide which papers to publish, and what changes need to be made to those papers before
publication.

How does peer review work?

It may surprise you to learn that this is not a standardized thing. Peer review evolved out of the informal practice of sending research to friends and colleagues to be critiqued, and it's never really been codified as a single process. It's still done on a voluntary basis, in scientists' free time. Such as that is. And most journals do not pay scientists for the work of peer review. For the most part, scientists are not formally trained in how to do peer review, nor given continuing education in how to do it better. And they usually don't get direct feedback from the journals or other scientists about the quality of their peer reviewing.

Instead, young scientists learn from their advisors—often when that advisor delegates, to the grad students, papers he or she had volunteered to review. Your peer-review education really depends on whether your advisor is good at it, and how much time they choose to spend training you. Meanwhile, feedback is usually indirect. Journals do show all the reviews to all of a paper's reviewers. So you can see how other scientists reviewed the same paper you reviewed. That gives you a chance to see what flaws you missed, and compare your work with others'. If you're a really incompetent peer reviewer, journals might just stop asking you to review, altogether.

Different journals have different guidelines they ask peer reviewers to follow. But there are some commonalities. First, most journals weed out a lot of the papers submitted to them before those papers are even put up for peer review. This is because different journals focus on publishing different things. No matter how cool your findings are, if they aren't on-topic, then 'Acute Pain' won't publish them. Meanwhile, a journal like 'Science' might prefer to publish papers that are likely to be very original, important to a field, or particularly interesting to the general public. In that case, if your results are accurate, but kind of dull, you probably will get shut out.

Second, peer reviews are normally done anonymously. The editors of the journal will often give the paper's author an opportunity to recommend, or caution against, a specific reviewer. But, otherwise, they pick who does the reviewing.

Reviewers are not the people who decide which papers will be published and which will not. Instead, reviewers look for flaws—like big errors in reasoning or methodology, and signs of plagiarism. Depending on the journal, they might also be asked to rate how novel the paper's findings are, or how important the paper is likely to be in its field. Finally, they make a recommendation on whether or not they think the specific paper is right for the specific journal.

After that, the paper goes back to the journal's editors, who make the final call.

If a paper is peer reviewed does that mean it's correct?

In a word: Nope.

Papers that have been peer reviewed turn out to be wrong all the time. That's the norm. Why? Frankly, peer reviewers are human. And they're humans trying to do very in-depth, time-consuming work in a limited number of hours, for no pay. They make mistakes. They rush through, while worrying about other things they're trying to get done. They once had to share a lab with the guy whose paper they're reviewing and they didn't like him. They get frustrated when a paper they're reviewing contradicts research they're working on. By sending every paper to several peer-reviewers, journals try to cancel out some of the inevitable slip-ups and biases, but it's an imperfect system. Especially when, as I said, there's not really any way to know whether or not you're a good peer reviewer, and no system for improving if you aren't. There's some evidence that, at least in the medical field, the quality and usefulness of reviews actually goes down as the reviewers get older. Nobody knows exactly why that is, but it could have to do with the lack of training and follow-up, the tendency to get more set in our ways as we age, and/or reviewers simply feeling burnt out and too busy.

It's also worth noting that peer review is really not set up to catch deliberate fraud. If you fake your results, and do it convincingly, there's not really any good reason why a peer reviewer would catch you. Instead, that's usually something that happens after a paper has been published—usually when other scientists try to replicate the fraudster's spectacular results, or find that his research contradicts their own in a way that makes no sense.

If a paper isn't peer-reviewed, does that mean it's incorrect?

Technically, no. But, here's the thing. Flawed as it is, peer review is useful. It's a first line of defense. It forces scientists to have some evidence to back up their claims, and it is likely to catch the most egregious biases and flaws. It even means that frauds can't be really obvious frauds.

Being peer reviewed doesn't mean your results are accurate. Not being peer reviewed doesn't mean you're a crank. But the fact that peer review exists does weed out a lot of cranks, simply by saying, 'There is a standard.' Journals that don't have peer review do tend to be ones with an obvious agenda. White papers, which are not peer reviewed, do tend to contain more bias and self-promotion than peer-reviewed journal articles.

You should think critically and skeptically about any paper—peer reviewed or otherwise—but the ones that haven't been submitted to peer review do tend to have more wrong with them.

What problems do scientists have with peer review, and how are they trying to change it?

Scientists do complain about peer review. But let me set one thing straight: The biggest complaints scientists have about peer review are not that it stifles unpopular ideas. You've heard this truthy factoid from countless climate-change deniers, and purveyors of quack medicine. And peer review is a convenient scapegoat for their conspiracy theories. There's just enough truth to make the claims sound plausible.

Peer review is flawed. Peer review can be biased. In fact, really new, unpopular ideas might well have a hard time getting published in the biggest journals right at first. You saw an example of that in my interview with sociologist Harry Collins. But those sort of findings will often published by smaller, more obscure journals. And, if a scientist keeps finding more evidence to support her claims, and keeps submitting her work to peer review, more often than not she's going to eventually convince people that she's right. Plenty of scientists, including Harry Collins, have seen their once-shunned ideas published widely.

So what do scientists complain about? This shouldn't be too much of a surprise. It's the lack of training, the lack of feedback, the time constraints, and the fact that, the more specific your research gets, the fewer people there are with the expertise to accurately and thoroughly review your work.

Scientists are frustrated that most journals don't like to publish research that is solid, but not ground-breaking. They're frustrated that most journals don't like to publish studies where the scientist's hypothesis turned out to be wrong.

Some scientists would prefer that peer review not be anonymous—though plenty of others like that feature. Journals like the British Medical Journal have started requiring reviewers to sign their comments, and have produced evidence that this practice doesn't diminish the quality of the reviews.

There are also scientists who want to see more crowd-sourced, post-publication review of research papers. Because peer review is flawed, they say, it would be helpful to have centralized places where scientists can go to find critiques of papers, written by scientists other than the official peer-reviewers. Maybe the crowd can catch things the reviewers miss. We certainly saw that happen earlier this year, when microbiologist Rosie Redfield took a high-profile peer-reviewed paper about arsenic-based life to task on her blog. The website Faculty of 1000 is attempting to do something like this. You can go to that site, look up a previously published peer-reviewed paper, and see what other scientists are saying about it. And the Astrophysics Archive has been doing this same basic thing for years.

So, what does all this mean for me?

Basically, you shouldn't canonize everything a peer-reviewed journal article says just because it is a peer-reviewed journal article. But, at the same time, being peer reviewed is a sign that the paper's author has done some level of due diligence in their work. Peer review is flawed, but it has value. There are improvements that could be made. But, like the old joke about democracy, peer review is the worst possible system except for every other system we've ever come up with.

If you're interested in reading more about peer review, and how scientists are trying to change and improve it, I'd recommend checking out Nature's Peer to Peer blog. They recently stopped updating it, but there's lots of good information archived there that will help you dig deeper.

Journals have also commissioned studies of how peer review works, and how it could be better. The British Medical Journal is one publication that makes its research on open access, peer review, research ethics, and other issues, available online. Much of it can be read for free.

_____________________________________________________________

The following people were instrumental in putting this explainer together: Ivan Oransky, science journalist and editor of the Retraction Watch blog; John Moore, Professor of Microbiology and Immunology at Weill Cornell Medical College; and Sara Schroter, senior researcher at the British Medical Journal.

Image: Some rights reserved by Nic's events

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Michael Chabon's introduction to The Phantom Tollbooth 50th anniversary edition

Michael Chabon's introduction to The Phantom Tollbooth 50th anniversary edition: "Michael Chabon has written a special introduction for the fiftieth anniversary edition of Norman Juster's wonderful, classic kids' book The Phantom Tollbooth. As you might expect, it's a lovely piece of work.

I am the son and grandson of helpless, hardcore, inveterate punsters, and when I got to Milo getting lost in The Doldrums where he found a (strictly analog) watchdog named Tock, it was probably already too late for me. I was gone on the book, riddled like a body in a crossfire by its ceaseless barrage of wordplay--the arbitrary and diminutive apparatchik, Short Shrift; the kindly and feckless witch, Faintly Macabre; the posturing Humbug, and, of course, the Island of Conclusions, reachable only by jumping. Puns--the word's origin, like the name of some pagan god, remains unexplained by etymologists--are derided, booed, apologized for.

When my father and grandfather committed acts of punmanship they were often, generally by the women at the table or in the car with them, begged if not ordered to cease at once. 'Every time I see you,' my grandfather liked to tell me, grinning, during the days of my growth spurt, 'you grusomer!' Maybe puns are a guy thing; I don't know. I can't see how anybody who claims to love language can fail to marvel at the beautiful slipperiness of meaning that puns, like aquarium nets, momentarily catch and bring shimmering to the surface. Puns act to shatter or at least compromise meaning; a pun condenses unrelated, even opposing meanings, like a collapsing dwarf star, into a singularity. Maybe it's this antisemantic vandalism that leads so many people to shun and revile them.

And yet I would argue--and it's a lesson I learned first from my grandfather and father and then in the pages of The Phantom Tollbooth--that puns, in fact, operate to generate new meanings, outside and beyond themselves. Anyone who jumps to conclusions, as to the island of Conclusions, is liable to find himself isolated, alone, unable to reconnect easily with the former texture and personages of his life. Without the punning island first charted by Norton Juster, we might not understand the full importance of maintaining a cautionary distance toward the act of jumping to conclusions, as Mr. Juster implicitly recommends.

'The Phantom Tollbooth' and the Wonder of Words


(Thanks, Zack!)




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Room-sized spirograph

Room-sized spirograph: "

Drawingmachine by Eske Rex from Core77 on Vimeo.

I love the way this thing looks like a cross between some kind of medieval engineering project and the best playground equipment ever. Made by Eske Rex—a Swedish-born designer who'd never heard of the toy Spirograph—it's based on a piece of 19th-century technical equipment.

Instead, he was inspired by the harmonograph, a mid-19th century mechanical apparatus that produces Lissajous curves, a complex family of shapes studied by mathematicians. While the harmonograph uses one pendulum to control a drawing device and a second to control a canvas, Rex's design calls for a two-pendulum device with a static canvas.

The Drawingmachine, Eske's name for his device, which produces art but is also itself considered an installation piece, uses two pendulums supported by large structures that stand at two ends of a similarly large canvas. The pendulums are connected to support systems (drawing arms) that meet in the middle of the canvas at a 90-degree angle and hold a single ballpoint pen, as you can see in the embedded images.

Video Link

Via The Atlantic

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Suwappu

Suwappu: "

Dentsu London and BERG are developing a suite of augmented-reality-enabled toys called Suwappu:

Suwappu is a range of toys, animal characters that live in little digital worlds. The physical toys are canvasses upon which we can paint worlds, through a phone (or tablet) lens we can see into the narratives, games and media in which they live.

The first part of this film imagines and explores the Suwappu world. Here we are using film to explore how animation and behaviours can draw out character and narrative in physical toy settings. The second part is an explanation of how Suwappu products might work, from using animal patterns as markers for augmented reality, to testing out actual Augmented Reality (AR) worlds on a mobile phone.

We wanted to picture a toy world that was part-physical, part-digital and that acts as a platform for media. We imagine toys developing as connected products, pulling from and leaking into familiar media like Twitter and Youtube. Toys already have a long and tenuous relationship with media, as film or television tie-ins and merchandise. It hasn’t been an easy relationship. AR seems like a very apt way of giving cheap, small, non-interactive plastic objects an identity and set of behaviours in new and existing media worlds.

Also, the badger is fucked in the head. Suwappu:

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Andy sends this amazing vintage advertisement. Apparently it was...

Andy sends this amazing vintage advertisement. Apparently it was...: "

Andy sends this amazing vintage advertisement. Apparently it was part of his American Studies curriculum - a segment on the insanity of advertising parables. Still, even seventy five years later, this is a pretty good argument for over-the-calf socks, I’d say.

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Matt Ridley's talk at Long Now: "The story of history is of more for less."

Matt Ridley's talk at Long Now: "The story of history is of more for less.": "Here's Stewart Brand's recap of science author Matt Ridley's (The Rational Optimist, Genome, The Red Queen) talk at the Long Now's Seminar About Long-term Thinking in San Francisco on Tuesday.

Hominids had upright walking, stone tools, fire, even language but still remained in profound stasis. What led to humanity's global takeoff, Ridley argues, was the invention of exchange about 120,000 years ago. 'That's ten times older than agriculture.'

The beginnings of trade encouraged specialization and innovation, which encouraged further innovation, specialization, and trade, and the unending virtuous cycle of progress was set in motion. The quality and speed of the progress depends on the size of the population doing the exchanging. 'It's not how clever we are but how much in contact we are with each other.' Thus the 5,000 Australians who became isolated on Tasmania 10,000 years ago didn't just stop progressing, they forgot how to make and use bone tools and even how to clothe themselves against cold weather. Their individual brains were fine, 'but there was something wrong with their collective brains.'

What really is being exchanged is ideas. The Pill-cam (for shooting video of your gut) was invented, Ridley points out, when a gastroenterologist had a conversation with guided missile designer.

The acceleration of progess can be measured in objective terms such as the amount of labor it takes to earn an hour of reading light. In 1997, with CF bulbs, it was half a second. In 1950, with incandescent bulbs, eight seconds. In 1880, with kerosene lamps, fifteen minutes. In 1800, with candles, six hours. In every decade various intellectuals keep saying that progress has stopped or is about to stop, but Ridley showed chart after chart chronicling constant improvement in everything we care about. Life expectancy is increasing by five hours a day. IQ keeps going up by three points a decade. Agriculture gets ever more productive, leaving more land to remain wild. Even economic inequality is decreasing, with poor countries getting rich faster than rich countries are getting richer.

On the subject of climate change, Ridley has a similar set of detailed charts showing that sea level has been rising slowly for a long time, but it is not accelerating. The same with the retreat of glaciers. Overall global warming is proceeding slower than was predicted. Humanity has been decarbonizing its energy supply steadily for 150 years as we progressed from wood to coal to oil to natural gas. A few years ago it was thought that only 25 years of natural gas was left, but with the invention of hydrofracking shale gas, the supply is suddenly 250 years worth, and it is a hugely cleaner source than coal. (Among nuclear innovations, Ridley is particularly intrigued by thorium reactors.)

'The story of history is of more for less.' Paul Ehrlich's formula (I=PAT--- environmental Impact equals Population times Affluence times Technology) is better stated as I=P/AT--- Impact equals Population divided by Affluence times Techology. As affluence and technology increase, and population levels off, environmental impact can go ever down.

An historian once wrote, 'On what principle is it that when we see nothing but improvement behind us, we are to expect nothing but deterioration before us?' That was English historian Thomas Babington Macaulay in 1830, even before the industrial revolution.

Matt Ridley on 'Deep Optimism'



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Stingray X-ray

Stingray X-ray: "

This is an x-ray of a newly discovered species of stingray, native to the Amazon. You can't tell from this shot of its innards, but the Heliotrygon gomesi actually resembles a "pancake with a nose"—big, round, flat, and beige. Read more about this creature at Our Amazing Planet.

Image: Ken Jones

Submitterated by Ajourneyroundmyskull

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