Tuesday, March 27, 2007

I've been so out of the loop!

` I would have had this up yesterday, but my computer is behaving so badly and erasing everything I've done in Blogger (or Word, for that matter) that I think I need to take it back into the shop.

` I regret not being there 'in time' to catch the latest Nature articles (or at least News Flashes, for the most part.) So many I've lost, and most of them look fascinating! Check it out:

Wipe out a single memory-Drug can clear away one fearful memory while leaving another intact.-11 March 2007
Earth's magnetic field reversals mimicked in the lab-The switching of the poles can be studied in a tub of molten metal.-9 March 2007
Quantum cryptography goes wireless-Single entangled photons travel 144 km through the air.-8 March 2007
Rose-scented sleep improves memory-Bursts of scent during the night can help solidify learning.-8 March 2007
Robo-salamander goes swimming-Bot throws light on the evolution of walking.-8 March 2007
Pollution decreases rainfall-Mountains in haze get less rain.-8 March 2007
Dozens of new cancer genes found-Genome sweep shows cancer-driving mutations more common than thought.-7 March 2007
Did a 'light' genome help birds take flight?-A smaller genome evolved in dinosaurs, long before birds learned to fly.-7 March 2007
Not a sea, but a seep, on Mars-Salt deposits could have come from groundwater, not standing water.-7 March 2007
Breath test for diabetes-Non-invasive test can pick up the whiff of disease.-6 March 2007
Turning sweat into light-Could 'gym generators' power the way to green electricity?-2 March 2007
Antarctic 'sandbags' may protect ice-Glacial deposits could help to protect against sea-level rise.-1 March 2007
None more black-Engineers make the most anti-reflective coating yet.-1 March 2007
Graphene steps up to silicon's challenge-Tiny transistor uses a single electron to turn off and on at room temperature.-28 February 2007
Electric switch could turn on limb regeneration-Tadpoles use a proton pump to direct tissue regrowth.-28 February 2007
The more, the wikier-The secret to the quality of Wikipedia entries is lots of edits by lots of people-27 February 2007
Ancient DNA solves milk mystery-Analysis of fossilized bones suggests milk-drinking mutations emerged after dairy herding.-26 February 2007

` There's also a bunch I would have missed anyway simply because I didn't pay the money:

Psychological attacks rank high on torture list-Watching a sham execution comes near the top of distressing assaults.-5 March 2007
The United States set its clocks back an hour last Sunday - three weeks earlier than usual, in an attempt to save on energy bills. Read our special report from January 2007 to see if the scheme will work.
Chinese ban on Internet cafes ducks the issue-If addiction's the problem, says Phil Ball, prohibition's not the answer.-9 March 2007
Scriptural violence can foster aggression-Elements of religious texts seem to inspire bad behaviour.-7 March 2007
Laser physics: Extreme light-Physicists are planning lasers powerful enough to rip apart the fabric of space and time. Ed Gerstner is impressed.-28 February 2007
Nature's X-files-Not all the correspondence to a top science journal contains top science. Some of it is very odd indeed.
The lab that asked the wrong questions-Closure of parapsychology lab throws spotlight on scientific taboos.-28 February 2007
Chimps make spears to catch dinner-Wooden weapons are a first in animal kingdom.
22 February 2007
Who were the first Americans?-Dating study suggests it wasn't the makers of the Clovis culture.-22 February 2007
Scrub-jays look ahead-Far-sighted birds plan breakfast the evening before.-21 February 2007
Monkeys hug it out to avoid fights-Embraces calm tension between rival gangs.-21 February 2007
Quantum computing at 16 qubits-Programmable computer solves sudoku and sets seating charts.-15 February 2007
Scientific treasure found in junk pit-Archaeological dig reveals high-tech medieval instrument.-14 February 2007
Squid vid shows swimming surprise-Pictures from the depths reveal luminous and speedy animal.-14 February 2007
Bird-eating bats pinned down-Bat blood shows that they can attack migrating birds.-14 February 2007
Oldest chimp tools found in West Africa-Apes could have passed down skills for thousands of years.-12 February 2007
Carbon goes deep-Studies show CO2 has reached the bottom of the ocean.-12 February 2007

` However, there are many more articles I have been able to access in the past week, and I promise you, they're just as interesting. But, if you're not into that, you can just stop right here and... and... go... watch Ryan vs. Dorkman 2!
` I just saw this video and was very impressed at how professional the martial arts and special effects were! Excellent work, guys!

` Now, as for more current editions, ones that I can access, I'll go over a few of them - I seriously have NO TIME AT ALL to write about them, so I'll have to reproduce chunks for you here: Not seeing is believing Hmm, this looks promising....
'Bond's invisible Aston Martin and Potter's invisibility cloak aside, what have metamaterials done for us? Not much in the real world yet, but from relatively mundane beginnings in all-optical communications technologies, that could all change. Just wait and see, or not.'
` Grrr, I should hope so!
` 'Unexpected tricks of the light-The buzz over invisibility cloaks is fun — while it lasts. But metamaterials are likely to transform optics through more mundane applications. Katharine Sanderson reports.'
` Ohhhh... I hope you don't think I'm a bastard for saying 'boring'....

Published online: 26 March 2007
'Semi-identical' twins discovered-Hermaphrodite reveals previously unknown type of twinning.-John Whitfield

` Now this is just insane!

Researchers have discovered a pair of twins who are identical through their mother's side, but share only half their genes on their father's side.

The 'semi-identical' twins are the result of two sperm cells fusing with a single egg — a previously unreported way for twins to come about, say the team that made the finding. The twins are chimaeras, meaning that their cells are not genetically uniform. Each sperm has contributed genes to each child.

"Their similarity is somewhere between identical and fraternal twins," says geneticist Vivienne Souter, of the Banner Good Samaritan Medical Center in Phoenix, Arizona. "It makes me wonder whether the current classification of twins is an oversimplification."...

Souter and her colleagues investigated the twins' genetic makeup because one was born with ambiguous genitalia. This twin turned out to be a 'true hermaphrodite', with both ovarian and testicular tissue. The other twin is anatomically male.

Genetic tests revealed that each twin contained some 'female' cells with two X chromosomes, and some 'male' cells with an X and a Y. The proportion of each type varies from tissue to tissue in each twin, the researchers report in Human Genetics....

...Occasionally, two sperm are known to fertilize a single egg; this 'double fertilization' is thought to happen in about 1% of human conceptions. An embryo created this way doesn't usually survive, but a few cases are known to have made it — these children are chimaeras of cells with X and Y chromosomes.

...It had been previously predicted that this might happen. Biologist Michael Golubovsky, for example, now at the University of California, Berkeley, suggested in 2003 that twins intermediate between identical and fraternal might result from double fertilizations2. The new discovery confirms his theory.

` Fancy that! Who would have ever thought it could work like that? (Besides Golubovsky....)

Published online: 22 March 2007-Mice made to see a rainbow of colours-All you need to see more is more pigments in the eye.-Lucy Odling Smee

` I already get the idea that some crazy scientist has tweaked a mouse's genes for opsin to allow it to have trichromatic color vision....

Simply by inserting a piece of DNA that codes for a human eye pigment into the genome of a mouse, scientists have introduced a rainbow array of colour to the dull mix of yellows, blues and greys that normally make up a mouse's visual world....

Gerald Jacobs from the University of California in Santa Barbara and his colleagues have genetically engineered mice with a human pigment in their eye as well as the normal mouse pigments and shown that this does appear to give the mice the ability to see colours they could not see before....

In looking at the evolution of full colour, or trichromatic, vision in humans, most scientists turn to New World monkeys, which have an arrangement mid-way between the two- and three-photopigment systems. They have only one photopigment gene on their X chromosome, but there are different versions of the gene, producing different pigments. As a result, female monkeys (which carry two X chromosomes, and so can potentially have two different pigment genes) can end up with three different photopigments in their eyes.

The team made female mice in which one X chromosome carries a normal mouse photopigment gene, while the other X chromosome has a human pigment gene. Like female New World monkeys, these mice were able to produce three types of photopigment, the team reports in Science1.

...They presented the mice with three circular panels each of which was lit up by light with a wavelength within the 500-600 nm range - that's the bit of the visual spectrum that looks green, yellow or red to us. In each trial, one panel was lit up differently from the other two; pressing on the odd-one-out would result in the mouse getting a soy milk reward.

Most of the transgenic mice could clearly see a difference when the lights were more than 10 nm different: three out of five of them pushed the correct panel with their nose or paw 80% of the time during 10,000 trials. As for the two transgenic mice who didn't do so well, the researchers speculate that they didn't have a good mix of the different photopigments in their eyes.

That means that the mouse brain is perfectly capable of deciphering a stream of new information from the eye. "This is a beautiful demonstration that fairly sophisticated processing can arise from a single change at the front end of the visual system," says Williams.

The result also hints that perhaps the right kind of photopigment is all that's needed for humans to get owl-like night vision, or to see ultraviolet colours.

` Mua ha ha ha ha haaaaa!

Degrees in homeopathy slated as unscientific-Alternative therapies are now a degree subject at some British universities. But do they deserve these credentials? Jim Giles reports.-21 March 2007

` Indeed!

As debate rages in the United States over whether intelligent design should be taught in science classes, another topic that many researchers see as a pseudoscience is claiming scientific status within the British education system.

...Many scientists and advocates of evidence-based medicine feel that giving homeopathy scientific status is unjustified. Aside from the fact that there is no known mechanism by which this treatment could work, they argue that the evidence against it is conclusive.
` Of the many rigorous systematic reviews conducted in the past decade, only a handful have produced evidence, marginal at best, in favour of homeopathy, with the authors in each case stating that the data were weak. Several reviewers found no effect, and a prominent study suggesting that homeopathy does work (L. Linde et al. Lancet 350, 834–843; 1997), and which is frequently cited by homeopaths, has had its methodology extensively criticized since publication.

...Ben Goldacre, a London-based medical doctor, journalist and frequent critic of homeopathy, says that several universities have refused to let him see their course materials. "I can't imagine what they're teaching," he says. "I can only imagine that they teach that it's OK to cherry-pick evidence. That's totally unacceptable."

One university that is willing to discuss its teaching is the University of Westminster in London. Brian Isbell, head of Westminster's department of complementary therapies, defends the BSc description, arguing that as with all of the university's complementary therapy degrees, students also have to study the health-sciences model of disease, so that they can "work safely and effectively within the healthcare system". Students are required to do research and produce critiques of the literature.

...One assignment asks students to critique a paper that assessed the health changes reported by patients suffering from a range of chronic diseases when they attended follow-up appointments after receiving homeopathic treatment at a hospital in Bristol. Almost three-quarters of the 6,500 patients reported that their condition had improved (D. S. Spence et al. The Journal of Alternative and Complementary Medicine 11, 793–798; 2005).

The paper generated significant media coverage when it was published, but its methodology has been widely criticized. No control group was used, prompting Colquhoun to note that the study is not even capable of showing that homeopathy was producing a placebo effect. So what happens when students critique the paper? Do they get full marks for showing that it provides no evidence at all for homeopathy?

Not quite, says Isbell, who says the paper was chosen precisely because of the controversy over its methodology. Students would be expected to discuss the problems with the lack of controls and to suggest ways to run better studies. But Isbell says that the Bristol researchers still collected useful 'outcome measures' — basically a set of reports from individual patients about how they improved. "It doesn't have the rigour of other methods," Isbell says, "but it is part of the picture."

The differing opinions over the paper highlight an issue at the centre of the dispute about the evidence for homeopathy, and which explains in part why lecturers feel they can teach the subject as science. For advocates of evidence-based medicine, the double-blind randomized clinical trial (in which neither the doctor nor the patient knows who is getting active treatment and who is getting a placebo) is the best form of evidence available to practitioners. When regulators take decisions on drug safety, for example, they usually rely on such studies. But for homeopaths, there is a serious flaw in this approach.

When a patient visits a homeopath, the practitioner asks questions that go beyond the symptoms and probe other aspects of the patient's life, such as whether they are feeling stressed or unhappy. The result is an individualized treatment that takes longer than the ten or so minutes that the patient would get with a government-funded family doctor. This personal interaction is critical to homeopathy, both in tailoring the medicine and in gaining the patient's confidence. Homeopaths say that if there is a chance that the patient might receive a placebo at the end of it, the necessary trust can break down.

...For advocates of evidence-based medicine, such arguments are equivalent to admitting that homeopathy is nothing more than a strong placebo effect brought on by an attentive practitioner. If the treatment cannot work unless the patient and practitioner believe in it, then it cannot be due to the physical properties of the remedy. Homeopaths disagree, insisting that the remedy itself does have an effect independent of the practitioner. But by ruling out what scientists consider the best mechanism available to test this assertion, it is hard to see how homeopaths will ever convince their opponents.

` I could mention here, that Lou says even though homeopathy isn't proven in studies, and that you can't tell the difference between placebos and homeopathic remedies, the fact that it's so hard to test and the overwhelming anecdotal and personal evidence is what keeps him believing.

'Here boy' makes dogs wag to the right-Direction of tail wagging highlights different tasks of brain halves.-21 March 2007

Dogs wag their tails to the right when they see something they want to approach, and to the left when confronted with something they want to back away from, say researchers in Italy.

` Now that's vaguely interesting!

Shown a human or a cat, tails wagged consistently to the right. The unfamiliar person elicited less wagging than the owner, and the cat the least wagging of all — probably because the dog was so interested in giving chase that it was distracted from wagging, says Vallortigara.

Shown a large, unfamiliar and intimidating dog, the dogs wagged their tails more to the left. Dogs also wagged to the left when left on their own without anyone to look at, the researchers report in Current Biology1.

...Previous studies have shown that, in humans, strong activity in the brain's left hemisphere (which controls the right side of the body) is associated generally with a sunny disposition. Human studies have also linked left-brain activity with approach behaviour, and right-brain activity with retreat.

Biases for right- or left-'handed' behaviours have been seen in fish, amphibians, reptiles, birds, reptiles and mammals. "The evidence is that brain asymmetry is quite ancient," says Vallortigara. "It seems to have started early in the vertebrates."

Parcelling out tasks to one side of the brain or the other avoids duplication, and may help decision-making by reducing conflict between brain regions.

More puzzling, says Rogers, is why such biases also arise in behaviours such as escape. Toads and chicks, for example, are both more likely to leap away from something seen in the left eye — suggesting that a predator could learn to sneak up from the right. Why such biases do not vary at random from animal to animal is still uncertain.

A chip in the eye boosts sight - Amplification of light restores limited vision in some damaged retinas. - 21 March 2007

` Hooray for cyborgdom!

Eberhart Zrenner, executive director of the Eye Hospital at the University of Tübingen in Germany, announced at a recent press conference that his team had surgically implanted a 3-millimetre-square chip behind the retina of one eye in seven legally blind patients between the ages of 26 and 58. The chips restored limited vision to three of the patients, Zrenner said. The group will present its results at the Association for Research in Vision and Ophthalmology annual meeting in Fort Lauderdale, Florida, in May.

For two of the patients who showed no improvement in the trial there were technical problems with the chips; two others had been blind for more than 10 years, and so seemed to have lost the ability to interpret the light signals.

The three patients in whom the chip worked reported seeing "sort of an illuminated window frame", in which they had limited vision. One was able to locate white dinner plates on a dark tablecloth, for example, but could not locate white plastic packages of coffee creamer.

"The patients were absolutely enthusiastic about it, to see light or find a plate on the table in front of them," says Wrobel. "For them, it was tremendous progress." A key to future success will be teaching patients to interpret the images better, he says.

Alan Chow at Rush University Medical Center in Chicago is a co-founder of Optobionics of Naperville, Illinois. His team has a sub-retinal implant that works without amplification, and is powered only by the incoming light. "We have demonstrated that a passive device works," Chow says, adding: "With ours there is no need for an exit wire."

An artificial silicon retina developed by Optobionics, with 5,000 microscopic solar cells, each with its own stimulating electrode, has been tested in ten people in a trial that began in 2000. The company says that sight improved for all of them. Chow says some have seen colours and others have been able to see their own face in a mirror. But Wrobel still argues that amplification is necessary to truly restore sight.

` ...Ear chips, eye chips, motor chips... what's next?

To kill one, or watch many die?-Brain damage takes the emotion out of decisions.-21 March 2007

` If this is what I think it is....

A runaway train is speeding down the tracks towards five workmen. You and a stranger are standing on a bridge over the track. The only way to save the five is to push the stranger in front of the train to his death, and his body will stop it from reaching them.

` It is!!

Antonio Damasio at the University of Southern California in Los Angeles and his colleagues used a battery of dilemmas like this one to explore the role of emotion in moral decisions. Healthy subjects rejected most of the solutions that involved harming one person to save many lives, but the team found that people with damage to the ventromedial prefrontal cortex (VMPC), a brain area just behind the forehead, endorsed such decisions.

These patients, whose brain damage resulted from stroke or the removal of a brain tumour, made perfectly normal decisions when the scenarios didn't have a moral component (is it all right to change a cake recipe if you don't like it?) or were asked to make less personal decisions (is it all right to push a heavy sculpture off a bridge to save the five workmen?). But when patients responded to more personal moral dilemmas, they were more than twice as likely as both normal controls and patients with brain damage that didn't include the VMPC to decide to harm one person — even their own child — to save more lives in the future.

"Social emotions were really the scaffolding for what we came to construct as ethics," he says. How those social emotions are taken into account in the process of decision-making seems to be very biological. "When things get complicated, we engage an emotional system — it's not reason alone," Damasio says.

` And now... time for dinosaurs!!!!

Burrowing dinosaur unearthed - Fossilized family broadens picture of extinct reptiles. - 21 March 2007

The discovery of a dinosaur family fossilized in its burrow could make us rethink where the animals lived, how they behaved, and even what wiped them out, say researchers.

David Varricchio of Montana State University in Bozeman and his colleagues found the jumbled remains of two juveniles and an adult together in what looks to be the remains of a custom-built hole in southern Montana.

The team has named the beast Oryctodromeus cubicularis, meaning 'digging runner of the lair'. It belongs to a group of small herbivorous dinosaurs, and lived 95 million years ago during the mid-Cretaceous period.

The skeletons are incomplete, but they show that when fully grown, the animal was about 2.1 metres long, of which more than half was tail. The dinosaur had a broad snout and powerful shoulders well adapted for digging, and sturdy hips that would help it to brace itself as it dug. It could also run on its back legs.

The den was just over two metres long, with a pronounced s-bend — making it harder for predators to enter — opening out into a terminal chamber. The close fit between the sizes of burrow and beast convinced the team that Oryctodromeus had dug its own den, rather than simply displacing a previous occupant. "It's not just a random attempt," says Martin. "It's very well constructed."

Varricchio and his colleagues had previously found what seemed to be a family of dinosaurs in what could have been a collapsed burrow in China (see 'Fossil hints at devoted parenting in dinosaurs'), but no one had seen an actual tunnel space until now.

` What a charming find! I myself have always thought that some small dinosaurs must have dug burrows to keep warm in during the winter, but this is beyond my expectations!

` Anyway, I have many a this, that and other thing going on, but I have to get my computer to the shop quickly (hence the rush job) because of its fondness for crashing whenever I open a program. I don't know why it hasn't done this yet today, but it had about thirty times yesterday.
` So, I hope you see it's important for me to get going. However, when I come back - I promise you! - I'll have a really big surprise!! (In fact, it might be done now if my computer would stop so rudely interrupting me with a Blue Screen of Death!)
` See you later! And if I'm not back before April Fool's Day, wish me a good 25th birthday!


Galtron said...

You can make people see UV? I can't wait until we get infrared vision! Bwa ha ha!

I hope your computer gets well soon and I wish it a speedy recovery!

S E E Quine said...

` Thanks!! I was about to take it down to the shop when Lou said he had to finish his actor's profile online. I said, "No, I don't think it's going to work for you." But he didn't listen, so after spending all morning ignoring the fact that he kept getting a Blue Screen of Death right when he was in the middle of what he was doing, he finally relented and said "No, this isn't working!"
` So here we are at the library - we just got everything else on his profile that needed to be gotten on it, so that's good, but this is no place to write blog posts in! The sooner my computer gets fixed, the better!

Galtron said...

Yes, the sooner your computer gets fixed, the quicker you can write things to entertain me! ...I mean, me and your faithful readers!

S E E Quine said...

` Though my computer was ready to go last night, I picked it up this morning because I went camping.

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