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charlesarthur : science   71

A code glitch may have caused errors in more than 100 published scientific studies • VICE
<p>Yuheng Luo, a graduate student at the University of Hawaiʻi at Mānoa, discovered the glitch this summer when he was verifying the results of research conducted by chemistry professor Philip Williams on cyanobacteria. The aim of the project was to "try to find compounds that are effective against cancer,” Williams said.

Under supervision of University of Hawaiʻi at Mānoa assistant chemistry professor Rui Sun, Luo used a script written in Python that was published as part of a 2014 paper by Patrick Willoughby, Matthew Jansma, and Thomas Hoye in the journal Nature Protocols. The code computes chemical shift values for NMR, or nuclear magnetic resonance spectroscopy, a common technique used by chemists to determine the molecular make-up of a sample.

Luo’s results did not match up with the NMR values that Williams’ group had previously calculated, and according to Sun, when his students ran the code on their computers, they realized that different operating systems were producing different results. Sun then adjusted the code to fix the glitch, which had to do with how different operating systems sort files.

Willoughby, the first author of the 2014 study who wrote the script, called the new study “a beautiful example of science working to advance the work we reported in 2014.”</p>

Here's <a href="">the paper on discovering the glitch</a>. Windows 10 and MacOS Mavericks (10.13) give the same result; Ubuntu 16 and MacOS Mojave (10.14) give results that don't agree with the other two, or each other. The reason: the way they sort files. The script expects pairs of data files to process. If the file pairing goes wrong, the outputs are wrong.
code  python  science 
5 days ago by charlesarthur
Novelist Cormac McCarthy’s tips on how to write a great science paper • Nature
Van Savage and Pamela Yeh:
<p>Van Savage, a theoretical biologist and ecologist, first met McCarthy in 2000, and they overlapped at the Sante Fe Institute (SFI) for about four years while Savage was a graduate student and then a postdoc. Savage has received invaluable editing advice from McCarthy on several science papers published over the past 20 years. While on sabbatical at the SFI during the winter of 2018, Savage had lively weekly lunches with McCarthy. They worked to condense McCarthy’s advice to its most essential points so that it could be shared with everyone. These pieces of advice were combined with thoughts from evolutionary biologist Pamela Yeh and are presented here. McCarthy’s most important tip is to keep it simple while telling a coherent, compelling story. The following are more of McCarthy’s words of wisdom, as told by Savage and Yeh.</p>

I'd have to say that the authors break McCarthy's rule about paragraphs in the above paragraph. But in general his rules are solid ones that anyone can benefit from - not just science paper writers.
science  research  writing 
10 days ago by charlesarthur
Human speech may have a universal transmission rate: 39 bits per second • AAAS
Catherine Matacic:
<p>Italians are some of the fastest speakers on the planet, chattering at up to nine syllables per second. Many Germans, on the other hand, are slow enunciators, delivering five to six syllables in the same amount of time. Yet in any given minute, Italians and Germans convey roughly the same amount of information, according to a new study. Indeed, no matter how fast or slowly languages are spoken, <a href="">they tend to transmit information at about the same rate: 39 bits per second</a>, about twice the speed of Morse code.

“This is pretty solid stuff,” says Bart de Boer, an evolutionary linguist who studies speech production at the Free University of Brussels, but was not involved in the work. Language lovers have long suspected that information-heavy languages—those that pack more information about tense, gender, and speaker into smaller units, for example—move slowly to make up for their density of information, he says, whereas information-light languages such as Italian can gallop along at a much faster pace. But until now, no one had the data to prove it.

Scientists started with written texts from 17 languages, including English, Italian, Japanese, and Vietnamese. They calculated the information density of each language in bits—the same unit that describes how quickly your cellphone, laptop, or computer modem transmits information. They found that Japanese, which has only 643 syllables, had an information density of about 5 bits per syllable, whereas English, with its 6949 syllables, had a density of just over 7 bits per syllable. Vietnamese, with its complex system of six tones (each of which can further differentiate a syllable), topped the charts at 8 bits per syllable.</p>

Now I'm wondering about a world where there's a language which transmits information more quickly. And also about how quickly reading transmits information. Plus: what about folk who listen to podcasts at 2x speed?
science  information  language  bitrate  speech 
4 weeks ago by charlesarthur
The end of the world: a history of how a silent cosmos led humans to fear the worst • The Conversation
Thomas Moynihan:
<p>Nestled within the university’s medieval spires, Nick Bostrom’s institute [Oxford’s Future of Humanity Institute] scrutinises the long-term fate of humanity and the perils we face at a truly cosmic scale, examining the risks of things such as climate, asteroids and AI. It also looks into less well-publicised issues. Universe destroying physics experiments, gamma-ray bursts, planet-consuming nanotechnology and exploding supernovae have all come under its gaze.

So it would seem that humanity is becoming more and more concerned with portents of human extinction. As a global community, we are increasingly conversant with increasingly severe futures. Something is in the air.

But this tendency is not actually exclusive to the post-atomic age: our growing concern about extinction has a history. We have been becoming more and more worried for our future for quite some time now. My PhD research tells the story of how this began. No one has yet told this story, yet I feel it is an important one for our present moment.

I wanted to find out how current projects, such as the Future of Humanity Institute, emerge as offshoots and continuations of an ongoing project of “enlightenment” that we first set ourselves over two centuries ago. Recalling how we first came to care for our future helps reaffirm why we should continue to care today.</p>

science  survival 
10 weeks ago by charlesarthur
Mathematician solves computer science conjecture in two pages • Quanta Magazine
Erica Klarreich:
<p>A <a href="">paper posted online</a> this month has settled a nearly 30-year-old conjecture about the structure of the fundamental building blocks of computer circuits. This “sensitivity” conjecture has stumped many of the most prominent computer scientists over the years, yet the new proof is so simple that one researcher summed it up in a single tweet.

“This conjecture has stood as one of the most frustrating and embarrassing open problems in all of combinatorics and theoretical computer science,” wrote Scott Aaronson of the University of Texas, Austin, in a blog post. “The list of people who tried to solve it and failed is like a who’s who of discrete math and theoretical computer science,” he added in an email.</p>

I'll be honest: I understand the problem (at least as described by Klarreich in her excellent explanatory metaphor - an achievement which deserves some sort of prize itself), but I don't understand the answer. However, I'm sure plenty of you will lap it up.
maths  computing  science 
11 weeks ago by charlesarthur
If this type of dark matter existed, people would be dying of unexplained ‘gunshot’ wounds • Science | AAAS
Juanita Bawagan:
<p>Dark matter makes up about 85% of the mass of the universe, but the substance itself remains a mystery. One theory posits that it consists of weakly interacting massive particles (WIMPs). These particles would be abundant, but so shy about interacting with ordinary matter that only very sensitive detectors would have a crack at catching them. So far, they’ve evaded detection in large tanks of liquid xenon and argon; kept in underground laboratories, these tanks would be able to sense the signals from WIMPs without interference from sources such as cosmic rays.

A less mainstream dark matter candidate, known as macros, would form heavier particles. While macros would be much rarer than WIMPs, any collisions with ordinary matter would be violent, leaving an obvious trace. The new study explores what those traces might look like if the macros hit people.

Glenn Starkman and Jagjit Singh Sidhu, theoretical physicists at Case Western Reserve University in Cleveland, Ohio, were originally searching for traces of macros in granite slabs when a colleague made a suggestion. “Why can’t you just use humans as a detector?” they recall Robert Scherrer, a co-author and theoretical physicist at Vanderbilt University in Nashville saying. “The energies you’re talking about, these things would probably at best maim a person, at worst kill a person.”

The team forged ahead with the idea and modeled macros that would have a similar effect to a fatal shot from a .22 caliber rifle. Such particles would be minuscule, but very heavy, and thus release the same amount of energy as a bullet as it passes through a person.</p>

science  darkmatter 
12 weeks ago by charlesarthur
The plan to mine the world’s research papers • Nature
Priyanka Pulla:
<p>Over the past year, [American technologist Carl] Malamud has — without asking publishers — teamed up with Indian researchers to build a gigantic store of text and images extracted from 73 million journal articles dating from 1847 up to the present day. The cache, which is still being created, will be kept on a 576-terabyte storage facility at Jawaharlal Nehru University (JNU) in New Delhi. “This is not every journal article ever written, but it’s a lot,” Malamud says. It’s comparable to the size of the core collection in the Web of Science database, for instance. Malamud and his JNU collaborator, bioinformatician Andrew Lynn, call their facility the JNU data depot.

No one will be allowed to read or download work from the repository, because that would breach publishers’ copyright. Instead, Malamud envisages, researchers could crawl over its text and data with computer software, scanning through the world’s scientific literature to pull out insights without actually reading the text.

The unprecedented project is generating much excitement because it could, for the first time, open up vast swathes of the paywalled literature for easy computerized analysis. Dozens of research groups already mine papers to build databases of genes and chemicals, map associations between proteins and diseases, and <a href="">generate useful scientific hypotheses</a>. But publishers control — and often limit — the speed and scope of such projects, which typically confine themselves to abstracts, not full text. Researchers in India, the United States and the United Kingdom are already making plans to use the JNU store instead. </p>
science  data  offshore 
july 2019 by charlesarthur
With little training, machine-learning algorithms can uncover hidden scientific knowledge • Techxplore
<p>Sure, computers can be used to play grandmaster-level chess (chess_computer), but can they make scientific discoveries? Researchers at the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have shown that an algorithm with no training in materials science can scan the text of millions of papers and uncover new scientific knowledge.

A team led by Anubhav Jain, a scientist in Berkeley Lab's Energy Storage & Distributed Resources Division, collected 3.3 million abstracts of published materials science papers and fed them into an algorithm called Word2vec. By analyzing relationships between words the algorithm was able to predict discoveries of new thermoelectric materials years in advance and suggest as-yet unknown materials as candidates for thermoelectric materials.

"Without telling it anything about materials science, it learned concepts like the periodic table and the crystal structure of metals," said Jain. "That hinted at the potential of the technique. But probably the most interesting thing we figured out is, you can use this algorithm to address gaps in materials research, things that people should study but haven't studied so far."

…"The paper establishes that text mining of scientific literature can uncover hidden knowledge, and that pure text-based extraction can establish basic scientific knowledge," said [Gerbrand] Ceder, who also has an appointment at UC Berkeley's Department of Materials Science and Engineering</p>

What happens when the machines start finding out things that we can't understand? What do we do with that discovered knowledge? Happened with Go, happening with chess.
knowledge  science  theory 
july 2019 by charlesarthur
We tried to publish a replication of a Science paper in Science. The journal refused • Slate
Kevin Arceneaux, Bert N. Bakker, Claire Gothreau, Gijs Schumacher:
<p>The researchers behind the Science article had shown a series of images to 46 participants in Nebraska and used equipment to record how much the participants’ palms sweated in response. The images included scary stuff, like a spider on a person’s face. We conducted two “conceptual” replications (one in the Netherlands and one in the U.S.) that used different images to get at the same idea of a “threat”—for example, a gun pointing at the screen. Our intention in these first studies was to try the same thing in order to calibrate our new equipment. But both teams independently failed to find that people’s physiological reactions to these images correlated with their political attitudes.

Our first thought was that we were doing something wrong. So, we asked the original researchers for their images, which they generously provided to us, and we added a few more. We took the step of “pre-registering” a more direct replication of the Science study, meaning that we detailed exactly what we were going to do before we did it and made that public. The direct replication took place in Philadelphia, where we recruited 202 participants (more than four times than the original sample size of 46 used in the Science study). Again, we found no correlation between physiological reactions to threatening images (the original ones or the ones we added) and political conservatism—no matter how we looked at the data.

By this point, we had become more skeptical of the rationale animating the original study. </p>

As you've guessed, Science didn't feel like publishing their non-replication. There have been proposals for a Journal of Non-Replication, but the problem is that you have to be sure that the replication attempt was good in every aspect, and that the failure isn't due to some other reason. Not as easy as it sounds.
science  replication 
june 2019 by charlesarthur
The dark side of Dark Mode • TidBITS
Adam Engst:
<p>To summarize, a dark-on-light display like a Mac in Light Mode provides better performance in focusing of the eye, identifying letters, transcribing letters, text comprehension, reading speed, and proofreading performance, and it results in less visual fatigue and increased visual comfort. The benefits apply to both the young and the old, as that paper concludes:
<p>In an ageing society, age-related vision changes need to be considered when designing digital displays. Visual acuity testing and a proofreading task revealed a positive polarity advantage for younger and older adults. Dark characters on light background lead to better legibility and are strongly recommended independent of observer’s age.</p>

I've never understood the attraction of Dark Mode. I had enough years of green-on-black terminals and MS-DOS's white-on-black to recognise that black-on-white text is how it's meant to be. (Plus you can't have an effective serif font in a white-on-black setting.) Engst is right. Steve Sinofsky pointed out on Twitter that the interest in Dark Mode also means two problems: it leads to new bugs through its own implementation, and the effort spent implementing it means other existing bugs don't get fixed.
science  vision  ergonomics  darkmode 
june 2019 by charlesarthur
Not just Party City: why helium shortages worry scientists and researchers • NBC News
Mary Pflum:
<p>“Helium is used in MRIs, it’s used in nuclear magnetic resonance, and the semiconductor industry uses a lot of helium,” Elsesser said.

“Helium is the workhorse of chemistry. Because of a helium shortage, some important experiments are being forced to shut down. The development of some drugs is being impacted. We’re losing time in research efforts.”

Liquid helium is like liquid gold to scientists, according to Sophia Hayes, a professor of chemistry at Washington University in St. Louis and one of the nation’s leading helium experts.

“It’s the coldest substance in the world,” Hayes said, explaining it plummets to minus 450 degrees Fahrenheit. “It’s almost as cold as outer space. There is no substitute. There is nothing else that can create those low temperatures.”

Scientists have been issuing warnings for years about the world’s shrinking helium supply. This year, the American Physical Society said that addressing the helium crisis is one of its top priorities.

Even fictitious scientists, like the ones featured on the popular sitcom, "The Big Bang Theory," have devoted entire episodes to the search for the gas. In an episode that aired in October 2015, entitled “The Helium Insufficiency,” two of the show’s main characters, Leonard and Sheldon, resort to shady dealings in a dark alley to source helium for an experiment.

But while the characters have been well aware of the helium shortage, it’s taken a while for the public and government officials to catch up.

“The helium shortage has hit us really hard,” Hayes said. “The situation is urgent.”</p>

An unexpected thing to run short of. This is (also) why we need fusion reactors so they can make more.
helium  science 
may 2019 by charlesarthur
The day the dinosaurs died • The New Yorker
Douglas Preston on a find - in south west North Dakota (try saying it out loud) - of fossils from the day when the asteroid struck and wiped out the dinosaurs:
<p>[Robert] DePalma returned to do a preliminary excavation of the site. “Almost right away, I saw it was unusual,” he told me. He began shovelling off the layers of soil above where he’d found the fish. This “overburden” is typically material that was deposited long after the specimen lived; there’s little in it to interest a paleontologist, and it is usually discarded. But as soon as DePalma started digging he noticed grayish-white specks in the layers which looked like grains of sand but which, under a hand lens, proved to be tiny spheres and elongated ­droplets. “I think, Holy shit, these look like microtektites!” DePalma recalled. Micro­tektites are the blobs of glass that form when molten rock is blasted into the air by an asteroid impact and falls back to Earth in a solidifying drizzle. The site appeared to contain micro­tektites by the million.

As DePalma carefully excavated the upper layers, he began uncovering an extraordinary array of fossils, exceedingly delicate but marvellously well preserved. “There’s amazing plant material in there, all interlaced and interlocked,” he recalled. “There are logjams of wood, fish pressed against cypress-­tree root bundles, tree trunks smeared with amber.” Most fossils end up being squashed flat by the pressure of the overlying stone, but here everything was three-dimensional, including the fish, having been encased in sediment all at once, which acted as a support. “You see skin, you see dorsal fins literally sticking straight up in the sediments, species new to science,” he said. As he dug, the momentousness of what he had come across slowly dawned on him. If the site was what he hoped, he had made the most important paleontological discovery of the new century.</p>

The thought at the back of one's mind is always what struck one of the first people to realise what wiped out the dinosaurs: one day, this could easily happen to us. A 300-metre object would end world agriculture.
science  dinosaurs 
april 2019 by charlesarthur
How artificial intelligence is changing science • Quanta Magazine
Rachel Suggs:
<p>In a <a href="">paper</a> published in December in Astronomy & Astrophysics, Schawinski and his ETH Zurich colleagues Dennis Turp and Ce Zhang used generative modeling to investigate the physical changes that galaxies undergo as they evolve. (The software they used treats the latent space somewhat differently from the way a generative adversarial network [GAN] treats it, so it is not technically a GAN, though similar.) Their model created artificial data sets as a way of testing hypotheses about physical processes. They asked, for instance, how the “quenching” of star formation — a sharp reduction in formation rates — is related to the increasing density of a galaxy’s environment.

For [Galaxy Zoo creator Kevin] Schawinski, the key question is how much information about stellar and galactic processes could be teased out of the data alone. “Let’s erase everything we know about astrophysics,” he said. “To what degree could we rediscover that knowledge, just using the data itself?”

First, the galaxy images were reduced to their latent space; then, Schawinski could tweak one element of that space in a way that corresponded to a particular change in the galaxy’s environment — the density of its surroundings, for example. Then he could re-generate the galaxy and see what differences turned up. “So now I have a hypothesis-generation machine,” he explained. “I can take a whole bunch of galaxies that are originally in a low-density environment and make them look like they’re in a high-density environment, by this process.”  Schawinski, Turp and Zhang saw that, as galaxies go from low- to high-density environments, they become redder in color, and their stars become more centrally concentrated. This matches existing observations about galaxies, Schawinski said. The question is why this is so.

The next step, Schawinski says, has not yet been automated: “I have to come in as a human, and say, ‘OK, what kind of physics could explain this effect?’”</p>

If you'd forgotten Galaxy Zoo, it was a <a href="">crowdsourcing method of cataloguing galaxies</a>, launched 12 years ago. Now, the article says, you'd get it done by an AI system in an afternoon.
ai  data  science 
march 2019 by charlesarthur
It’s not that your teeth are too big: your jaw is too small • Aeon Ideas
Professor Peter Ungar is a dental anthropologist at the University of Arkansas:
<p>[The jaw's] size depends both on genetics and environment; and it grows longer with heavy use, particularly during childhood, because of the way bone responds to stress. The evolutionary biologist Daniel Lieberman at Harvard University conducted an elegant study in 2004 on hyraxes fed soft, cooked foods and tough, raw foods. Higher chewing strains resulted in more growth in the bone that anchors the teeth. He showed that the ultimate length of a jaw depends on the stress put on it during chewing.

Selection for jaw length is based on the growth expected, given a hard or tough diet. In this way, diet determines how well jaw length matches tooth size. It is a fine balancing act, and our species has had 200,000 years to get it right. The problem for us is that, for most of that time, our ancestors didn’t feed their children the kind of mush we feed ours today. Our teeth don’t fit because they evolved instead to match the longer jaw that would develop in a more challenging strain environment. Ours are too short because we don’t give them the workout nature expects us to.

There’s plenty of evidence for this. The dental anthropologist Robert Corruccini at Southern Illinois University has seen the effects by comparing urban dwellers and rural peoples in and around the city of Chandigarh in north India – soft breads and mashed lentils on the one hand, coarse millet and tough vegetables on the other. He has also seen it from one generation to the next in the Pima peoples of Arizona, following the opening of a commercial food-processing facility on the reservation. Diet makes a huge difference. I remember asking my wife not to cut our daughters’ meat into such small pieces when they were young. ‘Let them chew,’ I begged. She replied that she’d rather pay for braces than have them choke. I lost that argument.</p>

Good to know that even professors can lose arguments at home even in their specialist subject.
teeth  evolution  science  health 
march 2019 by charlesarthur
AAAS: Machine learning 'causing science crisis' • BBC News
<p>Machine-learning techniques used by thousands of scientists to analyse data are producing results that are misleading and often completely wrong.

Dr Genevera Allen from Rice University in Houston said that the increased use of such systems was contributing to a “crisis in science”.

She warned scientists that if they didn’t improve their techniques they would be wasting both time and money. Her research was presented at the American Association for the Advancement of Science in Washington.

A growing amount of scientific research involves using machine learning software to analyse data that has already been collected. This happens across many subject areas ranging from biomedical research to astronomy. The data sets are very large and expensive.

But, according to Dr Allen, the answers they come up with are likely to be inaccurate or wrong because the software is identifying patterns that exist only in that data set and not the real world.

“Often these studies are not found out to be inaccurate until there's another real big dataset that someone applies these techniques to and says ‘oh my goodness, the results of these two studies don't overlap‘," she said.

“There is general recognition of a reproducibility crisis in science right now. I would venture to argue that a huge part of that does come from the use of machine learning techniques in science.”</p>

Reproducibility means what it says: can you get the same result starting from the same data? This <a href="">isn't a new problem</a> - it's just becoming more visible.
machinelearning  science  alienminds 
february 2019 by charlesarthur
The exercise “recovery” industry is largely bogus • Vox
Julia Belluz:
<p>When health journalist Christie Aschwanden was traveling the world as a competitive ski racer in the 1990s and 2000s, recovery between training sessions basically meant doing nothing — taking a day to sleep in or lie around with a good book.

About a decade ago, she noticed something had changed: recovery became a thing athletes actively performed — with foam rollers, cryotherapy, or cupping — as part of their training routines. These recovery tools were heavily marketed to athletes, including amateur ones, as a means to boost performance and bust muscle aches.

In a new book, Good to Go: What the Athlete in All of Us Can Learn from the Strange Science of Recovery, Aschwanden walks through all the biggest recovery fads of the past decade — and exposes the shoddy science backing most of them.

It’s an intelligent and entertaining tour of fitness research for anyone who exercises, with clear advice on what actually works to aid recovery. I won’t give away all the juicy details in the book, but I did ask Aschwanden to walk me through three of the most dubious recovery methods she uncovered. Here’s what she told me.</p>

Hydration overhyped, cold post-exercise bad, cupping nonsense. Relaxing baths good.
fitness  science 
february 2019 by charlesarthur
A hole opens up under Antarctic glacier — big enough to fit two-thirds of Manhattan
Denise Chow:
<p>The discovery is described in a paper published Jan. 30 in the journal Science Advances. The researchers expected to see significant loss of ice, but the scale of the void came as a shock.

“The size of the cavity is surprising, and as it melts, it’s causing the glacier to retreat,” said Pietro Milillo, a radar scientist at NASA’s Jet Propulsion Laboratory in Pasadena, California, and the paper’s lead author. He said the ice shelf encompassing the Florida-sized glacier is retreating at a rate in excess of 650 feet per year, and that most of the melting that led to the void occurred during the past three years.

<img src="" width="100%" />
<em>Sinking areas at Thwaites Glacier are shown here in red and rising areas in blue. The growing cavity (red mass, center) caused the greatest sinking.NASA/JPL-Caltech</em>

Previous research showed that meltwater from Thwaites accounts for about 4% of the global sea level rise, said Ted Scambos, a senior research scientist at the National Snow and Ice Data Center in Boulder, Colorado, who was not involved with the new study.

If the loss of ice becomes so severe that the glacier collapses — something computer models predict could happen in 50 to 100 years — sea levels would rise by two feet. That’s enough to inundate coastal cities across the globe.</p>

Worth declaring a state of emergency for the crisis on the US's south-eastern sea border?
science  climate  environment 
february 2019 by charlesarthur
Have Aliens found us? An Interview with the Harvard Astronomer Avi Loeb About the Mysterious Interstellar Object ‘Oumuamua | The New Yorker
Isaac Chotiner talks to Loeb, who thinks that the mysterious object dubbed ‘Oumuamua is an alien artefact:
<p>the evidence in this particular case is that there are six peculiar facts. And one of these facts is that it deviated from an orbit shaped by gravity while not showing any of the telltale signs of cometary outgassing activity. So we don’t see the gas around it, we don’t see the cometary tail. It has an extreme shape that we have never seen before in either asteroids or comets. We know that we couldn’t detect any heat from it and that it’s much more shiny, by a factor of ten, than a typical asteroid or comet. All of these are facts. I am following the facts.

Last year, I wrote a paper about cosmology where there was an unusual result, which showed that perhaps the gas in the universe was much colder than we expected. And so we postulated that maybe dark matter has some property that makes the gas cooler. And nobody cares, nobody is worried about it, no one says it is not science. Everyone says that is mainstream—to consider dark matter, a substance we have never seen. That’s completely fine. It doesn’t bother anyone.

But when you mention the possibility that there could be equipment out there that is coming from another civilization—which, to my mind, is much less speculative, because we have already sent things into space—then that is regarded as unscientific…

…Given the data that we have, I am putting this on the table, and it bothers people to even think about that, just like it bothered the Church in the days of Galileo to even think about the possibility that the Earth moves around the sun. Prejudice is based on experience in the past. The problem is that it prevents you from making discoveries. If you put the probability at zero per cent of an object coming into the solar system, you would never find it!</p>

Weirdly compelling. If it comes back... everyone hide.
science  astronomy  space  alien  Oumuamua 
january 2019 by charlesarthur
Strongest opponents of GM foods know the least but think they know the most • The Guardian
Ian Sample:
<p>The most extreme opponents of genetically modified foods know the least about science but believe they know the most, researchers have found.

The findings from public surveys in the US, France and Germany suggest that rather than being a barrier to the possession of strongly held views, ignorance of the matter at hand might better be described as a fuel.

“This is part and parcel of the psychology of extremism,” said Philip Fernbach, a researcher at the University of Colorado and co-author of the 2017 book The Knowledge Illusion. “To maintain these strong counter-scientific consensus views, you kind of have to have a lack of knowledge.”

Fernbach and others analysed surveys completed by nationally representative samples of the US, French and German public. Those who took part were asked about their attitudes to GM foods and given instructions on how to judge their understanding of the topic. Next, they completed a scientific literacy test. Among the statements the participants had to wrestle with were: “Ordinary tomatoes do not have genes, whereas genetically modified tomatoes do” (false), and “the oxygen we breathe comes from plants” (true).

The results from more than 2,500 respondents revealed the curious trend. “What we found is that as the extremity of opposition increased, objective knowledge went down, but self-assessed knowledge went up,” Fernbach said.</p>

When I was writing a lot about GM foods, about 20 years ago, it was noticeable that many of the arguments against them came from emotion. (There are some legitimate arguments against GM, around intellectual property on seeds.) But I suspect this result could be generalised; it's something of a <a href="–Kruger_effect">Dunning-Kruger</a> corollary.
genetics  gm  food  science 
january 2019 by charlesarthur
Is sunscreen the new margarine? • Outside Online
Rowan Jacobsen:
<p>In November, one of the <a href="">largest and most rigorous trials</a> of [Vitamin D supplements] ever conducted—in which 25,871 participants received high doses for five years—found no impact on cancer, heart disease, or stroke.

How did we get it so wrong? How could people with low vitamin D levels clearly suffer higher rates of so many diseases and yet not be helped by supplementation?

As it turns out, a rogue band of researchers has had an explanation all along. And if they’re right, it means that once again we have been epically misled.

These rebels argue that what made the people with high vitamin D levels so healthy was not the vitamin itself. That was just a marker. Their vitamin D levels were high because they were getting plenty of exposure to the thing that was really responsible for their good health—that big orange ball shining down from above.

One of the leaders of this rebellion is a mild-mannered dermatologist at the University of Edinburgh named Richard Weller. For years, Weller swallowed the party line about the destructive nature of the sun’s rays. “I’m not by nature a rebel,” he insisted when I called him up this fall. “I was always the good boy that toed the line at school. This pathway is one which came from following the data rather than a desire to overturn apple carts.”

Weller’s doubts began around 2010, when he was researching nitric oxide, a molecule produced in the body that dilates blood vessels and lowers blood pressure. He discovered a previously unknown biological pathway by which the skin uses sunlight to make nitric oxide.

It was already well established that rates of high blood pressure, heart disease, stroke, and overall mortality all rise the farther you get from the sunny equator, and they all rise in the darker months. Weller put two and two together and had what he calls his “eureka moment”: Could exposing skin to sunlight lower blood pressure?</p>

Sounds bonkers but: uh-huh.
science  vitamind  sunlight 
january 2019 by charlesarthur
What is the highest point on Earth as measured from Earth's center? • NOAA
<p>Mount Everest, located in Nepal and Tibet, is usually said to be the highest mountain on Earth. Reaching 29,029 feet at its summit, Everest is indeed the highest point above global mean sea level—the average level for the ocean surface from which elevations are measured. But the summit of Mt. Everest is not the farthest point from Earth’s center.</p>

You'll have to read on to find out. You've probably never heard of the mountain whose summit is the one. Remembering that the Earth is an oblate spheroid. And no, it's not Kilimanjaro.
geography  science  mountain 
november 2018 by charlesarthur
Once paralyzed, three men take steps again with spinal implant • The New York Times
Benedict Carey:
<p>David Mzee broke his neck in 2010. He was a college student in Zurich at the time, an athlete who enjoyed risk and contact, and he flipped off a trampoline and onto a foam pad. “The foam pad, it didn’t do its job,” he said.

Mr. Mzee, now 33, is one of three men who lost the use of their legs years ago after severe spinal injuries, but who now are able to walk without any supports, if briefly and awkwardly, with the help of a pacemaker-like implant, scientists reported on Wednesday.

The breakthrough is the latest achievement in the scientific effort to understand and treat such life-changing injuries. Several recent studies have restored motion to paralyzed or partially paralyzed patients by applying continuous electrical stimulation to the spinal cord.

The new report, <a href="">described in the journal Nature</a>, is the first demonstration of so-called patterned stimulation: an implant sends bursts of targeted stimulation to the muscles that intend to move. In effect, the stimulation occurs on an as-needed basis, roughly mimicking the body’s own signaling mechanism.</p>

The <a href="">BBC report, with video</a>, is truly amazing.
paralysis  science  spine 
october 2018 by charlesarthur
The extremely mad professors • The Outline
Christian McCrea:
<p>Pluckrose, Lindsay, and Boghossian [who perpetrated the "Sokhal Squared" effort to get hoax papers published in social science journals] will tell you that the crisis in the humanities they’ve ginned up is very current and real, but things get real curious when you scratch the surface. <a href="">Jason Wilson’s piece in the Guardian from March</a> outlines how the right-wing outrage machine draws in media hucksters and funds right-wing campus activists alike. In that piece, Boghossian is quoted as saying that the target of his hoaxes is “all disciplines infected by postmodernism, and women’s studies and gender studies in particular.” That’s right — hoaxes, plural. Last year, Boghossian and Lindsay employed the same tactic with a fake paper that argued the penis is less of a physical organ than it is something “a social construct isomorphic to performative toxic masculinity.”

Sensing a theme yet? Their long-running, multi-year media circus, based upon a deeply-held well... grievance, resonates with the broadly-held suspicions that some of the stuff that happens on campus is a bit crap — and anything remotely feminist comes first. Because looking around at the world in late 2018, gender doesn’t seem to be any kind of problem for anybody.

But — and I say this confidently — nobody in the humanities actually reads journals the way they do in science. You search journal databases by keywords. You read one paper from a new journal issue. You use what works. You skip over the paper that’s obviously rushed. You know that, in many areas, much more effort goes into book chapters. You know that some journals barely peer-review at all. This includes science journals, where hoaxes have also been perpetrated.

The hoaxers know all of this very well; they’re anything but stupid. The goal is plainly obvious: They don’t want these fields to exist.</p>
Hoax  science  publishing 
october 2018 by charlesarthur
What if everything we know about dark matter is totally wrong? • Wired
Katia Moskvitch:
<p>Despite huge pots of money being poured since the 1970s into dark matter experiments on, under or above Earth, despite endless late nights spent doing calculations, and despite plenty of media coverage, researchers keep getting nowhere. Apart from SNOLAB, there is the LUX experiment in Lead, South Dakota, one mile underground in an abandoned gold mine. It has obtained zero results. In France, the EDELWEISS experiment in a lab under the French Alps, under 1.7 km of rock, has found nothing. The PandaX experiment in the Jin-Ping sub-terrain laboratory in China hasn't spotted any particles either. In India, Jaduguda Underground Science Laboratory opened last year, 550 meters below the surface at an operating uranium mine. So far, they have found nothing (well, they've only been looking for a year). And on, and on, and on.

The leading theory is that dark matter is made out of particles that interact with normal, atomic, matter or light only through gravity - by exerting a gravitational pull. SuperCDMS will be looking for a very specific type of such exotic particles, so-called WIMPs, or weakly interacting massive particles. That’s the main (some say most obvious) dark matter candidate several detectors are searching for. Scientists are even trying to create these particles in the largest and most powerful particle accelerator in the world, the Large Hadron Collider (LHC) near Geneva (which cost nearly $7bn to build). But all in vain.

So just how much longer can researchers justify that they are looking for something unknown and finding nothing, but still get away with asking for more money to look for nothing... just a little bit longer? Well, turns out that for the researchers who have devoted their whole life to dark matter, null results are ultra-important – nearly as important as finding something.</p>

If we stopped looking for dark matter, what would happen to all the dark matter articles? I mean, we'd know that the desire to write them was out there, but how would we prove it existed?
Darkmatter  science 
september 2018 by charlesarthur
Bizarre particles keep flying out of Antarctica's ice, and they might shatter modern physics • Live Science
Rafi Letzer:
<p>Physicists don't know what it is exactly. But they do know it's some sort of cosmic ray — a high-energy particle that's blasted its way through space, into the Earth, and back out again. But the particles physicists know about — the collection of particles that make up what scientists call the Standard Model (SM) of particle physics — shouldn't be able to do that. Sure, there are low-energy neutrinos that can pierce through miles upon miles of rock unaffected. But high-energy neutrinos, as well as other high-energy particles, have "large cross-sections." That means that they'll almost always crash into something soon after zipping into the Earth and never make it out the other side.

And yet, since March 2016, researchers have been puzzling over two events in Antarctica where cosmic rays did burst out from the Earth, and were detected by NASA's Antarctic Impulsive Transient Antenna (ANITA) — a balloon-borne antenna drifting over the southern continent.

ANITA is designed to hunt cosmic rays from outer space, so the high-energy neutrino community was buzzing with excitement when the instrument detected particles that seemed to be blasting up from Earth instead of zooming down from space. Because cosmic rays shouldn't do that, scientists began to wonder whether these mysterious beams are made of particles never seen before.</p>

As long as it's only particles, I'm OK with it.
science  neutrinos 
september 2018 by charlesarthur
The war over supercooled water • Physics Today
Ashley Smart:
<p>[Renowned chemist David Chandler] and a graduate student, David Limmer [from UCal Berkeley], had used simulations to explore what happens when liquid water is cooled far below its freezing point. It was well known that pristine water—free of dust and other impurities on which ice crystals can nucleate—can be supercooled tens of degrees below 0 °C without freezing. But below what’s called the homogeneous nucleation temperature, around –40 °C, the liquid crystallizes almost instantly, no matter the purity. Chandler and Limmer wanted to know what that deeply supercooled water looks like in the instant before it freezes. What they found was seemingly unremarkable: at every temperature and pressure, the liquid basically resembled ordinary water.

To Princeton University’s Pablo Debenedetti, however, that result was mind-boggling. Two years earlier, Debenedetti and his coworkers had done their own simulations of supercooled water, at temperatures and pressures similar to those Chandler described. The Princeton simulations had revealed something far more intriguing. Yes, the liquid could take a high-density form that resembled water. But it could also take a low-density form, with the molecules arranged into airy hexagons reminiscent of those in ice. The water could morph back and forth between those two forms in much the same way it morphs between ice and liquid, or liquid and vapor.

In his 20-minute presentation, attended by many of the biggest names in condensed-matter theory, Chandler was essentially declaring that the Princeton team had gotten it wrong. “It was a matter of people saying, ‘Who are you going to believe, Chandler or Debenedetti?’” recalls Angell. “And Chandler carried the bigger stick.”

Over the next seven years, the perplexing discrepancy would ignite a bitter conflict, with junior scientists caught in the crossfire. At stake were not only the reputations of the two groups but also a peculiar theory that sought to explain some of water’s deepest and most enduring mysteries. Earlier this year, the dispute was finally settled. And as it turns out, the entire ordeal was the result of botched code.</p>

Now go back to the first paragraph, and the second: ah yes, that word "simulations". With so much science now relying on code, journals surely should insist on the publication of the source code used to reach conclusions. (Though read the comments on the story too, which point out that often it's impossible, because many use commercial code - and Matlab isn't going to publish its source.)

And yes, the whole story is a bit like a novella in the leadup to Kurt Vonnegut's Cat's Cradle.
software  science  coding  water  physics 
august 2018 by charlesarthur
The truth sometimes hurts • Scientific American Blog Network
Kate Marvel on the problem of being a scientist who tries to communicate with the public:
<p>every time I talk about the uncertainties inherent in climate projections, I feel attacked from all sides of the climate mitigation debate. I admit that in the current landscape, any expression of uncertainty is immediately weaponized by those who want to delay climate action.

Still, I’m a scientist, and I love to think about things I don’t understand. Being honest means acknowledging we don’t know everything. It also means being open about the problems of science itself, from a broken incentive system to the pervasive racial and sexual harassment that drives out brilliant minds. I struggle with how to talk about these things in a world where merchants of doubt will find a way to convert my science into their product.

I suspect this piece will be shared by some of those bad-faith actors. Unfortunately, there seems to be no way to construct an un-twistable argument. SCIENTIST SUPPRESSES INCONVENIENT RESULTS, they’ll say. CENSORSHIP! GROUPTHINK! This is, of course, the opposite of what I want to do. All I can ask is that if people insist on spreading false rumors about me, they also note that I have an evil twin, used to be an astronaut, and once killed a man in a bar fight. 

All I know is this: science communication is hard. There are no institutional rewards for doing it. Almost no one gets promoted for talking to the public. But we rely on scientists to choose to talk about their work, and to deal with the sometimes-overwhelming consequences of speaking in public. No other industry does this.  McDonalds does not force their cooks to engage in Hamburger Communication; they hire highly paid PR professionals instead.

So I want to approach this with something the stereotypical scientist is not known for: humility. Please don’t just tell us to be honest, help us to understand how to be transparent in an opaque world. </p>
science  understanding 
august 2018 by charlesarthur
US opposition to breast-feeding resolution stuns world health officials • The New York Times
Andrew Jacobs:
<p>A resolution to encourage breastfeeding was expected to be approved quickly and easily by the hundreds of government delegates who gathered this spring in Geneva for the United Nations-affiliated World Health Assembly.

Based on decades of research, the resolution says that mother’s milk is healthiest for children and countries should strive to limit the inaccurate or misleading marketing of breast milk substitutes.

Then the United States delegation, embracing the interests of infant formula manufacturers, upended the deliberations.

American officials sought to water down the resolution by removing language that called on governments to “protect, promote and support breastfeeding” and another passage that called on policymakers to restrict the promotion of food products that many experts say can have deleterious effects on young children.

When that failed, they turned to threats, according to diplomats and government officials who took part in the discussions. Ecuador, which had planned to introduce the measure, was the first to find itself in the crosshairs.

The Americans were blunt: If Ecuador refused to drop the resolution, Washington would unleash punishing trade measures and withdraw crucial military aid. The Ecuadorean government quickly acquiesced…

…In the end, the Americans’ efforts were mostly unsuccessful. It was the Russians who ultimately stepped in to introduce the measure — and the Americans did not threaten them.</p>

Very strange. Strong suspicion: lobbying by the US baby food industry.
breastfeeding  science  health  politics 
july 2018 by charlesarthur
Mysterious IceCube event may be caused by a tau neutrino • Eureakalert
Ranjan Laha is a postdoc at the Mainz-based team working at the PRISMA Cluster of Excellence:
<p>It was just eight years ago that the IceCube detector, a research center located at the South Pole to detect neutrinos emanating from the cosmos, was commissioned. Three years later, it began to register the first momentous results. The detection of high-energy neutrinos by IceCube made viable completely new options for explaining how our universe works. "These neutrinos with their considerable energy are cosmic messengers we have never encountered before and it is extremely important that we understand exactly what they are telling us," explained Dr. Ranjan Laha of Johannes Gutenberg University Mainz (JGU). Working in collaboration with a colleague at Stanford University in the USA, the Mainz-based physicist has put forward a new hypothesis on what this interstellar message carrier might be. The two physicists have calculated that what has been detected could be the track of a high-energy tau particle that transited the IceCube detector.</p>

A tau neutrino - if that's what it has found - would have far higher energy than any neutrino previously observed, and means something important about the universe, though it doesn't quite enable dilithium crystals and photon torpedoes just yet. Noted in passing, rather like a neutrino in the night. (Also, "Cluster of Excellence" would be a good name for a band.)
Neutrino  science 
june 2018 by charlesarthur
I worked at Theranos, and this is a glimpse of my story. : tech • Reddit
A person who says they were at Theranos in 2013 makes a number of points, but key among them was is this:
<p>They treated the company like a software company. They launched way too early. Sept 2013 they launched their Edison device which was nowhere near ready. Why did they launch too early? In meetings #2 [on the hierarchy, ie Balwani] would create timelines and deadlines like they do in software development. He would ask for very hard and fixed deadlines for things in R&D. Anyone who has done science knows that timelines constantly change, are usually always extended due to the development process. #2 thought he could ignore the setbacks. He would openly tell engineers in meetings, "Engineers are the most valued in this company." It showed because they spoiled the engineers by giving them a lot of perks other people did not observe. At the end of the day they never realized that the science was just as important as the engineering.</p>

Again and again it's clear that the company's aims ran miles ahead of the science - but because Holmes didn't really understand the science at a deep level, she couldn't see this fundamental flaw.
science  theranos 
june 2018 by charlesarthur
Reproducibility in machine learning: why it matters and how to achieve it •
JEnnifer Villa and Yoav Zimmerman:
<p>You’ve been handed your first project at your new job. The inference time on the existing ML model is too slow, so the team wants you to analyze the performance tradeoffs of a few different architectures. Can you shrink the network and still maintain acceptable accuracy?

The engineer who developed the original model is on leave for a few months, but not to worry, you’ve got the model source code and a pointer to the dataset. You’ve been told the model currently reports 30.3% error on the validation set and that the company isn’t willing to let that number creep above 33.0%.

You start by training a model from the existing architecture so you’ll have a baseline to compare against. After reading through the source, you launch your coworker’s training script and head home for the day, leaving it to run overnight.

The next day you return to a bizarre surprise: the model is reporting 52.8% validation error after 10,000 batches of training. Looking at the plot of your model’s validation error alongside that of your teammate leaves you scratching your head. How did the error rate increase before you even made any changes?

<img src="" width="100%" /></p>

Via Pete Warden, who is one of Google's people working on AI. A topic that one would imagine is close to his heart.
machinelearning  science  data 
may 2018 by charlesarthur
A controversial scientific study suggests octopuses came from outer space • Quartz
Ephrat Livni on a <a href="">bizarre speculative paper published</a> in "Progress in Biophysics and Molecular Biology":
<p>The octopus, for example, is traditionally considered to come from the nautiloid, having evolved about 500 million years ago. But that relationship doesn’t explain how these odd cephalopods got all their awesome characteristics or why <a href="">octopuses are so very different</a>, genetically speaking, from their alleged nautiloid ancestors. The paper states:
<p>The <a href="">genetic divergence</a> of Octopus from its ancestral coleoid sub-class is very great … Its large brain and sophisticated nervous system, camera-like eyes, flexible bodies, instantaneous camouflage via the ability to switch color and shape are just a few of the striking features that appear suddenly on the evolutionary scene.</p>

The transformative genes leading from the consensus ancestral nautilus to the common cuttlefish to squid to the common octopus can’t be found in any pre-existing life form, the authors say.

So far, so good. But then the paper gets highly speculative. The researchers continue, “It is plausible then to suggest they [octopuses] seem to be borrowed from a far distant ‘future’ in terms of terrestrial evolution, or more realistically from the cosmos at large.”</p>

Nope. Nope nope nope. This is not a "scientific study"; it's a bit of handwaving. Just because you don't know how the genes came to be present doesn't mean that they're alien, because they're not. Or else <em>everyone</em> is alien, which gets us back to square one.
science  genetics  octupus 
may 2018 by charlesarthur
Engineering a plastic-eating enzyme • University of Portsmouth News
<p>Professor John McGeehan at the University of Portsmouth and Dr Gregg Beckham at NREL solved the crystal structure of PETase—a recently discovered enzyme that digests PET— and used this 3D information to understand how it works. During this study, they inadvertently engineered an enzyme that is even better at degrading the plastic than the one that evolved in nature.

The researchers are now working on improving the enzyme further to allow it to be used industrially to break down plastics in a fraction of the time.

Professor McGeehan, Director of the Institute of Biological and Biomedical Sciences in the School of Biological Sciences at Portsmouth, said: “Few could have predicted that since plastics became popular in the 1960s huge plastic waste patches would be found floating in oceans, or washed up on once pristine beaches all over the world.

“We can all play a significant part in dealing with the plastic problem, but the scientific community who ultimately created these ‘wonder-materials’, must now use all the technology at their disposal to develop real solutions.”

The researchers made the breakthrough when they were examining the structure of a natural enzyme which is thought to have evolved in a waste recycling centre in Japan, allowing a bacterium to degrade plastic as a food source.</p>

BRB just writing a screenplay about how humanity subsists on paper bags and wood boats after the enzyme mutates and eats everything plastic everywhere so it eats our TVs and computers and screens and keyboards and
science  plastic  enzyme 
april 2018 by charlesarthur
People notice there’s something wrong with the rock’s new movie poster, and things escalate quickly • Bored Panda
<p>People are calling Dwayne Johnson ‘The Rock-et’ after he shared a poster of his upcoming movie. The action thriller is set in the not-so-distant future, where his character, Will Ford, is called in to inspect the security at the tallest building in the world, called The Pearl. And yes, films like these don’t always rely on the laws of physics, but the internet believes this one is stretching it a wee bit too much.

<blockquote class="twitter-tweet"><p lang="en" dir="ltr">I’ve mocked up some parabolas for The Rock’s SKYSCRAPER jump. Red is assuming he jumped up a bit first; green assuming he ran forward and somehow didn’t lose momentum; yellow for a sort of squat-thrust thing. <br><br>Whichever you choose, rest in peace The Rock, as you are dead now. <a href=""></a></p>&mdash; James Smythe (@jpsmythe) <a href="">February 2, 2018</a>
<script async src="" charset="utf-8"></script></p>
This is simply wonderful.
Film  science 
february 2018 by charlesarthur
Wikipedia has become a science reference source even though scientists don’t cite it • Science News
Bethany Brookshire on how scientists don’t cite Wikipedia - but they do seem to look at it very closely:
<p>the researchers created new Wikipedia articles from scratch to find out if the language in them affected the scientific literature in return. Hanley and Thompson had graduate students in chemistry and in econometrics write up new Wikipedia articles on topics that weren’t yet on the site. The students wrote 43 chemistry articles and 45 econometrics articles. Then, half of the articles in each set got published to Wikipedia in January 2015, and the other half were held back as controls. The researchers gave the articles three months to percolate through the internet. Then they examined the next six months’ worth of published scientific papers in those fields for specific language used in the published Wikipedia entries, and compared it to the language in the entries that never got published.

In chemistry, at least, the new topics proved popular. Both the published and control Wikipedia page entries had been selected from graduate level topics in chemistry that weren’t yet covered on Wikipedia. They included entries such as the synthesis of hydrastine (the precursor to a drug that stops bleeding). People were interested enough to view the new articles on average 4,400 times per month.

The articles’ words trickled into to the scientific literature. In the six months after publishing, the entries influenced about 1 in 300 words in the newly published papers in that chemical discipline. And scientific papers on a topic covered in Wikipedia became slightly more like the Wikipedia article over time. For example, if chemists wrote about the synthesis of hydrastine — one of the new Wikipedia articles — published scientific papers more often used phrases like “Passarini reaction,” a term used in the Wikipedia entry. But if an article never went on to Wikipedia, the scientific papers published on the topic didn’t become any more similar to the never-published article (which could have happened  if the topics were merely getting more popular).</p>

The depth of Wikipedia on some topics is amazing. I had to look up a specific ligament injury recently. The related pages had clearly been written by medical students regurgitating textbooks. Definitely one of the wonders of the internet.
Wikipedia  science 
february 2018 by charlesarthur
Checkmate: how do climate science deniers' predictions stack up? • The Guardian
Graham Readfearn:
<p>some [people] remain convinced that the whole thing is an elaborate hoax and readily find a home for their conspiracy theories and pseudoscience in conservative media outlets and, too often, on publicly funded ones too.

Climate-science deniers love to fling around accusations that climate change models are massively over-egging the global warming pudding and should not be trusted (climate scientist Zeke Hausfather has a great technical explainer on this).

While many pseudo-sceptics are quick with an unfounded criticism, it’s rare for them to put their own alchemy to the test by making firm projections about what’s to come.

But sometimes they do and the results are often spectacularly and comically bad. Let’s have a look at a few.</p>

This is an overlooked point: what do climate sceptics predict? They're so busy denying that anything's happening, or that it's for other reasons, they don't get asked what they think will happen. This is the tactic to take with deniers: ask them what they forecast, and hold them to it.
climatechange  prediction  science 
december 2017 by charlesarthur
What a nerdy debate about p-values shows about science — and how to fix it • Vox
Brian Resnick:
<p>Most casual readers of scientific research know that for results to be declared “statistically significant,” they need to pass a simple test. The answer to this test is called a p-value. And if your p-value is less than .05 — bingo, you got yourself a statistically significant result.

Now a group of 72 prominent statisticians, psychologists, economists, sociologists, political scientists, biomedical researchers, and others want to disrupt the status quo. A <a href="">forthcoming paper in the journal Nature Human Behavior</a> argues that results should only be deemed “statistically significant” if they pass a higher threshold.

“We propose a change to P< 0.005,” the authors write. “This simple step would immediately improve the reproducibility of scientific research in many fields.”

This may sound nerdy, but it’s important. If the change is accepted, the hope is that fewer false positives will corrupt the scientific literature. It’s become too easy — using shady techniques known as p-hacking and outcome switching — to find some publishable result that reaches the .05 significance level.

“There’s a major problem using p-values the way we have been using them,” says John Ioannidis, a Stanford professor of health research and one of the authors of the paper. “It’s causing a flood of misleading claims in the literature.”</p>

That sort of threshold would put a ton of social scientists out of work, or at least out of research. A colossal move if implemented.
science  statistics  pvalue 
october 2017 by charlesarthur
Emails show how an Ivy League prof tried to do damage control for his bogus food science • Buzzfeed
Stephanie Lee:
<p>The Smarter Lunchrooms Movement, a $22m federally funded program that pushes healthy-eating strategies in almost 30,000 schools, is partly based on studies that contained flawed — or even missing — data.

The main scientist behind the work, Cornell University professor Brian Wansink, has made headlines for his research into the psychology of eating. His experiments have found, for example, that women who put cereal on their kitchen counters weigh more than those who don’t, and that people will pour more wine if they’re holding the glass than if it's sitting on a table. Over the past two decades he’s written two popular books and more than 100 research papers, and enjoyed widespread media coverage (including on BuzzFeed).

Yet over the past year, Wansink and his “Food and Brand Lab” have come under fire from scientists and statisticians who’ve spotted all sorts of red flags — including data inconsistencies, mathematical impossibilities, errors, duplications, exaggerations, eyebrow-raising interpretations, and instances of self-plagiarism — in 50 of his studies.

Journals have so far retracted three of these papers and corrected at least seven. Now, emails obtained by BuzzFeed News through public information requests reveal for the first time that Wansink and his Cornell colleague David Just are also in the process of correcting yet another study, “Attractive names sustain increased vegetable intake in schools,” published in Preventive Medicine in 2012.</p>

Who could have guessed that headline-friendly "science" might be flawed?
science  bogus 
september 2017 by charlesarthur
"The moon blew up without warning and for no apparent reason" • Almost looks like work
Jason Cole:
<p>Intriguing title, no? These are the first eleven words of Neal Stephenson’s novel Seveneves, which set up the remaining 600 pages as an extended treatise on the future of humanity as it copes with certain annihilation. I thoroughly recommend it, as long as you can deal with hundreds of pages of orbital mechanics. In this post I will numerically explore this post-lunar age, to verify for myself if it would be as deadly as described.

In the novel, one day the moon breaks up into 7 roughly equal-sized pieces. These pieces continue peacefully orbiting the Earth for a while, and eventually two pieces collide. This collision causes a piece to fragment, making future collisions more likely. The process repeats, at what Stephenson says is an exponential rate, until the Earth is under near-constant bombardment from meteorites, wiping out (nearly) all life on Earth.

How likely is this? Let’s simulate the process numerically.</p>

Now I want to read the book.
science  meteorites  moon  simulation 
september 2017 by charlesarthur
First human embryos edited in US • MIT Technology Review
Steve Connor:
<p>The first known attempt at creating genetically modified human embryos in the United States has been carried out by a team of researchers in Portland, Oregon, MIT Technology Review has learned.

The effort, led by Shoukhrat Mitalipov of Oregon Health and Science University, involved changing the DNA of a large number of one-cell embryos with the gene-editing technique CRISPR, according to people familiar with the scientific results.

Until now, American scientists have watched with a combination of awe, envy, and some alarm as scientists elsewhere were first to explore the controversial practice. To date, three previous reports of editing human embryos were all published by scientists in China.

Now Mitalipov is believed to have broken new ground both in the number of embryos experimented upon and by demonstrating that it is possible to safely and efficiently correct defective genes that cause inherited diseases.</p>

This would allow one to get rid of genetic disease, of course. A sidenote: Steve Connor is one of the best science journalists in the world. So this exclusive is reliable, and remarkable.
science  mit  genetics  crispr  embryo 
july 2017 by charlesarthur
Sci-Hub’s cache of pirated papers is so big, subscription journals are doomed, data analyst suggests • Science
Lindsay McKenzie:
<p>There is no doubt that Sci-Hub, the infamous—and, according to a U.S. court, illegal—online repository of pirated research papers, is enormously popular. (See Science’s investigation last year of who is downloading papers from Sci-Hub.) But just how enormous is its repository? That is the question biodata scientist Daniel Himmelstein at the University of Pennsylvania and colleagues recently set out to answer, after an assist from Sci-Hub.

Their findings, <a href="">published in a preprint on the PeerJ journal site</a> on 20 July, indicate that Sci-Hub can instantly provide access to more than two-thirds of all scholarly articles, an amount that Himmelstein says is “even higher” than he anticipated. For research papers protected by a paywall, the study found Sci-Hub’s reach is greater still, with instant access to 85% of all papers published in subscription journals. For some major publishers, such as Elsevier, more than 97% of their catalog of journal articles is being stored on Sci-Hub’s servers—meaning they can be accessed there for free.

Given that Sci-Hub has access to almost every paper a scientist would ever want to read, and can quickly obtain requested papers it doesn’t have, could the website truly topple traditional publishing? In a chat with ScienceInsider, Himmelstein concludes that the results of his study could mark “the beginning of the end” for paywalled research.</p>

The "beginning of the end" has been predicted for science paywalls many times. We'll see if this marks that true start.
science  academia 
july 2017 by charlesarthur
I’m a scientist. I’m blowing the whistle on the Trump administration. • The Washington Post
Joel Clement was director of the Office of Policy Analysis at the US Interior Department for seven years - and then was moved abruptly to an unrelated job "in the accounting office that collects royalty checks from fossil fuel companies":
<p>On Wednesday, I filed two forms — a complaint and a disclosure of information — with the U.S. Office of Special Counsel. I filed the disclosure because eliminating my role coordinating federal engagement and leaving my former position empty exacerbate the already significant threat to the health and the safety of certain Alaska Native communities. I filed the complaint because the Trump administration clearly retaliated against me for raising awareness of this danger. Our country values the safety of our citizens, and federal employees who disclose threats to health and safety are protected from reprisal by the Whistleblower Protection Act and Whistleblower Protection Enhancement Act.

Removing a civil servant from his area of expertise and putting him in a job where he’s not needed and his experience is not relevant is a colossal waste of taxpayer dollars. Much more distressing, though, is what this charade means for American livelihoods. The Alaska Native villages of Kivalina, Shishmaref and Shaktoolik are perilously close to melting into the Arctic Ocean. In a region that is warming twice as fast as the rest of the planet, the land upon which citizens’ homes and schools stand is newly vulnerable to storms, floods and waves. As permafrost melts and protective sea ice recedes, these Alaska Native villages are one superstorm from being washed away, displacing hundreds of Americans and potentially costing lives. The members of these communities could soon become refugees in their own country.</p>

Trump got 51.3% of votes cast in Alaska in November 2016, slightly increasing the margin from 2012.
science  climate  trump 
july 2017 by charlesarthur
Is the staggeringly profitable business of scientific publishing bad for science? • The Guardian
Stephen Buranyi writing in 2017 about the £19bn business of scientific publishing:
<p>The [science] publishing business is “perverse and needless”, the Berkeley biologist Michael Eisen <a href="">wrote in a 2003 article for the Guardian</a>, declaring that it “should be a public scandal”. Adrian Sutton, a physicist at Imperial College, told me that scientists “are all slaves to publishers. What other industry receives its raw materials from its customers, gets those same customers to carry out the quality control of those materials, and then sells the same materials back to the customers at a vastly inflated price?” (A representative of RELX Group, the official name of Elsevier since 2015, told me that it and other publishers “serve the research community by doing things that they need that they either cannot, or do not do on their own, and charge a fair price for that service”.)

Many scientists also believe that the publishing industry exerts too much influence over what scientists choose to study, which is ultimately bad for science itself. Journals prize new and spectacular results – after all, they are in the business of selling subscriptions – and scientists, knowing exactly what kind of work gets published, align their submissions accordingly. This produces a steady stream of papers, the importance of which is immediately apparent. But it also means that scientists do not have an accurate map of their field of inquiry. Researchers may end up inadvertently exploring dead ends that their fellow scientists have already run up against, solely because the information about previous failures has never been given space in the pages of the relevant scientific publications. A 2013 study, for example, reported that half of all clinical trials in the US are never published in a journal.

According to critics, the journal system actually holds back scientific progress. In a 2008 essay, Dr Neal Young of the National Institutes of Health (NIH), which funds and conducts medical research for the US government, argued that, given the importance of scientific innovation to society, “there is a moral imperative to reconsider how scientific data are judged and disseminated”.</p>

It seems to me that the whole "Sokal Squared" thing is about this: perverse incentives created by science publishers, together with for-profit universities which want to collect more fees but aren't judged by outcomes any more rigorous than how many people they graduate.
Sokal  publishing  science 
june 2017 by charlesarthur
How to fight the bloatware of AI • Medium
Peter Sweeney is an entrepreneur and inventor of AI technologies, and he takes issue with the idea that we need a human-like AI. What we need, he argues, is one which narrowly does the rational part we've only recently learned to do:
<p>it’s only within the past few centuries, beginning with the scientific revolution, that humans began making consistent, predictable progress through the creation of good knowledge. Earlier humans produced a wealth of bad knowledge, most of it long forgotten.

<img src="*ON3aD6G9UXvGAg-vJfgTtQ.png" width="100%" />

This isn’t to say humans were incapable of producing good knowledge. The point is that good knowledge creation was exceedingly rare. We wouldn’t model flight using a bird that failed to fly at such a spectacular rate. As a model for machine intelligence, shouldn’t humans be subject to the same standard of criticism?

We can further hone our expectations for good knowledge to scientific disciplines. According to Gary Marcus, “What society most needs is automated scientific discovery.” Demis Hassabis [founder and CEO of Google's DeepMind] holds similar ambitions. “I’ve always hoped that A.I. could help us discover completely new ideas in complex scientific domains.”

We expect machines to embody superhuman intelligence. Only scientific progress embodies the sort of revolutionary knowledge creation that we imagine for our machines. It’s knowledge that arrives in conjectural leaps, defies our past experiences, and redefines what’s possible.
This process of knowledge creation is a human invention, not a natural phenomenon. Yet on closer inspection, our knowledge of how scientific knowledge is created is younger still! It was only in the 20th century, with Karl Popper’s philosophy of science, that there emerged a strong consensus of how scientific knowledge is created.

Naturally irrational humans are deeply flawed knowledge creation machines. We’ve only recently acquired the skills we need from machines and our knowledge of how we do it has not been broadly disseminated. Nature doesn’t provide a model of what we want from intelligent machines, namely revolutionary scientific knowledge, nor is the process that humans use to create this knowledge a naturally occurring phenomenon.</p>

Or as Lewis Wolpert used to put it, "science isn't common sense. It's usually the direct opposite." (Think of Earth revolving around the sun, or the reason for gravity. Common sense doesn't predict them.)
science  ai 
june 2017 by charlesarthur
“Mindless Eating,” or how to send an entire life of research into question • Ars Technica
Cathleen O'Grady:
<p>Things began to go bad late last year when [Brian] Wansink posted some advice for grad students on his blog. The post, which has subsequently been removed (although a cached copy is available), described a grad student who, on Wansink’s instruction, had delved into a data set to look for interesting results. The data came from a study that had sold people coupons for an all-you-can-eat buffet. One group had paid $4 for the coupon, and the other group had paid $8.

The hypothesis had been that people would eat more if they had paid more, but the study had not found that result. That’s not necessarily a bad thing. In fact, publishing null results like these is important—failure to do so leads to publication bias, which can lead to a skewed public record that shows (for example) three successful tests of a hypothesis but not the 18 failed ones. But instead of publishing the null result, Wansink wanted to get something more out of the data.

“When [the grad student] arrived,” Wansink wrote, “I gave her a data set of a self-funded, failed study which had null results... I said, ‘This cost us a lot of time and our own money to collect. There’s got to be something here we can salvage because it’s a cool (rich & unique) data set.’ I had three ideas for potential Plan B, C, & D directions (since Plan A had failed).”

The responses to Wansink’s blog post from other researchers were incredulous, because this kind of data analysis is considered an incredibly bad idea. As <a href="">this very famous xkcd strip</a> explains, trawling through data, running lots of statistical tests, and looking only for significant results is bound to turn up some false positives. This practice of “<a href="">p-hacking</a>”—hunting for significant p-values in statistical analyses—is one of the many questionable research practices responsible for the replication crisis in the social sciences.</p>

O'Grady's article is not short. But it is very, very informative.
science  statistics 
april 2017 by charlesarthur
Legalized marijuana could help curb the opioid epidemic, study finds • NBC News
<p>In states that legalized medical marijuana, US hospitals failed to see a predicted influx of pot smokers, but in an unexpected twist, they treated far fewer opioid users, a new study shows.

Hospitalization rates for opioid painkiller dependence and abuse dropped on average 23% in states after marijuana was permitted for medicinal purposes, the <a href="">analysis</a> found. Hospitalization rates for opioid overdoses dropped 13% on average.

At the same time, fears that legalization of medical marijuana would lead to an uptick in cannabis-related hospitalizations proved unfounded, according to the report in Drug and Alcohol Dependence.

"Instead, medical marijuana laws may have reduced hospitalizations related to opioid pain relievers," said study author Yuyan Shi, a public health professor at the University of California, San Diego.

"This study and a few others provided some evidence regarding the potential positive benefits of legalizing marijuana to reduce opioid use and abuse, but they are still preliminary," she said in an email…

…Last week, U.S. Attorney General Jeff Sessions, the nation's top cop, reiterated his concerns about marijuana and heroin, an illegal opioid.

"I am astonished to hear people suggest that we can solve our heroin crisis by legalizing marijuana," he told law enforcement officers in Virginia, "so people can trade one life-wrecking dependency for another."</p>

Jeff Sessions, showing what belief disconnected from the scientific method looks like.
politics  science  marijuana  opioid 
april 2017 by charlesarthur
What geology has to say about building a 1,000-mile border wall • Smithsonian Science
Maya Wei-Haas:
<p>Dirt can also eat up the wall’s support system. Soils that are naturally acidic or have high chloride levels can rapidly degrade iron-rich metals, says McKinnon. These soils could “corrode any, say, nice big metal rebar that you're putting in there to stabilize your foundation,” she says. Other soils have a high amount of sulfates, a compound found in the common mineral gypsum that breaks down both metals and concrete. Sulfate-rich soils are common in what’s known as the Trans-Pecos soils along the border in the southwestern arm of Texas.

Upkeep of such a lengthy structure is challenging. And even if such a wall can be erected, the size of budget necessary to keep it standing remains unclear. (Kevin Foy / Alamy Stock Photo)
“You're going to encounter hundreds, if not thousands, of different types of soils along [such a lengthy] linear pathway,” says Clendenin. (In fact, there are over 1,300 kinds of soil in Texas alone.) And many of those soils aren’t going to be the right type to build on top of. At that point, would-be wall-builders have two options: Spend more time and money excavating the existing soils and replacing them with better dirt—or avoid the region altogether.

One thing they can’t always avoid, though, are regions at risk of earthquakes and floods. Rivers run along a sizeable portion of the U.S.-Mexico border, which can create a very real danger of flood. Building adjacent to rivers can also present unexpected legal issues: A 1970 treaty necessitates that the fence be set back from the Rio Grande river, which delineates the Texas-Mexico border. Because of this, the current fence crosscuts Texas landowner’s property and has gaps to allow landowners to pass.

Earthquakes are also relatively common in the western U.S. Depending on the build, some of these tremblors could cause cracks or breaks in the wall, says McKinnon. One example is the magnitude 7.2 quake that struck in 2010 near the California-Mexico Border, according to Austin Elliott, a postdoctoral student at the University of Oxford whose research is focused on the history of earthquakes. “If there had been a wall at El Centinela [a mountain in northern Mexico] it would have been offset,” Elliott writes on Twitter.

Even if all the proper surveys are completed and the boxes checked, success isn’t guaranteed. “There are just so many things that have to be done before you even shovel out the first scoop of dirt,” says Clendenin.</p>

Trump wants all the surveying done by mid-year (he signed an executive order in January). Ain't gonna happen. And then what?
wall  science  politics  trump 
february 2017 by charlesarthur
I am the scholar caught in Trump inauguration crowd controversy • Times Higher Education
Keith Still explains his (extensive) experience, which meant that...
<p>in the run-up to the inauguration, we were asked to provide an estimate of how many people were at the Abraham Lincoln inauguration and a comment on the historical analysis of the crowds at inaugurations down the years. We turned this around in less than a day, which led to the question: “Can you guys do this in real-time?”

At that time, there were various claims that 3 million people would attend the 2017 inauguration.

Hmmm…let me see. Three million people would need between 750,000 and 1,500,000 square metres. There isn’t enough space. To give you some idea of how this would look, I’ve marked out 1,200,000 in the diagram below.

We knew this would be extremely dangerous if the area was packed to this density. There needs to be provision for emergency services, infrastructures, media village, barriers to prevent forward surges and potential crushing. Consequently, this gave birth to our live inauguration analysis, which would later fuel the media fire – Marcel and me giving minute-by-minute crowd updates for the NYT.

<img src="" width="100%" /> 

As the minutes ticked towards noon in Washington and the oath of office, we watched the crowds arrive, monitoring the build-up and the areas the crowds were occupying. At 11am, we had a comparison image from the 2009 inauguration and were capturing images from seven live broadcast feeds, assessing the metro data and comparing this with previous inaugurations.</p>
inauguration  crowd  science 
february 2017 by charlesarthur
Scientific breakthrough reveals unprecedented alternative to battery power storage • University of Surrey
<p>Ground-breaking research from the University of Surrey and Augmented Optics Ltd., in collaboration with the University of Bristol, has developed potentially transformational technology which could revolutionise the capabilities of appliances that have previously relied on battery power to work.

This development by Augmented Optics Ltd., could translate into very high energy density super-capacitors making it possible to recharge your mobile phone, laptop or other mobile devices in just a few seconds.

The technology could have a seismic impact across a number of industries, including transport, aerospace, energy generation, and household applications such as mobile phones, flat screen electronic devices, and biosensors. It could also revolutionise electric cars, allowing the possibility for them to recharge as quickly as it takes for a regular non-electric car to refuel with petrol – a process that currently takes approximately 6-8 hours to recharge. Imagine, instead of an electric car being limited to a drive from London to Brighton, the new technology could allow the electric car to travel from London to Edinburgh without the need to recharge, but when it did recharge for this operation to take just a few minutes to perform.

Supercapacitor buses are already being used in China, but they have a very limited range whereas this technology could allow them to travel a lot further between recharges. Instead of recharging every 2-3 stops this technology could mean they only need to recharge every 20-30 stops and that will only take a few seconds.</p>

This is the sort of dense and uninformative stuff that lands in journalists' inboxes all the time. The idea of "transformational effect" is repeated multiple times; only once is the explanation given that they're polymers, and "based on large organic molecules composed of many repeated sub-units and bonded together to form a 3-dimensional network."

Basically, we're no wiser on why this material is a supercapacitor. But there might be some hope.
science  battery  polymer 
december 2016 by charlesarthur
Strange numbers found in particle collisions • Quanta Magazine
Kevin Hartnett:
<p>Over the last decade physicists and mathematicians have been exploring a surprising correspondence that has the potential to breathe new life into the venerable Feynman diagram and generate far-reaching insights in both fields. It has to do with the strange fact that the values calculated from Feynman diagrams seem to exactly match some of the most important numbers that crop up in a branch of mathematics known as algebraic geometry. These values are called “periods of motives,” and there’s no obvious reason why the same numbers should appear in both settings. Indeed, it’s as strange as it would be if every time you measured a cup of rice, you observed that the number of grains was prime.

“There is a connection from nature to algebraic geometry and periods, and with hindsight, it’s not a coincidence,” said Dirk Kreimer, a physicist at Humboldt University in Berlin.

Now mathematicians and physicists are working together to unravel the coincidence. For mathematicians, physics has called to their attention a special class of numbers that they’d like to understand: Is there a hidden structure to these periods that occur in physics? What special properties might this class of numbers have? For physicists, the reward of that kind of mathematical understanding would be a new degree of foresight when it comes to anticipating how events will play out in the messy quantum world.</p>

Long. You will be (a lot) wiser about Feynman diagrams and the rest by the end though.
mathematics  science  quantum  physics 
december 2016 by charlesarthur
Remarks by the President in opening remarks and panel discussion at White House Frontiers Conference •
This, from Barack Obama:
<p>The final thing I’ll say is that government will never run the way Silicon Valley runs because, by definition, democracy is messy.  This is a big, diverse country with a lot of interests and a lot of disparate points of view.  And part of government’s job, by the way, is dealing with problems that nobody else wants to deal with. 

So sometimes I talk to CEOs, they come in and they start telling me about leadership, and here’s how we do things.  And I say, well, if all I was doing was making a widget or producing an app, and I didn’t have to worry about whether poor people could afford the widget, or I didn’t have to worry about whether the app had some unintended consequences - setting aside my Syria and Yemen portfolio - then I think those suggestions are terrific.  (Laughter and applause.)  That's not, by the way, to say that there aren't huge efficiencies and improvements that have to be made. 

But the reason I say this is sometimes we get, I think, in the scientific community, the tech community, the entrepreneurial community, the sense of we just have to blow up the system, or create this parallel society and culture because government is inherently wrecked.  No, it's not inherently wrecked; it's just government has to care for, for example, veterans who come home. That's not on your balance sheet, that's on our collective balance sheet, because we have a sacred duty to take care of those veterans.  And that's hard and it's messy, and we're building up legacy systems that we can't just blow up.</p>

The whole speech and discussion are worth a look, especially his point about accepting scientific findings and fact: "Sixty years ago, when the Russians beat us into space, we didn’t deny that Sputnik was up there."
obama  government  politics  science 
october 2016 by charlesarthur
The detectives who never forget a face • The New Yorker
Patrick Radden Keefe:
<p>Studying the map, Porritt plotted the various routes and developed a hunch that the man [the police wanted to question] lived in Camden. Porritt grew up there, and he decided to go and ask around. He invited Alison Young, an officer who had just joined the unit, to tag along. Young is twenty-nine, with long red hair and an ebullient sense of humor. She had worked as a community-support officer for several years, but one day she was summoned to an auditorium at Scotland Yard, where dozens of officers were instructed to take a facial-recognition exam. Using a laptop, Young found matches in a series of faces that were presented like masks—without hair or other context. When the test was done, she was startled to learn that she had received the second-highest score.

By some estimates, as many as a million CCTV cameras are installed in London, making it the most surveilled metropolis on the planet. Boris Johnson, who before becoming Britain’s Foreign Secretary served as the city’s mayor, once said, “When you walk down the streets of London, you are a movie star. You are being filmed by more cameras than you can possibly imagine.”

Porritt thought that the cameras outside the Camden Road railway station might have caught the groper walking by, so he and Young visited the CCTV office there. As Porritt examined the equipment, Young gazed out a window at scores of rush-hour commuters streaming in and out of the station. Then, suddenly, she shouted, “Oh, my God. That’s him!”

Young was staring at a man just inside the entrance: he had a mustache and wore glasses. She watched him pick up a Metro from a stack on the floor and walk out of the station.

“We ran like maniacs,” Young recalled. They caught him, and after he was in handcuffs he muttered to Porritt, “I’m sorry, I’m sorry.” A fifty-six-year-old clerical worker named Ilhan Karatepe, he subsequently pleaded guilty to three counts of sexual assault and received a suspended sentence. (He was also barred from riding public transportation by himself.)</p>
crime  science 
august 2016 by charlesarthur
Why i hope the search for extraterrestrial life finds nothing • Nick Bostrom
From 2008, but still relevant after the latest discovery of an Earth-like planet near another sun:
<p>From these two facts [no observed alien civilisations; space is REALLY big] it follows that there exists a “Great Filter”. 1 The Great Filter can be thought of as a probability barrier. It consists of exist one of more highly improbable evolutionary transitions or steps whose occurrence is required in order for an Earth‐like planet to produce an intelligent civilization of a type that would be visible to us with our current observation technology. You start with billions and billions of potential germination points for life, and you end up with a sum total of zero extraterrestrial civilizations that we can observe. The Great Filter must therefore be powerful enough— which is to say, the critical steps must be improbable enough—that even with many billions rolls of the dice, one ends up with nothing: no aliens, no spacecraft, no signals, at least none that we can detect in our neck of the woods.

Now, an important question for us is, just where might this Great Filter be located? There are two basic possibilities: It might be behind us, somewhere in our distant past. Or it might be ahead of us, somewhere in the millennia or decades to come. Let us ponder these possibilities in turn.</p>

See if you can work out which of those two possibilities is preferable. Bostrom's essay is unhurried and thorough, yet economical.
evolution  science  space 
august 2016 by charlesarthur
Police asked this 3D printing lab to recreate a dead man’s fingers to unlock his phone • Fusion
Rose Eveleth:
<p>Last month, law enforcement officers showed up at the lab of Anil Jain, a professor at Michigan State University. Jain wasn’t in trouble; the officers wanted his help.

Jain is a computer science professor who works on biometric identifiers such as facial recognition programs, fingerprint scanners and tattoo matching; he wants to make them as difficult to hack as possible. But the police were interested in the opposite of this: they wanted his help to unlock a dead man’s phone.

Jain and his PhD student Sunpreet Arora couldn’t share details of the case with me, since it’s an ongoing investigation, but the gist is this: a man was murdered, and the police think there might be clues to who murdered him stored in his phone. But they can’t get access to the phone without his fingerprint or passcode. So instead of asking the company that made the phone to grant them access, they’re going another route: having the Jain lab create a 3D printed replica of the victim’s fingers. With them, they hope to unlock the phone.</p>

The fine details of how they're going to make it work is quite something.
science  3dprinting 
july 2016 by charlesarthur
Licensing agreement reached on brilliant new blue pigment discovered by happy accident • Oregon State University
<p><img src="" width="100%" />

A brilliant new blue pigment – discovered serendipitously by Oregon State University chemists in 2009 – is now reaching the marketplace, where it will be used in a wide range of coatings and plastics.

The commercial development has solved a quest that began thousands of years ago, and captured the imagination of ancient Egyptians, the Han dynasty in China, Mayan cultures and others – to develop a near-perfect blue pigment.

It happened accidently.</p>

ACCIDENTLY. Someone at Oregon State University's communications department let the word ACCIDENTLY go through into a document for publication.

<p>The new pigment is formed by a unique crystal structure that allows the manganese ions to absorb red and green wavelengths of light, while only reflecting blue. The vibrant blue is so durable, and its compounds are so stable – even in oil and water – that the color does not fade.</p>

Tories will be pleased. (In the UK the Conservative "Tory" party uses blue for its identifying colour.)
science  colour 
june 2016 by charlesarthur
The strange science of why airport security lines spiral out of control • NY Mag
Drake Baer:
<p>Queues are governed by <a href="">Little’s Law</a>, which states that the number of items in a queuing system (the length of a queue) is equal to the average waiting time per item (how long each interaction takes) times the number of items arriving per unit time (how many people/things are coming in).

For queues with “servers” — someone handling transactions with whomever’s at the front of the line — the server needs to have some idle time, otherwise the queue, according to the math, could grow without limit. For a queue with only a single server, the rule of thumb is about 15 percent to 20 percent idle time. If there’s lots of servers (like a call bank with hundreds of people taking calls), then they don’t need as much idle time, because there’s less of a chance of every server being occupied at once, causing the line to build and leading to the inevitable viral videos.

A lot of this, Larson says, has to do with the profoundly human quality of variability. If queues were mechanical — like in a well-run factory, where the time of arrival and the time of service for each transaction were highly predictable — then a server could be super busy and queues still wouldn’t form.

But people are neither predictable nor identical in how they approach airline travel.</p>

Damn people.
science  airport  queueing 
may 2016 by charlesarthur
Researcher illegally shares millions of science papers free online to spread knowledge » ScienceAlert
<p>A researcher in Russia has made more than 48 million journal articles - almost every single peer-reviewed paper every published - freely available online. And she's now refusing to shut the site down, despite a court injunction and a lawsuit from Elsevier, one of the world's biggest publishers.

For those of you who aren't already using it, the site in question is Sci-Hub, and it's sort of like a Pirate Bay of the science world. It was established in 2011 by neuroscientist Alexandra Elbakyan, who was frustrated that she couldn't afford to access the articles needed for her research, and it's since gone viral, with hundreds of thousands of papers being downloaded daily. But at the end of last year, the site was <a href="">ordered to be taken down by a New York district court</a> - a ruling that Elbakyan has decided to fight, triggering a debate over who really owns science. 

"Payment of $32 is just insane when you need to skim or read tens or hundreds of these papers to do research. I obtained these papers by pirating them," Elbakyan told Torrent Freak last year. "Everyone should have access to knowledge regardless of their income or affiliation. And that’s absolutely legal."…

… She also explains that the academic publishing situation is different to the music or film industry, where pirating is ripping off creators. "All papers on their website are written by researchers, and researchers do not receive money from what Elsevier collects. That is very different from the music or movie industry, where creators receive money from each copy sold," she <a href="">said</a>.</p>

The journals' argument is that they add value by getting papers peer-reviewed, and edited, and choosing the important ones to publish. The existence of free unpeered sites such as Arxiv hasn't noticeably dented their business.

But it always feels wrong when publicly funded research in particular ends up behind giant paywalls. If the public pays for the research, the public should be able to see its fruits.
science  publication 
february 2016 by charlesarthur
Gravitational waves exist: the inside story of how scientists finally found them » The New Yorker
Nicola Twilley:
<p>It took years to make the most sensitive instrument in history insensitive to everything that is not a gravitational wave. Emptying the tubes of air demanded forty days of pumping. The result was one of the purest vacuums ever created on Earth, a trillionth as dense as the atmosphere at sea level. Still, the sources of interference were almost beyond reckoning—the motion of the wind in Hanford, or of the ocean in Livingston; imperfections in the laser light as a result of fluctuations in the power grid; the jittering of individual atoms within the mirrors; distant lightning storms. All can obscure or be mistaken for a gravitational wave, and each source had to be eliminated or controlled for. One of LIGO’s systems responds to minuscule seismic tremors by activating a damping system that pushes on the mirrors with exactly the right counterforce to keep them steady; another monitors for disruptive sounds from passing cars, airplanes, or wolves.

“There are ten thousand other tiny things, and I really mean ten thousand,” Weiss said. “And every single one needs to be working correctly so that nothing interferes with the signal.” When his colleagues make adjustments to the observatory’s interior components, they must set up a portable clean room, sterilize their tools, and don what they call bunny suits—full-body protective gear—lest a skin cell or a particle of dust accidentally settle on the sparkling optical hardware.</p>

This is the one story to read today about this amazing finding. Detail and insight.
astronomy  science  gravity 
february 2016 by charlesarthur
Riddle of cement’s structure is finally solved » MIT News
<p>Concrete forms through the solidification of a mixture of water, gravel, sand, and cement powder. Is the resulting glue material (known as cement hydrate, CSH) a continuous solid, like metal or stone, or is it an aggregate of small particles?

As basic as that question is, it had never been definitively answered. In a paper published this week in the Proceedings of the National Academy of Sciences, a team of researchers at MIT, Georgetown University, and France’s CNRS (together with other universities in the U.S., France, and U.K.) say they have solved that riddle and identified key factors in the structure of CSH that could help researchers work out better formulations for producing more durable concrete.</p>

What a time to be alive, eh? That solid/particle question had been bugging me for ages. Seriously, though, it's an important topic: this stuff is <em>everywhere</em>.
concrete  structure  science 
february 2016 by charlesarthur
As Flint fought to be heard, Virginia Tech team sounded alarm » The New York Times
Mitch Smith:
<p>as government officials were ignoring and ridiculing residents’ concerns about the safety of their tap water, a small circle of people was setting off alarms. Among them was the team from Virginia Tech.

The team began looking into Flint’s water after its professor, Marc Edwards, spoke with LeeAnne Walters, a resident whose tap water contained alarming amounts of lead. Dr. Edwards, who years earlier had helped expose lead contamination in Washington, D.C., had his students send testing kits to homes in Flint to find out if the problem was widespread. Lead exposure can lead to health and developmental problems, particularly in children, and its toxic effects can be irreversible.

Their persistence helped force official to acknowledge the crisis and prompted warnings to residents not to drink or cook with tap water.</p>
community  science 
february 2016 by charlesarthur
Mesmerizing migration: watch 118 bird species migrate across a map of the western hemisphere » All About Birds
Pat Leonard:
<p>For the first time, scientists at the Cornell Lab of Ornithology have documented migratory movements of bird populations spanning the entire year for 118 species throughout the Western Hemisphere. The study finds broad similarity in the routes used by specific groups of species—vividly demonstrated by animated maps showing patterns of movement across the annual cycle.</p>

<img src="" width="100%" />

There's also a version <a href="">showing which species is which</a>.
maps  migration  science 
january 2016 by charlesarthur
The muscular dystrophy patient and the Olympic medallist with the same genetic disorder » ProPublica
David Epstein, who wrote a book about genes and sport, and was then contacted out of the blue:
<p>It seemed absolutely crazy. The idea that an Iowa housewife, equipped with the cutting-edge medical tool known as Google Images, would make a medical discovery about a pro athlete who sees doctors and athletic trainers as part of her job?

I consulted Harvard geneticist Robert C. Green to get his thoughts, in part because he has done important work on how people react to receiving information about their genes. Green was open to discussing it, but he recalls a justifiable concern that had nothing to do with science: “Empowering a relationship between these two women could end badly,” he says. “People go off the deep end when they are relating to celebrities they think they have a connection to.” I was skeptical too. Maybe she was a nutjob.

I had no idea yet that Jill, just by investigating her own family, had learned more about the manifestations of her disease than nearly anyone in the world, and that she could see things that no one else could.</p>

Open this in another tab, and make the time to read it today - you'll need about 15 minutes. It's stunning. And (for any criticism of Google's tax affairs below) it's also testament to the power of Google Images and search engines and the power of having the world's scientific information available to everyone. Jill extended two peoples' lives, including her father's (and probably her own), because she could access information easily.
health  science  genetics 
january 2016 by charlesarthur
As freezing persons recollect the snow: first chill, then stupor, then the letting go » Outside Online
Peter Clark with a scary description of what happens as hypothermia sets in:
<p>When your Jeep spins lazily off the mountain road and slams backward into a snowbank, you don't worry immediately about the cold. Your first thought is that you've just dented your bumper. Your second is that you've failed to bring a shovel. Your third is that you'll be late for dinner. Friends are expecting you at their cabin around eight for a moonlight ski, a late dinner, a sauna. Nothing can keep you from that.

Driving out of town, defroster roaring, you barely noted the bank thermometer on the town square: minus 27 degrees at 6:36. The radio weather report warned of a deep mass of arctic air settling over the region. The man who took your money at the Conoco station shook his head at the register and said he wouldn't be going anywhere tonight if he were you. You smiled. A little chill never hurt anybody with enough fleece and a good four-wheel-drive.

But now you're stuck.</p>

(Via <a href="">Eugene Wei</a>.)
science  hypothermia 
november 2015 by charlesarthur
In the 1970s, scientists discovered a two billion-year-old nuclear reactor in west Africa » Medium
The Physics ArXiv blog explains:
<p>When the ore in Gabon was laid down some 2 billion years ago, the concentration of uranium-235 would have been about 4%, more than enough for a self-sustaining nuclear reaction.

The idea is that when a neutrons hits an atom of uranium-235, the atom splits producing two smaller nuclei and several neutrons. These neutrons go on to split other atoms in an ongoing chain reaction.

However, the liberated neutrons are high-energy particles that tend to fly away rapidly. So nuclear reactors usually contain a moderating material that slows down the neutrons so that they can interact with other uranium atoms.

It turns out that water is a reasonable neutron moderator. So an important component of this natural reactor was the presence of water seeping through the uranium ore. And this had an interesting impact on the way the reactors operated.

Nuclear scientists believe that the Oklo reactors operated in pulses. As water flowed into the rock, it moderated the neutrons, allowing a chain reaction to occur. But this increased the temperature of the rock, boiling the water into steam which escaped.</p>

Kept running for 300,000 years. More useful than that is what it taught scientists about how fission waste products migrate from burial sites. Turns out the answer is: not that much.
science  fission 
november 2015 by charlesarthur
See the Milky Way anew »Chromoscope
The Milky Way, viewed at different light frequencies - from gamma ray to radio. It looks very different depending on how your eyes work, as you quickly realise. Fun (though possibly not so much on mobile)
astronomy  science  space 
october 2015 by charlesarthur
The earthquake that will devastate Seattle » The New Yorker
Kathryn Schulz:
Under pressure from Juan de Fuca, the stuck edge of North America is bulging upward and compressing eastward, at the rate of, respectively, three to four millimetres and thirty to forty millimetres a year. It can do so for quite some time, because, as continent stuff goes, it is young, made of rock that is still relatively elastic. (Rocks, like us, get stiffer as they age.) But it cannot do so indefinitely. There is a backstop—the craton, that ancient unbudgeable mass at the center of the continent—and, sooner or later, North America will rebound like a spring. If, on that occasion, only the southern part of the Cascadia subduction zone gives way—your first two fingers, say—the magnitude of the resulting quake will be somewhere between 8.0 and 8.6. That’s the big one. If the entire zone gives way at once, an event that seismologists call a full-margin rupture, the magnitude will be somewhere between 8.7 and 9.2. That’s the very big one.

Flick your right fingers outward, forcefully, so that your hand flattens back down again. When the next very big earthquake hits, the northwest edge of the continent, from California to Canada and the continental shelf to the Cascades, will drop by as much as six feet and rebound thirty to a hundred feet to the west—losing, within minutes, all the elevation and compression it has gained over centuries. Some of that shift will take place beneath the ocean, displacing a colossal quantity of seawater.

Last earthquake involving Juan de Fuca: 315 years ago. Usual frequency of earthquakes involving Juan de Fuca: every 243 years. Variance of quake timing: not given (but known by someone at Oregon State University). Value of real estate in Seattle and Oregon: probably falling by the time you read this. (To put the tech lens on this, consider that Microsoft and Amazon are both headquartered in Seattle. Now wipe them off the map. Pause.)
earthquake  seattle  science 
july 2015 by charlesarthur
Universities Inc. in the UK
After yesterday's link about <a href="">Proctor & Gamble's disruptive capacity</a>, David Colquhoun from University College London pointed out that it's not all sweetness and light - far from it:
Dr Aubrey Blumsohn MBBCh, PhD, MSc, BSc(hons), FRCPath was, until 2006, a senior lecturer and honorary consultant in metabolic bone diseases at Sheffield University. He, and his boss, Richard Eastell, were doing a clinical study of a Procter & Gamble Pharmaceuticals (P&G) drug, Actonel (risedronate), The work was funded by Procter & Gamble.

Richard Eastell is Professor of Bone Metabolism, and was Research Dean.

Proctor & Gamble refused, from 2002 onwards, to release the randomisation codes for the trial to the authors whose names appear on the paper. After trying to see the data for years, and getting little support from his employer, Blumsohn subsequently got hold of it in 2005, and then discovered flaws in the analysis provided by P&G’s statistician. P&G wrote papers on which the names of university academics as authors. Blumsohn did the only thing that any honest scientist could do: he went public with his complaint.

Bad things ensued.
proctorgamble  science 
april 2015 by charlesarthur
Global warming is now slowing down the circulation of the oceans — with potentially dire consequences » The Washington Post
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Chris Mooney:
Welcome to this week’s installment of “Don’t Mess with Geophysics.”

Last week, we learned about the possible destabilization of the Totten Glacier of East Antarctica, which could unleash over 11 feet of sea level rise in coming centuries.

And now this week brings news of another potential mega-scale perturbation. According to a new study just out in Nature Climate Change by Stefan Rahmstorf of the Potsdam Institute for Climate Impact Research and a group of co-authors, we’re now seeing a slowdown of the great ocean circulation that, among other planetary roles, helps to partly drive the Gulf Stream off the U.S. east coast. The consequences could be dire – including significant extra sea level rise for coastal cities like New York and Boston.

Somehow just linking to this feels insufficient. Equally, we're talking about the world's oceans here, and it's hard to know quite what to do.
climate  science  thermohaline 
march 2015 by charlesarthur
Why science is so hard to believe » The Washington Post
Joel Achenbach:
In the United States, climate change has become a litmus test that identifies you as belonging to one or the other of these two antagonistic tribes. When we argue about it, Kahan says, we’re actually arguing about who we are, what our crowd is. We’re thinking: People like us believe this. People like that do not believe this.

Science appeals to our rational brain, but our beliefs are motivated largely by emotion, and the biggest motivation is remaining tight with our peers. “We’re all in high school. We’ve never left high school,” says Marcia McNutt. “People still have a need to fit in, and that need to fit in is so strong that local values and local opinions are always trumping science. And they will continue to trump science, especially when there is no clear downside to ignoring science.”

That's the key point: you can be an idiot, and it doesn't have any effect. Well, apart from vaccination, and if you're in charge of the country. (With luck, most of the commenters on the article will never be in a position where they can make any difference to anything.)
science  belief 
february 2015 by charlesarthur
Unique in the shopping mall: On the reidentifiability of credit card metadata >> Science
<a href="">Science magazine</a> has a special this week on data and privacy. Here, it looks at how many data points are needed to identify someone uniquely:
To provide a quantitative assessment of the likelihood of identification from financial data, we used a data set D of 3 months of credit card transactions for 1.1 million users in 10,000 shops in an Organisation for Economic Co-operation and Development country (Fig. 1). The data set was simply anonymized, which means that it did not contain any names, account numbers, or obvious identifiers. Each transaction was time-stamped with a resolution of 1 day and associated with one shop. Shops are distributed throughout the country, and the number of shops in a district scales with population density (r2 = 0.51, P < 0.001) (fig. S1).

How many data points for identification? Three.
privacy  data  science 
january 2015 by charlesarthur
Chemists find a way to unboil eggs >> Phys Org
Janet Wilson on news that will delight, well, anyone?
Like many researchers, he has struggled to efficiently produce or recycle valuable molecular proteins that have a wide range of applications but which frequently "misfold" into structurally incorrect shapes when they are formed, rendering them useless.

"It's not so much that we're interested in processing the eggs; that's just demonstrating how powerful this process is," [Gregory] Weiss [professor of chemistry and molecular biology at UCal at Irvine] said. "The real problem is there are lots of cases of gummy proteins that you spend way too much time scraping off your test tubes, and you want some means of recovering that material."

But older methods are expensive and time-consuming: The equivalent of dialysis at the molecular level must be done for about four days. "The new process takes minutes," Weiss noted. "It speeds things up by a factor of thousands."

To re-create a clear protein known as lysozyme once an egg has been boiled, he and his colleagues add a urea substance that chews away at the whites, liquefying the solid material. That's half the process; at the molecular level, protein bits are still balled up into unusable masses. The scientists then employ a vortex fluid device, a high-powered machine designed by Professor Colin Raston's laboratory at South Australia's Flinders University. Shear stress within thin, microfluidic films is applied to those tiny pieces, forcing them back into untangled, proper form.

Unspilling milk next, I hope.
eggs  science  protein 
january 2015 by charlesarthur

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