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Thursday, November 5, 2009

Percentages and Vote Counts

Posted by Jonathan Golob on Thu, Nov 5, 2009 at 6:31 PM

Today was a good day for McGinn, right? The difference in vote counts went up from yesterday, from 462 to 515. Fifty-three more votes went to McGinn.

Counts in the way of McGinn!
  • Counts in the way of McGinn

Wrong.

This is one of the most annoying fallacies of election reporting. While the final result is determined by the absolute counts, as we're using the ongoing vote totals as a sample of that final count we should be paying attention to percentages. By this more accurate measure, the mayoral race has tightened a bit since yesterday, from 0.44% to 0.40% (when excluding write-ins from the total).

... but the percentage tightens
  • ... but the percentage tightens

Given the (innovative in city elections) use of last-minute get out the vote efforts by the McGinn campaign, I suspect these ongoing totals might not be as reflective of the true final counts as in the past. But for now, today's results are actually looking better for Mallahan, not worse.

(Don't even get me started about the foolishness of expecting machine or hand recounts to resolve an election whose final counts are within the margin of counting error. We might as well just flip a coin, if we're going to rely upon entropy to make our decisions.)

Wednesday, November 4, 2009

News from the Animal Kingdom: Some Animals Can Display Grief for the Dead

Posted by Charles Mudede on Wed, Nov 4, 2009 at 9:29 AM

Here is how gorillas grieve:

Gorillas are known to hold wakes for dead friends, something that some zoos have formalized in a ceremony when one of their gorillas passes away. Donna Fernandes, now president of the Buffalo Zoo, tells the story of being at Boston's Franklin Park Zoo ten years ago during the wake for a female gorilla, Babs, who had died of cancer. She describes seeing the gorilla's longtime mate say good-bye: "He was howling and banging his chest,... and he picked up a piece of her favorite food — celery — and put it in her hand and tried to get her to wake up. I was weeping, it was so emotional." Later, the scene at Babs's December funeral was similarly moving. As reported by local news, gorilla family members "one by one ... filed into" the room where "Babs's body lay," approaching their "beloved leader" and "gently sniffing the body."

Here is how elephants express their grief:

[These] are the actions of the members of an elephant family... after a group member had been shot: "Teresia and Trista became frantic and knelt down and tried to lift her up. They worked their tusks under her back and under her head. At one point they succeeded in lifting her into a sitting position but her body flopped back down. Her family tried everything to rouse her, kicking and tusking her, and Tullulah even went off and collected a trunkful of grass and tried to stuff it in her mouth."

Finally, wolves:

[A] wolf pack after the loss of the low-ranking omega female wolf, Motaki, to a mountain lion. The pack lost their spirit and their playfulness. They no longer howled as a group, but rather they "sang alone in a slow mournful cry." They were depressed — tails and heads held low and walking softly and slowly — when they came upon the place where Motaki was killed. They inspected the area and pinned their ears back and dropped their tails, a gesture that usually means submission. It took about six weeks for the pack to return to normal. The Dutchers also tell of a wolf pack in Canada in which one pack member died and the others wandered about in a figure eight as if searching for her. They also howled long and mournfully.

As for humans, some of us can completely contain our emotions and turn the grief into a dark, inner sea that's wide and deep. We know the depths of death. No crying, no smelling, no stomping about—just the silent sea of grief.

Almost All of the Universe Is Dark

Posted by Charles Mudede on Wed, Nov 4, 2009 at 8:13 AM

Just 5% of everything is normal:

A detailed picture of the seeds of structures in the universe has been unveiled by an international team co-led by Sarah Church of the Kavli Institute for Particle Astrophysics and Cosmology, jointly located at the Department of Energy's SLAC National Accelerator Laboratory and Stanford University, and by Walter Gear, of Cardiff University in the United Kingdom. These measurements of the cosmic microwave background — a faintly glowing relic of the hot, dense, young universe — put limits on proposed alternatives to the standard model of cosmology and provide further support for the standard cosmological model, confirming that dark matter and dark energy make up 95% of everything in existence, while ordinary matter makes up just 5%
Such discoveries, discoveries that decenter and belittle humans, gives us a terrific sense of what Terry Eagleton calls "the sublime negative." To use Martin Rees words: "The distinctive details of our universe, and of everything in it (ourselves included), seem to be the outcome of what might be called an accident."

From the accident of the universe, the sublime negativity itself, we get this other accidental universe, the accident of Miss Universe 2009:

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Even her dress is a universe.

Wednesday, October 28, 2009

Red in...

Posted by Charles Mudede on Wed, Oct 28, 2009 at 9:54 AM

If you hate mosquitoes as much as I do, you will draw as much pleasure as I did from this image for this Science News story:

A jumping spider feasts on a mosquito, living up to researchers' nickname of "Mosquito Terminator" for this Evarcha culicivora spider. Eating a mosquito engorged on blood makes both males and females of this species more appealing to potential mates
.

The Other Way Around

Posted by Charles Mudede on Wed, Oct 28, 2009 at 9:26 AM

Nonstop is the news about diseases jumping from other animals (birds, pigs) to us (frightful!). For once, a story about diseases jumping from us to other animals:

Researchers from The Roslin Institute of the University of Edinburgh have shown that a strain of bacteria has jumped from humans to chickens.

It is believed to be the first clear evidence of bacterial pathogens crossing over from humans to animals and then spreading since animals were first domesticated some 10,000 years ago.

The study identified a form of the bacteria Staphylococcus aureus — of which MRSA is a subtype — in chickens, and found that the bacteria originally came from humans.

Monday, October 26, 2009

Recently on Mars

Posted by Grant Brissey on Mon, Oct 26, 2009 at 3:23 PM

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  • NASA, HiRISE, MRO, LPL (U. Arizona)
  • (Click to enlarge image)

This high-resolution picture from the HiRISE camera on board the Mars Reconnaissance Orbiter shows twisting dark trails criss-crossing light-colored terrain on the Martian surface. Newly formed trails like these had presented researchers with a tantalizing mystery but are now known to be the work of miniature wind vortices known to occur on the red planet, in other words Martian dust devils. Such spinning columns of rising air heated by the warm surface are also common in dry and desert areas on planet Earth. Typically lasting only a few minutes, dust devils become visible as they pick up loose red-colored dust leaving the darker and heavier sand beneath intact. Ironically, dust devils have been credited with unexpectedly cleaning the solar panels of the Mars rovers.

h/t: nasa.gov and Slog commenter Peter F.

Friday, October 23, 2009

Flying Anvils Are Incredibly Satisfying

Posted by Paul Constant on Fri, Oct 23, 2009 at 2:30 PM

Here, via Super Punch, we have someone who enjoys launching anvils some 200 feet into the air:

Thursday, October 22, 2009

Who Rules the World?

Posted by Charles Mudede on Thu, Oct 22, 2009 at 11:56 AM

The Vancouver Sun reports:

There is life in the planet's expanding dead zones, say researchers, who have uncovered a remarkable microbe thriving in toxic waters off the B.C. coast.

The bacteria takes up carbon dioxide like a plant, consumes sulphide that is deadly to most other lifeforms, and exhales nitrous oxide which is a potent greenhouse gas.

The microbe may be small but it appears to be an important global player impacting the chemistry of both the atmosphere and the oceans, says lead researcher Steven Hallam, of the University of British Columbia, who likes to point out that it is microbes that "really rule the world."

But a human being is a nation of microbes. The genome is only a part of the picture. The real picture is a meta-genome. What rules the world? Life rules this world.

Wednesday, October 21, 2009

The Ares 1-X Rumbles to the Launchpad

Posted by Jonathan Golob on Wed, Oct 21, 2009 at 11:36 AM

Ares1x.jpg

The Ares 1-X rocket rumbled out to Launch Pad 39B in preps for an absolutely critical test launch next week. The Ares rocket is meant to replace the shuttle and provide a safer way to send people into orbit—cannibalizing components from both the shuttle program and the Saturn V rockets. This will be the tallest rocket launched since the Saturn V during the Apollo era.

Keep your eyes peeled on October 27th for the launch. It should be a good show, either way.

Thursday, October 15, 2009

The Strings of Life

Posted by Charles Mudede on Thu, Oct 15, 2009 at 4:51 PM

This passage about the epigenome, "the first manual to show how genes are orchestrated inside cells" (it appeared today in a science article in the Guardian)...

If the genetic code were a keyboard, the epigenome would be the pianist. Different chords become the various cell types, and all the notes have to be played perfectly to produce a healthy human being. Damage to the epigenome — the pattern of chemicals that controls our genes — has been linked to medical conditions as diverse as asthma, schizophrenia and cancer.
...this passage reminded me of Dr. Michio Kaku's description of String Theory:
So the particles we see in nature are musical notes; if the rubber bands vibrate one way, it’s called an electron; if it vibrates another way, it’s called a quark; if it vibrates another way, it’s called a neutrino. So we have a musical analogy. So, the melodies you could play on the string is the laws of chemistry; the harmonies of the string is what we call physics. The universe is a symphony of strings. And then the mind of God; the mind of God that so fascinated Einstein for the last 30 years of his life — the mind of God — we now have a candidate for it, believe it or not; it is cosmic music resonating through 11 dimensional hyperspace.


And also a passage from Gilles Delueze's short but brilliant essay "Spinoza and Us":

The important thing is to understand life, each living individuality, not as a form, or a development of each living individuality, but as a complex relation between differential velocities, between deceleration and acceleration of particles. A composition of speeds and slowness on a plane of immanence. In the same way, a musical form will depend on a complex relationship between speeds and slownesses of sound particles...

Biology, physics, and philosophy—it all comes down to music:

Come With Me If You Want to Live

Posted by Paul Constant on Thu, Oct 15, 2009 at 2:01 PM

The New York Times presents the most awesome theory ever about why the Large Hadron Collider hasn't worked properly:

Then it will be time to test one of the most bizarre and revolutionary theories in science. I’m not talking about extra dimensions of space-time, dark matter or even black holes that eat the Earth. No, I’m talking about the notion that the troubled collider is being sabotaged by its own future. A pair of otherwise distinguished physicists have suggested that the hypothesized Higgs boson, which physicists hope to produce with the collider, might be so abhorrent to nature that its creation would ripple backward through time and stop the collider before it could make one, like a time traveler who goes back in time to kill his grandfather.

If I knew science was this cool when I was a kid, I wouldn't be fucking around with books today.

(Via The Rumpus.)

One Superconducting Ring to Bind Them All

Posted by Jonathan Golob on Thu, Oct 15, 2009 at 8:51 AM

The United States power grid is currently (get it? get it!?) split into three distinct chunks: an Eastern interconnection, a Western interconnection (of which Seattle and Washington State are members) and Texas. Why is Texas separate from the rest? Why indeed.

EnergyGrids.jpg
  • Public Domain

Surplus power generated in one interconnection, at this time, cannot be transferred to another. Further, the parts of the continent most promising for wind, solar and geothermal power (i.e. the greenest power choices available right now) are far from where the bulk of power is consumed (the East and West coasts).

Enter the Tres Amigas project—a plant build a superconducting triangle of powerlines to connect these three grids. Using high temperature superconductors allows the power to be transmitted as direct current with similar efficiencies to alternating current. (Mashing together alternating currents from disparate grids is quite problematic, due to issues of phase. Using DC to connect the grids alleviates this problem. Superconductors alleviate some of the inefficiencies of transmitting DC over long distances.)

This is good news from the perspective of green energy. Connecting the East and West coasts to the areas most promising for wind and solar power will boost the economic viability of such projects in the near future. In the negative, this allows for all sorts of new games to be played by energy traders in the largely unregulated energy market.

Friday, October 9, 2009

The Scientific Method

Posted by Dan Savage on Fri, Oct 9, 2009 at 2:30 PM

The feminized/masculinized guy from that study doesn't do it for me—ovulating or not, I'm just not into him (why does his fro grow when he gets masculinized?)—and, hey, it's not sound science if an experiment can't be duplicated to test the reliability of the results. So here in the interest of science...

2boyspillstudy.jpg

I want to fuck...

I am..

The results of Slog polls are scientifically valid and legally binding.

Re: In About Twelve Hours, We Smash a Part of the Moon

Posted by Grant Brissey on Fri, Oct 9, 2009 at 1:34 PM

Well, I guess I'm glad that I was too lazy to stay up until 4:30 am or get out of bed at 4:30 am to watch the LCROSS impact on the moon:

NASA's much anticipated LCROSS mission sent two spacecraft "bombing" into the moon early this morning. The craft successfully struck their target, a crater thought to harbor frozen water.

But the much-hyped moon show that had been expected to accompany the impact, however, turned out to be a flop—no billowing plumes of dust and ice visible through backyard telescopes or on NASA TV. The low-impact impact had one NASA expert musing that LCROSS may have struck a "dry hole."
Four minutes later LCROSS (Lunar Crater Observation and Sensing Satellite) performed its own kamikaze dive—the final act in its mission to detect evidence of water ice in the moon's shadowed craters.

Whether or not sky-watchers could see the LCROSS crashes, NASA insists they happened.

The only video I can find on the thing is sort of long and boring, and contains exactly zero explosions, but here it is:

Anyone else got interesting photos, video, or whatevers on LCROSS, let us know in the comments.

UPDATE: Wise commenter Peter F says:

The plume was pretty much invisible, even through observatory telescopes (haven't seen the Hubble observation yet) but NASA thinks they got the spectroscopic data they wanted from the instrumentation, though it will take a while to process.

And commenter Pissy Mcslogbot posted this image of the impact:

melies.gif

Via National Geographic

Re: Are You a Lady? On the Pill? Engaged To Be Married?

Posted by Dan Savage on Fri, Oct 9, 2009 at 12:59 PM

boysboysboys.jpg

Earlier in the week I wrote up the results of a study that showed that women who were on the pill when they were dating may wind up partnered with mates they're not all that into once they go off the birth control pill. The pill suppresses ovulation and studies have shown that ovulating women prefer men who are more masculine and "more... genetically unrelated," like the butch guy on the right; women who aren't ovulating prefer guys who are more feminine and genetically more similar, like the pansy on the left. From my post:

Alvergne and Lummaa theorize that all those suppressed ovulations may have dire consequences where sexual compatibility and long-term marital success are concerned. It can't be pleasant, after all, to realize you're not as attracted to your spouse as you thought you were once you stop taking the pill. And couples who are genetically similar—the kind of pairings the pill promotes—are more likely to have infertility issues. Which is, um, also bad. And then there's this: since men have been shown to find ovulating women more attractive, "...the use of oral contraceptives may influence a woman’s ability to attract a mate by reducing attractiveness to men, thereby disrupting her ability to compete with normally cycling women for access to mate."

I wrote the authors of the study—Dr. Alexandra Alvergne and Dr. Virpi Lummaa of the University of Sheffield—asked what they thought its implications were. Should women switch to the IUD? Should an engaged woman go off the pill to make sure she's not marrying a too-genetically-similar swish? Should we, you know, panic? Dr. Alvergne wrote me right back... but her email wound up in my spam folder. (Sorry about that, Dr. Alvergne.) Her letter—and her answers—after the jump...

Continue reading »

The HIV Vaccine... Success

Posted by Jonathan Golob on Fri, Oct 9, 2009 at 12:28 PM

Sixteen thousand people volunteered for the study—primarily Thai sex workers and IV drug users from the general population of two Thai provinces. All received condoms, HIV prevention counseling, and an offer for HAART therapy if they became positive. Eight thousand received a placebo shot, the other half six doses of two distinct (and previously failed) HIV vaccines. About five years later, 74 of the placebo recipients were newly HIV positive. Twenty-three fewer, 51 total, among the vaccine recipients were now HIV positive. It was a statistically significant reduction in infection among the vaccinated.

After years of struggle, and some truly distressing failures, this is the one and only successful HIV vaccine trial.

It definitely was an odd approach. Take two failed vaccines, combine them together, and see if they'll work. The first vaccine stuffed into a tamed Canarypox virus some of the critical functional proteins of the HIV virus. (Canarypox is in the same broad family of viruses that includes Smallpox. Birds are the desired home of Canarypox; it's capable of getting into human cells, but not properly replicating itself once in. As such, it has the ideal vaccine combination of really pissing off the human immune system while being incapable of causing injury.) The second, booster, vaccine was simply some of the purified and isolated surface protein (gp120) from the HIV virus. (This booster vaccine is a bit like going around the human immune system with a mugshot of the HIV virus. The isolated protein is incapable of causing disease, but gives the whiff of what the real deal is like.) When the study was first proposed, parts of the scientific community were non-plussed. Isn't zero times zero still zero?

Nope, it's one third. What do you do with a vaccine that only works sometimes, or only for some? For a vaccine to be considered clinically useful (i.e, after the shots are done, you can feel confident in telling someone they are vaccinated and protected against the infection), you'd hope to have at least 70-80% of those vaccinated to be protected. (Herd immunity takes care of the rest of the risk, eventually.) Further, this vaccine combination (bizarrely) failed to produce neutralizing antibodies even in the successfully vaccinated.

For the next few months and years, the results of this study will be torn into, trying to answer some of these questions. In the meantime, this is an extremely heartening sign—indicating a real potential to salvage other failed vaccines into successful combination therapies.

Thursday, October 8, 2009

In About Twelve Hours, We Smash a Part of the Moon

Posted by Jonathan Golob on Thu, Oct 8, 2009 at 4:19 PM

Question: Is there water on the moon?

Experiment:

The main LCROSS mission objective is to confirm the presence or absence of water ice in a permanently shadowed crater near a lunar polar region.

LCROSS launched with the Lunar Reconnaissance Orbiter (LRO) aboard an Atlas V rocket from Cape Canaveral, Fla., on June 18, 2009 at 2:32 p.m. PDT. The LCROSS shepherding spacecraft and the Atlas V’s Centaur upper stage rocket executed a fly-by of the moon on June 23, 2009 (LCROSS lunar swingby video stream coverage) and entered into an elongated Earth orbit to position LCROSS for impact on a lunar pole. On final approach, the shepherding spacecraft and Centaur will separate. The Centaur will act as a heavy impactor to create a debris plume that will rise above the lunar surface. Projected impact at the lunar South Pole is currently: Oct 9, 2009 at 4:30 a.m. PDT. Following four minutes behind, the shepherding spacecraft will fly through the debris plume, collecting and relaying data back to Earth before impacting the lunar surface and creating a second debris plume.

The debris plumes are expected to be visible from Earth- and space-based telescopes 10-to-12 inches and larger.

A small group is gathering at Cal Anderson park to observe. Bring your telescope and join in!

Updated:
At 6:40pm PDT, the Centaur will separate from the rest of the ship. You'll be able to watch it live, via NASA!

The countdown has begun.

Wednesday, October 7, 2009

Are You a Lady? On the Pill? Engaged To Be Married?

Posted by Dan Savage on Wed, Oct 7, 2009 at 9:25 AM

boysboysboys.jpg

Then you might want to read the results of a new study published this morning in Trends in Ecology and Evolution: "Does the Contraceptive Pill Alter Mate Choice In Humans?"

Dr. Alexandra Alvergne and Dr. Virpi Lummaa of the University of Sheffield review "emerging evidence suggesting that contraceptive methods which alter a woman’s natural hormonal cycles" may be messing up straight peoples' sex lives and married lives. It may also raise "evolutionary questions and concerns," write Alvergne and Lummaa. It goes like this: the type of man a woman finds attractive varies pretty widely according to her menstrual cycle. Women who are ovulating prefer men who are more masculine and "more... genetically unrelated," like the guy on the right, above; women who aren't ovulating prefer guys who are more feminine and genetically more similar, like the guy on the left. Since the pill suppresses ovulation, and since many women are on the pill when they're dating and sleeping around—or "selecting a mate," as the docs put it—women may be marrying men they find attractive on the pill but not so much once they've gone off the pill.

Which women tend to do once they're married and want to have children.

Alvergne and Lummaa theorize that all those suppressed ovulations may have dire consequences where sexual compatibility and long-term marital success are concerned. It can't be pleasant, after all, to realize you're not as attracted to your spouse as you thought you were once you stop taking the pill. And couples who are genetically similar—the kind of pairings the pill promotes—are more likely to have infertility issues. Which is, um, also bad. And then there's this: since men have been shown to find ovulating women more attractive, "...the use of oral contraceptives may influence a woman’s ability to attract a mate by reducing attractiveness to men, thereby disrupting her ability to compete with normally cycling women for access to mate." While their study is sure to be cited by religious nuts waging war on the pill, Alvergne and Lummaa cite all the good the pill has done for women:

Any such effects should be weighed against the multiple benefits that the invention of the pill has brought. This revolutionary contraceptive method has given women unprecedented control over their fertility with the possibility to sample different partners before reproduction, to control their number of children, to reach optimal birth spacing given circumstances or to end reproductive career before menopause if desired, which has had a considerable impact on their social life. For instance, a sharp increase in college attendance and graduation rates for women was observed after the pill was legalized.

Giving women control over their fertility, allowing them to sample different partners, more women going to college—you can see why religious conservatives have problem with the pill. You can download a PDF of the study here. I've also sent a some questions to the study's authors—should women switch to the IUD? should an engaged woman go off the pill to make sure she's not marrying a too-genetically-similar swish? and what does all of this mean for gay marriage? and the ballot booth that is their [RSVP] envelopes?—and I'll share their answers with you when I hear back.

Tuesday, October 6, 2009

Today in Outer Space

Posted by Grant Brissey on Tue, Oct 6, 2009 at 3:09 PM

(Click to Enlarge)
  • (Click to Enlarge)

This image from NASA's Mars Reconnaissance Orbiter shows gullies near the edge of Hale crater on southern Mars.

Martian gullies carved into hill slopes and the walls of impact craters were discovered several years ago. On Earth, gullies usually form through the action of liquid water — long thought to be absent on the Martian surface. Whether liquid water carves gullies under today's cold and dry conditions on Mars is a major question that planetary scientists are trying to answer.

Gullies at this site are especially interesting because scientists recently discovered actively changing examples at similar locations. Images separated by several years showed changes in the appearance of some of these gullies. Today, planetary scientists are using the HiRISE camera on MRO to examine gullies such as the one in this image for change that might provide a clue about whether liquid water occurs on the surface of Mars. The view covers an area about 1 kilometer, or 0.6 mile, across and was taken on Aug. 3, 2009.

h/t: nasa.gov

Friday, October 2, 2009

NASA's Waste Limitation and Management of Resources Design Challenge

Posted by Grant Brissey on Fri, Oct 2, 2009 at 12:06 PM

Despite the recent discovery of water traces on the moon, supplying water for consumption on the moon is still an issue:

Lori M. Feaga, a research scientist at the University of Maryland who is a member of the team that analyzed the Deep Impact data, said this process would work only to about one millimeter into the lunar surface. If correct, that would not give future astronauts much to drink.

“You would have to scrape the area of a baseball field or a football field to get one quart of water,” she said.

Thankfully, NASA has created the Waste Limitation and Management of Resources Design Challenge, recruiting kids from grades 5 through 8 to design and test a water recycling system for the moon. Presumably, some of this eventual waste water would involve urine, which is an abundant resource that has also been proven as a potential source of fuel.

(Click to Enlarge)
  • (Click to Enlarge)

No doubt fortunately for classroom hygiene, American nippers won't be required to self-source the "waste stream" as future Moon residents will. According to NASA, they will instead produce a synthetic urine/waste-water mixture. The formula will apparently call for "tap water, household ammonia cleaner, white distilled vinegar, baby shampoo, table salt and baking soda".

h/t: nytimes.com, the Register, and commenter Peter F

Thursday, October 1, 2009

Today in Kazakhstan/Outer Space

Posted by Grant Brissey on Thu, Oct 1, 2009 at 3:41 PM

I'm not sure I'd want to get into a rocket ship built in Kazakhstan, but apparently Jeffrey Williams and Maxim Suraev did yesterday when they launched off from the Plesetsk Cosmodrome in this Soyuz TMA-16.

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(click to enlarge)

The Facts

Posted by Charles Mudede on Thu, Oct 1, 2009 at 10:46 AM

Remember this post? And remember the last sentence in that post?

I would rather be shot down by a robber than be in a situation where I'm exchanging gunfire with a robber.
Well it looks like my extreme pacifism is not only morally excellent but also has logic on its side.
ScienceDaily (Sep. 30, 2009) — In a first-of its-kind study, epidemiologists at the University of Pennsylvania School of Medicine found that, on average, guns did not protect those who possessed them from being shot in an assault. The study estimated that people with a gun were 4.5 times more likely to be shot in an assault than those not possessing a gun.
Over four fucking times!
What Penn researchers found was alarming — almost five Philadelphians were shot every day over the course of the study and about 1 of these 5 people died. The research team concluded that, although successful defensive gun uses are possible and do occur each year, the chances of success are low.

Owning a gun is owning a stupidity.

Wednesday, September 30, 2009

Bad Brains

Posted by Charles Mudede on Wed, Sep 30, 2009 at 2:07 PM

Episode 61 of the Brain Science Podcast features the Chief Science Officer (Allen Jones) of the Allen Institute for Brain Research.

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The institute, which is based in Seattle, began by mapping where "the approximately 20,000 genes in the mouse genome are turned on in the adult mouse brain." The rich information from this inaugural project, which was completed in 2006, is now offered to the public for free. Jones explains the importance of the map:
The brain is really all about those functional divisions, and it’s very important to understand how those functional divisions relate to the underlying biochemistry of those places. The underlying biochemistry of those places is driven by the genes that are turned on in them.
The institute is currently doing for the human brain what it did for the mouse brain. But, of course, to map the human brain, you need human tissue; and to get human tissue, you need dead humans. No guessing is required to know why my favorite section of the generally excellent interview concerns this aspect of the institute's research—obtaining the brains of dead humans:
I would say that every aspect poses its own unique challenge in scaling to the human brain. Right out of the gate it’s just getting human brain tissue. Obviously human brain tissue is coming to us postmortem, and the postmortem tissue—especially from what we’re gunning for, which is normal human brain tissue from people that are between the ages of 20 and 60—those are typically coming from accidental death of some sort. So, there’s a lot of logistics that have to happen to make sure that you can get high-quality human The longer that a brain is sitting there after death and before we’re actually able to obtain the tissue and freeze it down, you have issues where the tissue is starting to degrade, and the RNAs that we would like to measure—which are telling us at what level a gene is turned on—are starting to degrade. So, there are important things that relate to that.

And what is a normal brain? Meaning, what is not a bad brain?

[One that has] no history of psychiatric disease. You certainly don’t want [one with] a history of drug abuse or a history of alcoholism. So, there are a number of things that we’re screening for up front that we want to avoid.
A good dead brain must be very hard to come by.

Monday, September 28, 2009

The Uncertainty of the All

Posted by Charles Mudede on Mon, Sep 28, 2009 at 10:13 AM

At the end of a review of a Skidelsky's new book on the British economist Keyens, the reviewer, the American economist Krugman, gets to his point, a point which has in it something that almost reaches (and possibly enters) the magic circle a truth:

Most strikingly, Skidelsky declares that the traditional division between microeconomics and macroeconomics, which is based on whether one focuses on individual markets or on the overall economy, is all wrong; macroeconomics should be defined as the field that studies those areas of economic life in which irreducible uncertainty, uncertainty that cannot be tamed with statistics, dominates. He goes so far as to call for a complete division of postgraduate studies: departments of macroeconomics should not even teach microeconomics, or vice versa, because macroeconomists must be protected "from the encroachment of the methods and habits of mind of microeconomics".

How far should we be willing to follow Skidelsky in this? I think we must trust the biographer in his assessment of Keynes himself; Skidelsky argues persuasively that Keynes spent much of his life deeply focused upon, even obsessed with, the question of how one acts in the face of uncertainty...

The unknown persists. No amount of information, computing, calculating can eradicate it from the future. But how is it we are able to live happily in the face of the unknown?


Even Krugman points this out:

...[Some behavioural] economists... drop the assumption of perfect rationality but don't seem much concerned by the essential unknowability of the future, [and] have done relatively well at making sense of this crisis...


One answer to this can be found in Brain Science, a podcast hosted by Ginger Campbell. Near the opening of podcast 48, the guest, a neuroscientist named Gary Lynch, explains what "point-to-point mapping and the random access circuits are":

Gary Lynch: ...So there's a map of the entire body up there. There's an area of the cortex that represents the hand and then an area that represents the wrist and then the forearm - all those areas are actually sitting adjacent to each other pretty much in the same form that they actually are in the body. This means that the fingers are projecting, in order, to an area of the cortex, and right next to that area is an area that the wrist is projecting to. OK, so that's point to point.

GC: Right.

GL: It's called topographic. It's like you have a map - you have a grid map here and you just
superimpose that grid map on the wall. It's just one point to one point.

The random access networks, which are certainly real - so for example, if you go into the olfactory
cortex you find none of that point to point stuff. In fact the olfactory system - some of the things that
launched all this - the olfactory system in fact throws it away rather aggressively. It is point to point design starting from the nose to the first stage of the olfactory system but beyond that it throws it away - it takes all the organization and it's as though it throws it all up in the air and makes it random Everything goes to wherever it wants to go, and nothing is point to point. And what we're arguing is, that basic olfactory design actually set a template for the evolution of the association regions of the cortex. OK.. so now why - what do you get with the point to point? Well, it's pretty straightforward. If this area of your cortex lights up suddenly you know that in a spatial map something happened in this region.

you have - your retina is a map of the external world there's something in the visual cortex on grid square x 1 y 3 lights up. The brain knows that there's something happening at 11 o'clock. There's
spatial information tells you where things are and it tells you a lot more than that. But what do you get with a random design? And what you get there is the ability to associate anything with anything else. See what I mean?

GC: Yeah.

GL: ...That ability to associate anything with anything else, that is in our argument a key ingredient of what we experience as cognition. Consciousness.

We are biologically wired to experience or encounter the unknown. A level of the brain's map of the body ("the mind is the idea of body") is open to the new. This is so because it can connect "anything with anything else." The unknown (anything) can become known (something), that is why we can live with a future that is partly unknown. What we might fear, then, is not the unknown as such, but the encounter with it. We fear the moment of translation or transition. I will deal with this fear in another post.

Friday, September 25, 2009

Recently in Outer Space

Posted by Grant Brissey on Fri, Sep 25, 2009 at 10:23 AM

This image taken by NASA's Moon Mineralogy Mapper, an insturment on the Indian Space Research Organization's Chandrayaan-1 mission, shows the signature of water (blue) concentrated at the poles. The orange and green represent different minerals.

ISRO/NASA/JPL-Caltech/Brown Univ./USGS
  • ISRO/NASA/JPL-Caltech/Brown Univ./USGS

(click to enlarge)

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