Tag Archives: Science

Data Analysts Captivated by R’s Power

data mining has entered a golden age, whether being used to set ad prices, find new drugs more quickly or fine-tune financial models. Companies as diverse as Google, Pfizer, Merck, Bank of America, the InterContinental Hotels Group and Shell use it.
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Close to 1,600 different packages reside on just one of the many Web sites devoted to R, and the number of packages has grown exponentially. One package, called BiodiversityR, offers a graphical interface aimed at making calculations of environmental trends easier.

Another package, called Emu, analyzes speech patterns, while GenABEL is used to study the human genome. The financial services community has demonstrated a particular affinity for R; dozens of packages exist for derivatives analysis alone. “The great beauty of R is that you can modify it to do all sorts of things,” said Hal Varian, chief economist at Google. “And you have a lot of prepackaged stuff that’s already available, so you’re standing on the shoulders of giants.”

R first appeared in 1996, when the statistics professors Ross Ihaka and Robert Gentleman of the University of Auckland in New Zealand released the code as a free software package. According to them, the notion of devising something like R sprang up during a hallway conversation. They both wanted technology better suited for their statistics students, who needed to analyze data and produce graphical models of the information. Most comparable software had been designed by computer scientists and proved hard to use.

R is another example of great, free, open source software. See R packages for Statistics for Experimenters.

via: R in the news

A Microscopic Layer of Diamonds Beneath the Surface of North America

Diamonds show comet struck North America, scientists say

A discovery of microscopic diamonds a few feet beneath the surface of North America reveals that a comet caused a cataclysm of fire, flood and devastation nearly 13,000 years ago that extinguished mammoths and mastodons and dealt a blow to early civilization, scientists said Friday.

The nanodiamonds, so small that they are barely visible in an electron microscope, are thought to be remnants of that comet, which would have hit about 65 million years after the much larger collision that wiped out the dinosaurs.
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Battered by fire and ice, as many as 35 species of mammals, including American camels, the short-faced bear, the giant beaver, the dire wolf and the American lion, either immediately vanished or were so depleted in number that humans hunted them to extinction.

The humans, a Paleo-Indian grouping known as the Clovis culture for the distinctive spear points they employed, suffered a major population drop, disappearing in many areas for hundreds of years.
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gems can only be created under the extreme temperatures and pressures of a massive explosion, such as a comet striking the Earth’s surface.

“There’s no other way we can interpret the presence of these diamonds other than an extraterrestrial impact,” said James Kennett, a paleooceanographer.

Such an impact would be the most likely source of nanodiamonds, critics agreed. But many argued that the one-page paper in Science did not provide enough evidence to support the authors’ claim.

“Nanodiamonds could be a good indicator of an impact event . . . but after reading the paper, I wasn’t convinced they found diamonds,” said physicist Tyrone Daulton of Washington University in St. Louis. “Maybe they found diamonds and maybe they didn’t.”

Post 2009

My first post in 2009 is the 2009th post for the blog. Here are some highlights from 2008:

Swarm of Yellowstone Quakes Baffles Scientists

photo of Yellowstone's Old Faithful by John Hunter

Photo of Old Faithful geyser in Yellowstone National Park by John Hunter

Swarm of Yellowstone Quakes Baffles Scientists

Swarms of small earthquakes happen frequently in Yellowstone, but it’s very unusual for so many earthquakes to happen over several days, said Robert Smith, a professor of geophysics at the University of Utah. “They’re certainly not normal,” Smith said. “We haven’t had earthquakes in this energy or extent in many years.”
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“There doesn’t seem to be anything to be alarmed about,” Vallie said. Smith said it’s difficult to say what might be causing the tremors. He pointed out that Yellowstone is the caldera of a volcano that last erupted 70,000 years ago.
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Yellowstone has had significant earthquakes as well as minor ones in recent decades. In 1959, a magnitude 7.5 quake near Hebgen Lake just west of the park triggered a landslide that killed 28 people.

So far the most powerful quake over the last few days has been one at 3.8 on the Richter scale. An earthquake of 4.0-4.9 “Noticeable shaking of indoor items, rattling noises. Significant damage unlikely.” The Richter scale is a logarithmic scale, meaning a measure of 4.0 is 10 times as powerful as 3.0 quake, and 5.0 is 100 times more powerful than a 3.o quake.

The Year in Bad Science

The Year in Bad Science Ben Goldacre reviews some of the science lowlights of the year.

In a world where rigorous evidence from scientific research languishes unpublicised, the media continued to churn out bogus wacky science stories. Britain’s happiest places were mapped by “scientists”, although the differences were just chance findings; there were innumerable “surveys” from unrepresentative populations; and the right wing press claimed that “Lord Nelson and Captain Cook’s ship logs question climate change theories,” although they did nothing of the sort, as the researchers themselves helpfully explained. We saw how the BBC misrepresented the statistics on parents’ choices about keeping a Down’s Syndrome pregnancy, producing their a publicity avalanche on the back of an incorrect story, and learnt along the way about confounding variables, baseline changes, and more.

In the world of evidence based social policy we saw how the government quietly dropped death as an outcome indicator for their drugs policy, the fascinating inconsistencies in food additive judgment calls, and more. We also watched with delight as right-wing think tank Reform produced a report on the crisis in maths in which they got their maths wrong.

Brain Reorganizes As It Learns Math

Brain reorganizes to make room for math

It takes years for children to master the ins and outs of arithmetic. New research indicates that this learning process triggers a large-scale reorganization of brain processes involved in understanding written symbols for various quantities.

The findings support the idea that humans’ ability to match specific quantities with number symbols, a skill required for doing arithmetic, builds on a brain system that is used for estimating approximate quantities. That brain system is seen in many nonhuman animals.

When performing operations with Arabic numerals, young adults, but not school-age children, show pronounced activity in a piece of brain tissue called the left superior temporal gyrus, says Daniel Ansari of the University of Western Ontario in London, Canada. Earlier studies have linked this region to the ability to associate speech sounds with written letters, and musical sounds with written notes. The left superior temporal gyrus is located near the brain’s midpoint, not far from areas linked to speech production and understanding.

In contrast, children solving a numerical task display heightened activity in a frontal-brain area that, in adults, primarily serves other functions.

Making Embryonic Stem Cells

photo of Junying Yu, an assistant scientist with the University of Wisconsin-Madison by Bryce Richter, 2007.

Holy Grail of stem cell research within reach by Mark Johnson

It was time to test the 14 genes she had selected as the best candidates to reprogram a cell.

Using viruses to deliver the genes, she inserted all 14 at once into human cells. On the morning of July 1, 2006, Yu arrived at the lab and examined the culture dishes. Her eyes focused on a few colonies, each resembling a crowded city viewed from space. They looked like embryonic stem cells.
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Cells must pass certain tests. They must multiply for weeks while remaining in their delicate, primitive state. When they are allowed to develop, they must turn into all the other cell types.

Bad things happen. Cells develop too soon. Cells die. There is no “aha!” moment, Thomson has said, only stress. He looked at the colonies and suppressed any excitement. He told Yu, essentially: OK, well get back to me in a couple of weeks.
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In the fall of 2006, Yu was preparing to whittle down her list of genes when she fell ill. The pain in her gut was awful. She struggled to eat. Her doctor thought it was a stomach flu. Instead, in late October, Yu’s appendix burst. She was laid up for a month. When she returned to the lab, the problem with the culture medium struck again.

Not until January 2007 was she able to begin narrowing the list of genes. She spent several months testing subsets of them, finally arriving at four. Two, Oct4 and Sox2, were “Yamanaka factors,” the name given to the genes the Japanese scientist had used to reprogram mouse cells. Two, Nanog and Lin28, were not.

Using a virus to deliver the four genes, she reprogrammed a line of fetal cells, then repeated the experiments with more mature cells. Although the process was inefficient, succeeding with only a small fraction of cells, it did work.

Dr. Junying Yu, an American trained scientist who entered the US as a foreign student from China. Which is somewhat ironic given the movement of USA based stem cell researches to China. Great article showing the process of scientific inquiry.

Online Education in Science, Engineering and Medicine

The National Academies state that they want to develop websites, podcasts, and printed information featuring the topics in science, engineering, and medicine that concern you the most, and that you’d like to understand better. Great. I am very disappointed in how little great material is available now (from them, and others).

Fill out their survey and hope they hire some people that actually understand the web. I must say the survey seems very lame to me.

The internet provides a fantastic platform for those that have an interest in increasing scientific literacy. But there is still very little great material available. There are a few great resources but there should be a great deal more. The National Academies of Science have a particularly stilted web presence – it is as though the web were just a way to distribute pages for people to print out. Though they are very slowly getting a bit better, adding a small amount of podcasts, for example. While hardly innovative, for them, it is a step into the 21st century, at least.

Some of the good material online: Public Library of Science – Science Blogs – Encyclopedia of Life – The Naked Scientists – Berkeley Course Webcasts – BBC Science News – MIT OpenCourseWare (though it is very lacking in some ways at least they are trying) – TED – Mayo Clinic – Nobel Prize – SciVee

It seems to me universities with huge endowments (MIT, Harvard, Yale, Standford…), government agencies (NSF, National Academies), museums and professional societies should be doing much more to create great online content. I would increase funding in this area by 5 to 10 times what is currently being dedicated right now, and probably much more would be wise. I believe funding this would be most effective way to spend resources of those organizations on what they say they want to support.

1,000 Species Discovered in Greater Mekong in Last Decade

Photograph of Gumprechts Green Pitviper courtesy Greater Mekong Programme/WWF International

While most species were discovered in the largely unexplored jungles and wetlands, some were first found in the most surprising places. The Laotian rock rat, for example, thought to be extinct 11 million years ago, was first encountered by scientists in a local food market, while the Siamese Peninsula pitviper was found slithering through the rafters of a restaurant in Khao Yai National Park in Thailand.

“This region is like what I read about as a child in the stories of Charles Darwin,” said Dr Thomas Ziegler, Curator at the Cologne Zoo. “It is a great feeling being in an unexplored area and to document its biodiversity for the first time… both enigmatic and beautiful,” he said.

The findings, highlighted in this report, include 519 plants, 279 fish, 88 frogs, 88 spiders, 46 lizards, 22 snakes, 15 mammals, 4 birds, 4 turtles, 2 salamanders and a toad. The region comprises the six countries through which the Mekong River flows including Cambodia, Lao PDR, Myanmar, Thailand, Vietnam and the southern Chinese province of Yunnan. It is estimated thousands of new invertebrate species were also discovered during this period, further highlighting the region’s immense biodiversity.

“It doesn’t get any better than this,” said Stuart Chapman, Director of WWF’s Greater Mekong Programme. “We thought discoveries of this scale were confined to the history books. This reaffirms the Greater Mekong’s place on the world map of conservation priorities.”

The report stresses economic development and environmental protection must go hand-in-hand to provide for livelihoods and alleviate poverty, and ensure the survival of the Greater Mekong’s astonishing array of species and natural habitats.

Full press release. I am a World Wildlife Fund member.

Before the Big Bang

Did our cosmos exist before the big bang?

The theory that the recycled universe was based on, called loop quantum cosmology (LQC), had managed to illuminate the very birth of the universe – something even Einstein’s general theory of relativity fails to do.
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LQC is in fact the first tangible application of another theory called loop quantum gravity, which cunningly combines Einstein’s theory of gravity with quantum mechanics. We need theories like this to work out what happens when microscopic volumes experience an extreme gravitational force, as happened near the big bang, for example.
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If LQC turns out to be right, our universe emerged from a pre-existing universe that had been expanding before contracting due to gravity. As all the matter squeezed into a microscopic volume, this universe approached the so-called Planck density, 5.1 Ã— 1096 kilograms per cubic metre. At this stage, it stopped contracting and rebounded, giving us our universe.

In classical cosmology, a phenomenon called inflation caused the universe to expand at incredible speed in the first fractions of a second after the big bang. This inflationary phase is needed to explain why the temperature of faraway regions of the universe is almost identical, even though heat should not have had time to spread that far – the so-called horizon problem. It also explains why the universe is so finely balanced between expanding forever and contracting eventually under gravity – the flatness problem. Cosmologists invoke a particle called the inflaton to make inflation happen, but precious little is known about it.