Obsidian Wings

The Big Bang Theory

Guest post by Gary Farber.  Gary's home blog is Amygdala, and he invites you to read him there. 

For my final guest post at Obsidian Wings, something completely different: a roundup of some recent science, or tech, or just downright weird, sci-tech news, or that's at least news to me, as well as an item or two of the fantastic.

Green your factories with electron beam particle accelerators:

[...] While environmental applications of particle accelerators have made little progress commercially in the United States in the last 40 years, a number of countries in Asia, Europe, and the Middle East are actively pursuing the technology.

In Daegu, Korea, an electron-beam accelerator in a textile factory removes toxic dyes from 10,000 cubic meters of wastewater per day. In Szczecin, Poland, the Pomorzany power station installed an electron-beam accelerator in its coal plant to simultaneously remove sulfur dioxides and nitrogen oxides from roughly 270,000 cubic meters of flue gas per hour. China has started to use electron beams to control air pollution, and a facility in Bulgaria is under construction. Saudi Arabia may soon follow.

All you have to do for more widespread use is ensmall them. 

[...] "We have proven that the technology works," says Andrzej Chmielewski, director of the Institute of Nuclear Chemistry and Technology in Warsaw, Poland. "The size of the accelerators can be huge, though. We need a technological breakthrough" to make accelerators smaller and easier to maintain.

But they're working on that!  With plasma wakefield acceleration and laser wakefield acceleration! 

Oh, and who do you have to thank for that?

[...] Thanks in great part to the American Recovery and Reinvestment Act, commonly known as the stimulus package,

Live from the UN Summit on Climate Change

By Lindsay Beyerstein

I'm posting from the UN Summit on Climate Change at UN HQ in New York. I'm wearing one of those special plastic translation earpieces.

World leaders are here to talk face-to-face before the big climate negotiations to be held in Copenhagen in December. President Obama is scheduled to address this morning's opening session.

The meeting is supposed to be an opportunity for all nations, from the richest emitters to the most vulnerable developing nations, to meet on neutral turf to discuss solutions to the climate crisis.

The one-day summit consists of public opening and closing sessions, separated by closed roundtable discussions among nearly 100 heads of state in attendance.

I'll be tweeting the proceedings. Follow me @beyerstein.

Swine Flu: What We Should Do for One Another

What follows is a guest post by Ruth A. Karron and Ruth R. Faden. Ruth A. Karron is the director of the Center for Immunization Research and Johns Hopkins Vaccine Initiative at the Johns Hopkins Bloomberg School of Public Health.  Ruth R. Faden is the executive director of the Johns Hopkins Berman Institute of Bioethics.

***

At this point, it is impossible to predict whether we are on the brink of an influenza pandemic.  The threat is real, however, and governments across the globe are working hard to mitigate the potential impact of swine flu.  

This is right and proper.  Our government has an obligation to protect the public’s health, which it exercised responsibly by declaring a national public health emergency on Sunday.  This declaration is the public face of countless actions that federal, state, and local health authorities are now undertaking on our behalf.  But these are not the only actions that will be needed. There are also actions that we as citizens must undertake to minimize the swine flu threat that will help us protect ourselves and our families.  These actions are not only prudent; they are a matter of moral and civic responsibility.  Just as our government has an obligation to protect the public’s health, we too have an obligation to our country and to our fellow human beings to do our share to minimize the burdens of this influenza outbreak. 

What can each of us do?

Stay informed: New information about swine flu will be generated rapidly in the near term, and possibly longer. DHS Secretary Napolitano has committed to providing daily briefings for the foreseeable future. It is important that we commit to accessing that information, as well as information that may pertain to our local settings, so that we understand what is happening and can take action as needed.

Abide by public health recommendations: As public health officials learn more about the extent and spread of swine flu, new recommendations may be made to limit public gatherings, close schools or workplaces, or restrict or modify travel. These “social distancing” measures should reduce the public health burden of influenza by slowing down the pace by which flu will spread, but they will only work if each of us does our part. 

Follow basic hygiene practices: Good hand hygiene is always important, but particularly so in this context. Wash your hands frequently with soap and water or with an alcohol-based cleanser. Use a tissue to cover your nose or mouth if you cough or sneeze, and dispose of the tissue properly or, if you don’t have a tissue, sneeze into your upper sleeve. Avoid touching your nose or mouth frequently.

Be vigilant and responsible if you or a loved one becomes ill: Contact a healthcare provider if you or a member of your household develops a fever and follow his or her instructions. Keep the person who is ill out of work or school. Unless someone is seriously ill, avoid using emergency rooms to evaluate possible flu symptoms. Even as we monitor this latest threat to public health, people will continue to have medical emergencies like heart attacks and car accidents, and it is important that emergency rooms be able to take care of those who need immediate medical attention. 

Prepare for the possibility of staying in your home: One possible social distancing measure that public health authorities could ask us to undertake is to stay at home for a period of time. A basic principle of emergency preparedness is that each of us should have sufficient food and water in our homes to last our families in such an eventuality. Now is the time to make sure that your family is well provisioned, not only to protect yourselves but also out of recognition that some families do not have the money or stable housing required to stockpile food. If those of us who have the means take care of our own needs, it will be easier for the government and community organizations to take care of those who do not.

Check on your neighbors: If you haven’t done so already, now is a good time to get to know your neighbors. Find out if any of them may need a little extra help dealing with this public health threat. People who live alone, for example, may appreciate your checking in with them from time to time, and elderly neighbors may need your help stocking up on food. Parents of school age children may want to talk through how they can help each other if schools in your area close but some workplaces stay open. 

In his inaugural address, President Obama declared: "What is required of us now is a new era of responsibility -- a recognition, on the part of every American, that we have duties to ourselves, our nation and the world." Our individual and collective response to this swine flu outbreak will be one important measure of whether we as Americans and as citizens of the global community are living up to what the President has asked of us.

Swine Flu

by hilzoy

From the Washington Post:

"The World Health Organization rushed to convene an emergency meeting Saturday to develop a response to the "pandemic potential" of a new swine flu virus that has sparked a deadly outbreak in Mexico and spread to disparate parts of the United States.

Health officials reported that at least eight students at a private high school in New York City had "probable" swine flu. They also confirmed three new cases -- two in Kansas and one in California -- bringing the total number of confirmed U.S. cases to 11. The president of Mexico, where the outbreak has killed as many as 81 people, issued an order granting his government broad powers to isolate patients and question travelers. (...)

The virus, for which there is no vaccine for humans, has nearly brought Mexico City to a halt. Normally congested downtown streets in this city of 20 million were almost empty Saturday, and of the few people who ventured outside, many said they did so only out of necessity. Soldiers posted at subway stations handed out face masks to passersby from the back of armored vehicles. Some pedestrians covered their mouths and noses with scarves and rags.

"We can't escape the air," said Antonio Gonzáles, 56, who wore a surgical mask outside a public hospital. "If it was something in the food, we'd have a chance."

The Mexican government reported more than 1,300 suspected cases of the virus, which mixes animal and human strains of flu. Bars and nightclubs, schools, gallery openings and sporting events were cancelled until further notice. Authorities advised people to wash their hands regularly and avoid the customary greeting of kissing on the cheek. The government issued a decree giving the Health Ministry power to enter people's homes, close public events, isolate patients, and inspect travelers and their baggage.

The Associated Press reported that 24 new cases of the flu emerged Saturday in Mexico."

Thus far, the Mexican version seems to be much more virulent than the US version, despite the fact that "partial comparisons of the genetic sequences of the Mexican and American cases shows them to be essentially the same". There could be any number of explanations for this: "some difference in the information (looking at severely ill versus routine surveillance of outpatients), some difference in the virus (while the viruses are said to be "genetically identical" this is true only in the parts that have so far been compared) or some co-factor (e.g., co-infection with another pathogen)."

However, it seems likely that there has been human-to-human transmission, which is worrisome. Moreover, the casualties in Mexico seem to have been disproportionately healthy young adults. On NPR today, Laurie Garrett gave two possible explanations for this: it might be that children and the elderly got the regular flu vaccine, and that it confers some protection to this new strain of influenza, which would be good; or it might be the dreaded cytokine storm: basically, a lethal overreaction by the immune system. This is thought to be the reason why young adults were disproportionately represented among the casualties of the pandemic of 1918: since they have stronger immune systems, the overreaction was more likely to be fatal.

If we're lucky, this will continue to be relatively mild in this country, and the steps Mexico is taking will do the trick. Just in case, though, now might be a good time to download this flu manual (pdf; h/t DemFromCT at dKos.) Unnecessary preparation beats being caught unprepared by a flu pandemic.

Good blogs on this topic: Effect Measure, H5N1, Aetiology, DemFromCT at dKos, ScienceInsider.

Animal Stories

by hilzoy

Recently, we've learned that chimpanzees stockpile weapons in anticipation of future attacks. We've discovered that they not only use tools, but modify them to make them better. But macaques teaching their infants to floss?

"Female monkeys in Thailand have been observed showing their young how to floss their teeth --using human hair.

Researchers from Japan said they watched seven long-tailed macaques cleaning the spaces between their teeth in the same manner as humans.

They spent double the amount of time flossing when they were being watched by their infants, the team said.

This suggests the mothers were deliberately teaching their young how to floss, Professor Nobuo Masataka of Kyoto University's Primate Research Institute said."

You should definitely click the link and watch the video -- at least, if the idea of watching a long-tailed macaque floss interests you in the slightest. 

***

While I'm on the subject: here's a wonderful anecdote about Alex the African Gray Parrot. Irene Pepperberg, the researcher who worked with Alex, had been training him to sound out phonemes, in the hopes that eventually she might be able to teach him to spell:

"Alex had already made progress on this task. If shown a tray of plastic letters, the kind parents affix to a refrigerator door to stimulate their kids' alphabet learning, he responded correctly to questions. Shown an array of letters that included, say, a red "Ch," a green "N," and a blue "S," and so on, when asked, "What sound is blue?," Alex answered "Ssss…."

That day, some of MIT’s corporate sponsors had flocked to watch Alex do a demo. Alex answered a phoneme question correctly, but then piped up with "Want a nut." Like students everywhere, Alex liked a good snack now and again, and to push his luck with his teachers.

Wanting to keep him on task, Irene pressed Alex with another question, and got the correct answer and immediately, another "Want a nut." A third Q&A round followed, but this time Alex underscored the seriousness of his craving with the avian equivalent of italics: "Want a nut."

At this point, Pepperberg writes, Alex "became very slitty-eyed, always a sign he was up to something." He looked at her and slowly said, "Want a nut. Nnn…uh….tuh.""

Teaching Alex that the phonemes went together to form words was supposed to be the next step, the one they hadn't gotten to yet. But no one told Alex that.

Stem Cell Orders for Dummies (Like Me)

by publius

In reading up on Obama’s stem cell decision, I got confused about what exactly it does.  This line, in particular, confused me (from the WSJ):

The new policy won't affect federal laws that prevent the use of federal money to destroy human embryos. So while it will substantially broaden research opportunities on established cell lines, it won't allow the creation of new ones.

Huh?  Wasn’t that Bush’s policy too?  This may be common knowledge to everyone but me.  But just in case anyone else was confused, here’s a basic rundown of legal landscape (most details come from this CRS report, via the most awesome OpenCRS):

In 1996, Congress passed the Dickey Amendment, which prohibits federal funds from being used to destroy embryos (which is of course what happens when you remove stem cells).  In 1999, Clinton’s HHS got around this ban by interpreting “embryo” as excluding already-created embryonic stem cells. 

The upshot was that while federal funds could be used for embryonic stem cell research, they couldn’t be used to obtain those cells in the first place.  My guess, though, is that most labs could do some fancy accounting (e.g., making sure extraction is covered by “non-federal” funds), and conduct as much research as they wanted.

Congressional Republicans, however, weren’t exactly thrilled with the HHS interpretation.  And so when the Decider retreated to a Zen-like meditative state to contemplate these weighty issues, he came up with a “compromise.”  Bush allowed funding for a few cell lines that had already been created.  But he banned funding for any stem cell lines created after August 2001.  He claimed there were about 60 lines at the time, but 58 of those turned out to be bread mold I think.

Anyway, that’s what Obama’s order presumably will do – the federal government will be able to fund research on any already-created stem cell lines, regardless of when they were created.  Maybe science wonks can jump in – but that’s probably all that research labs need.  The Dickey Amendment doesn’t seem like a big obstacle to me.

That said, it’s still probably worth getting rid of the Dickey Amendment at some point (or at least rewording it), even if it doesn’t pose a research obstacle.  The problem with leaving the definition in the hands of the executive branch is that Republicans will control the White House again one day.  If Governor Palin wins in 2012 (with an assist from Citigroup), the ban is back on. 

So the Democrats should eventually – maybe not in the middle of the current economic battle – get around to amending that statute while they have such strong majorities.  Once enacted, Republicans would have to break a filibuster to change the definition, and life-saving research would be more safe.

One More Reason Why I'm Glad I'm Not An Ant

by hilzoy

From the New York Review:

"Some ant species do not have queen ants in the strict sense. Instead, worker ants (which are all female) that have mated with a male ant become the dominant reproductive individuals. These are the gamergates, or "married workers," and their sex life can be brutal. In one species the gamergates venture outside of the nest to attract a male, engage him in copulation, then carry him into the nest before snipping off his genitals and throwing away the rest of his body. The severed genitals continue to inseminate the gamergate for up to an hour, after which they too are discarded."

I really wonder whether the argument from design would have survived a close acquaintance with the habits of insects around the world. This arrangement, at least, does not make the idea of a benevolent deity leap to mind.

Great News

by hilzoy

Wonderful news from the New England Journal of Medicine (1, 2), summarized by FP Passport:

Results of the latest malaria vaccine trials will be published today in The New England Journal of Medicine, and from the looks of it, the news is good--fantastic, in fact. "We are closer than every before to having a malaria vaccine for use by children in Africa, says Christian Lucq, director of the PATH Malaria Vaccine Initiative.

First, some background: The new trials use a vaccine candidate known as RTSS, the most clinically advanced malaria vaccine in development. The two tests took place in Kenya and Tanzania, and included 340 and 894 children, respectively. After vaccination, children were visited in their homes to follow up on their health and most importantly, their contraction (or not) of malaria.

Here are some highlights from the results:

* Unlike previous trials, these studies administered the malaria vaccine in conjunction with the normal WHO schedule of vaccines like polio, MMR, and others. There was no interference on either side. That matters because if a malaria vaccine is every to be administered, it is likely to be administered in tandem with others.

* In infants of 8, 12, and 16 weeks, the vaccine reduced malaria infections by 65%.

* In children aged five to 17 months, the incidence of clinical malaria was reduced by 53%.

The results today set the stage for more Phase 3 trials--the last needed before lisencing of the vaccine. Future trials will continue to test safety, efficacy, and the possibility of a "booster" shot lengthening the already lengthy 18-month protection observed. 16,000 children will be involved in 11 sites found in 7 countries."

According to the CDC, malaria is the fourth leading cause of death among children under five. It kills at least a million people a year, and sickens hundreds of times that number. Besides the horrific burden of disease, death, and misery that malaria places on large chunks of the world, it also puts a serious economic burden on those countries where it's endemic -- which are, as it happens, often the countries that can least afford it.

So a malaria vaccine that's 50-65% effective would be a wonderful, wonderful thing.

"Just Lowering My Risk Of Prostate Cancer, Heh Heh Heh..."

by hilzoy

The BBC brings good news for guys:

"Men could reduce their risk of developing prostate cancer through regular masturbation, researchers suggest.

They say cancer-causing chemicals could build up in the prostate if men do not ejaculate regularly.

And they say sexual intercourse may not have the same protective effect because of the possibility of contracting a sexually transmitted infection, which could increase men's cancer risk. (...)

The protective effect was greatest while the men were in their 20s.

Men who ejaculated more than five times a week were a third less likely to develop prostate cancer later in life."

Consider this an open thread.

Alex: RIP

by hilzoy

From the NYT:

"He knew his colors and shapes, he learned more than 100 English words, and with his own brand of one-liners he established himself in TV shows, scientific reports, and news articles as perhaps the world’s most famous talking bird.

But last week Alex, an African Grey parrot, died, apparently of natural causes, said Dr. Irene Pepperberg, a comparative psychologist at Brandeis University and Harvard who studied and worked with the parrot for most of its life and published reports of his progress in scientific journals. The parrot was 31. (...)

When, in 1977, Dr. Pepperberg, then a doctoral student in chemistry at Harvard, bought Alex from a pet store, scientists had little expectation that any bird could learn to communicate with humans. Most of the research had been done in pigeons, and was not promising.

But by using novel methods of teaching, Dr. Pepperberg prompted Alex to learn about 150 words, which he could put into categories, and to count small numbers, as well as colors and shapes. “The work revolutionized the way we think of bird brains,” said Diana Reiss, a psychologist at Hunter College who works with dolphins and elephants. “That used to be a pejorative, but now we look at those brains — at least Alex’s — with some awe.” (...)

Alex showed surprising facility. For example, when shown a blue paper triangle, he could tell an experimenter what color the paper was, what shape it was, and — after touching it — what it was made of. He demonstrated off some of his skills on nature shows, including programs on the BBC and PBS. He famously shared scenes with the actor Alan Alda on the PBS series, “Look Who’s Talking.” (...)

Even up through last week, Alex was working with Dr. Pepperberg on compound words and hard-to-pronounce words. As she put him into his cage for the night last Thursday, Dr. Pepperberg said, Alex looked at her and said: “You be good, see you tomorrow. I love you.”"

I'm not sure the astonishing nature of Alex's language-learning comes through here. He could answer questions like 'What color?', 'What shape?' and 'What number?' Given a tray with blocks and balls of several different colors, he can say how many blocks of a given color there are -- separating them out from the blocks of a different color, and the balls of the same color. He can use and understand the word 'none'.

My favorite story about Alex comes from The Alex Studies, p. 147. Alex had been asked to identify the color and material of various objects, and apparently he got bored. (Who can blame him?) Here's what happened:

"In each of two additional trials (one on color, one on material), however, he did not respond correctly on the second try. He produced instead each of the wrong possible answers from the appropriate category, repeated each wrong answer, then grabbed the tray liner and tossed all the objects to the floor."

Rest in peace, Alex.