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Thanks for the memories

Sunday, October 22, 2006

We're all pretty concerned about how well our memory works, right? There's now evidence that the quantity of the neurotransmitter acetylcholine present in the brains of test animals (rats, of course) is directly related to the level of detail of new memories:

Researchers discover mechanism that determines when detailed memories are retained
The levels of a chemical released by the brain determine how detailed a memory will later be, according to researchers at UC Irvine.

The neurotransmitter acetylcholine, a brain chemical already established as being crucial for learning and memory, appears to be the key to adding details to a memory. In a study with rats, Norman Weinberger, research professor of neurobiology and behavior, and colleagues determined that a higher level of acetylcholine during a learning task correlated with more details of the experience being remembered. The results are the first to tie levels of acetylcholine to memory specificity and could have implications in the study and treatment of memory-related disorders.

The findings appear in the November issue of the journal Neurobiology of Learning and Memory.

"This is the first time that direct stimulation of a brain region has controlled the amount of detail in a memory," said Weinberger, a fellow at UCI's Center for the Neurobiology of Learning and Memory. "While it is likely that the brain uses a number of mechanisms to store specific details, our work shows that the level of acetylcholine appears to be a key part of that process."

It isn't news that acetylcholine is related to memory. As a neurotransmitter, acetylcholine is released by presynaptic projections of a neuron's axon in order to cause activation (or inhibition) of a postsynaptic neuron. Normally, the neurotransmitter must be quickly degraded in the synapse so as not to continue to affect the postsynaptic neuron.

However, it was discovered that inhibiting the degradation of acetylcholine (which is normally done by the enzyme acetylcholinesterase) can improve memory performance of persons with early stage Alzheimer's disease. And so acetylcholinesterase inhibitors have turned out to be popular drugs for treating early Alzheimer's.

A little is known about how acetylcholine is involved in memory. It is generally assumed now that memory is a phenomenon of "synaptic plasticity" that occurs when the strengths of connections between neurons increase in proportion to how often signals pass between the neurons – so-called "long-term potentiation". (There has been experimental confirmation of this hypothesis only recently – see this report.) Acetylcholine has been shown to enhance the amplitude of synaptic potentials following long-term potentiation in many regions of the brain.

What the recent research reported here seems to show is that deliberately increasing the quantity of acetylcholine in the brain leads to the formation of more detailed memories.

Sounds like a useful thing to be able to do whenever one needs to cram for a crucial exam...

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Evidence that quasars are powered by black holes

Saturday, October 21, 2006

Astronomers see inside a quasar for the first time
For the first time, astronomers have looked inside quasars -- the brightest objects in the universe -- and have seen evidence of black holes.

The study lends further confirmation to what scientists have long suspected -- that quasars are made up of super-massive black holes and the super-heated disks of material that are spiraling into them.

The suspicion that quasars are powered by supermassive black holes has, until now, been based only on the fact that astrophysicists couldn't think of any other plausible explanation. The new evidence that supports this hypothesis is that it has been possible to observe what looks like a black hole accretion disk inside two quasars:
[The researchers] were able to measure the size of the so-called accretion disk around the black hole inside each quasar.

In each, the disk surrounded a smaller area that was emitting X-rays, as if the disk material was being heated up as it fell into the black hole in the center.

Further supporting their conclusion was the fact that the hightest-energy emissions (X-rays) occurred near the center of the quasar, while optical light originated much farther out. (Since gas and dust would be heated most near a central black hole.) It was possible to make these observations on two quasars only because they were magnified by gravitational lensing due to intervening massive objects, and only by by combining results from ground-based optical telescopes and the orbiting Chandra X-Ray Observatory.

Other references:

Black Holes Power the Brightest Cosmic Objects – Space.com

Quasars Under the Lens – ScienceNow (subscription rqd)

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Stellar birth control by supermassive black holes

This news item, which was mentioned in our article on black holes, suggests that the supermassive black hole at the center of the relatively nearby galaxy M87 might be responsible for a low rate of star birth in the galaxy.

There is also new evidence from the very early universe that the same suppression of star formation was already happening 11 billions years ago:

Stellar birth control in the early universe
Every year only a handful of new stars are born out of the gas that fills the space between the stars in galaxies like the Milky Way. To account for the large number of stars in the Universe today, about 400 billion in the Milky Way alone, it was thought that the "stellar birth rate" must have been much higher in the past.

Surprisingly, in this study appearing in the October 2 issue of Astrophysical Journal, astronomers using the 8.1m Gemini telescope in Chile report that many of the largest galaxies in the Universe had a very low stellar birth rate even when the Universe was only about 20 percent of its present age.

"Our new results imply that the stars in many large galaxies were born when the Universe was in its infancy, in the first few billion years after the Big Bang," said team leader Mariska Kriek, a PhD student from Leiden University and Yale. "The results confirm what some astronomers had suspected -- galaxies seem to have some method of 'birth control' that is very effective."

These new findings add to growing evidence that in big galaxies the formation of new stars was significantly suppressed after an initial period of vigorous activity. "These galaxies had a very violent early youth, but rose into stable adulthood well before many galaxies like the Milky Way were even in kindergarten," said Kriek."

And why might that have been?
One suggestion is that enormous black holes in the centers of large galaxies may be responsible for suppressing star formation. When material spirals into a black hole, huge amounts of energy are released and are rapidly injected into the galaxy's gas. This energy injection may dilute the gas sufficiently to prevent future star birth.

Another study of about 800 nearby elliptical and lenticular galaxies of various sizes has come to the same conclusion:

Huge Black Holes Stifle Star Formation
Supermassive black holes play a stealthy role in two major types of galaxies in the universe, bulking up until they are big enough to effectively shut down the formation of new stars, scientists have found.

The new results explain why scientists have observed in the past that massive galaxies have fewer young stars. Black holes, monstrous heaps of dense matter, grow at a different rate than the galaxies that surround them. But once a black holes reach a critical mass and become too large for its host galaxy, it zaps away nearly all the gas needed for young stars to form.

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Black holes in the news

No, this isn't metaphorically about censorship in the news media. It's about real black holes.

There's been a lot of new information coming out about black holes recently – some of which we're already discussed, such as this and this. (There's more if you search the archives.)

And just think – only a few years ago many astrophysicists weren't convinced that black holes (as usually conceived) really existed. A few are even still trying to come up with alternative explanations (e. g. here, here, here). Whatever.

Here are a few more news items, and that's not even getting into news about quasars and the effect of supermassive black holes on star birth – which we'll talk about separately.

Scientists Nudge Closer To The Edge Of A Black Hole
NASA scientists and their international partners using the new Japanese Suzaku satellite have collected a startling new set of black hole observations, revealing details of twisted space and warped time never before seen with such precision.

The observations include clocking the speed of a black hole's spin rate and measuring the angle at which matter pours into the void, as well as evidence for a wall of X-ray light pulled back and flattened by gravity

Another one:

Chandra reviews black hole musical: Epic but off-key
A gigantic sonic boom generated by a supermassive black hole has been found with NASA's Chandra X-ray Observatory, along with evidence for a cacophony of deep sound.

This discovery was made by using data from the longest X-ray observation ever of M87, a nearby giant elliptical galaxy. M87 is centrally located in the Virgo cluster of galaxies and is known to harbor one of the Universe's most massive black holes.

Scientists detected loops and rings in the hot, X-ray emitting gas that permeates the cluster and surrounds the galaxy. These loops provide evidence for periodic eruptions that occurred near the supermassive black hole, and that generate changes in pressure, or pressure waves, in the cluster gas that manifested themselves as sound.

"We can tell that many deep and different sounds have been rumbling through this cluster for most of the lifetime of the Universe," said William Forman of the Harvard-Smithsonian Center for Astrophysics (CfA).

The outbursts in M87, which happen every few million years, prevent the huge reservoir of gas in the cluster from cooling and forming many new stars. Without these outbursts and resultant heating, M87 would not be the elliptical galaxy it is today.

The next item has a little more about the "iron K-alpha" spectroscopic line that's mentioned in the previous article:

Astronomers use supercomputers to study atoms linked to black holes
The atom that most black-hole hunters are interested in is iron, and that's where Einstein's general theory of relativity comes in.

The immense gravity of a black hole should, according to relativity, distort the X-ray signal as seen from Earth, particularly for iron atoms. The signal is a spectrum, and looks like a series of lines, with each atom having its own line. One line in particular, called the iron K-alpha line, appears broadened for X-rays emanating from the center of active galaxies, and it is often cited as a key indication of a black hole.

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Intrinsically unstructured proteins

It's long been the conventional wisdom that proteins have rigidly fixed shapes which are crucial to their function – at least those proteins which actually have important functions. But now, apparently, not so much:

First Major Study Of Mammalian 'Disorderly' Proteins
Unlike the classic description of proteins described in science textbooks, IUPs are not completely locked into rigid, 3-D shapes that determine their function in the cell. Instead, IUPs have varying amounts of flexibility within their sometimes spaghetti-like structures that is critical for function. For example, one protein named p27 initially looks like a Slinky™ toy. However, when p27 goes to work, it puts a vise-like grip on an enzyme that otherwise would promote uncontrolled cell division.

The St. Jude team developed a technique that uses heat to isolate IUPs in large, purified quantities from extracts of a standard type of cultured mouse cells called NIH3T3 fibroblasts. The IUPs were resistant to the heat, unlike more structured proteins, which fell apart. Based on these studies, the investigators were able to classify all proteins into one of three categories: IUPs; intrinsically folded proteins (IFPs, i.e., fully folded into specific shapes); or mixed ordered or disordered proteins (MPs), which have both structured and unstructured parts.

The point isn't that protein scientists have been wrong all this time, so much as that nature will often be able to find a use for building blocks in order to take advantage of varying characteristics that are available.

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A Cosmology Calculator for the World Wide Web

Tuesday, October 17, 2006

Have you ever been frustrated, while reading a news article or scientific paper dealing with cosmology or extragalactic astronomy, to find some object (like a quasar) described as having a certain redshift, but without any indication as to the age of the universe at which the light we can now see was emitted? Or perhaps vice versa? I know I have, many times... but then maybe I'm a little odd.

However, if you've experienced the same frustration, then there is now help just a few clicks away: a Javascript cosmology calculator, by UCLA cosmologist Ned Wright.

You supply the red shift value (z) that you're interested in, and certain additional parameters (for which the best estimated values are supplied as defaults), and the calculator will tell you when the light was emitted (in billions of years since the big bang), how long the light has been traveling, and several other interesting but more arcane quantities. Links to brief explanations of many of the variables are provided.

By varying some of the parameters (such as Hubble's constant, H0, and ΩM) you can play with different cosmological models.

If you want to find a red shift value that corresponds to some given light travel time, you have to make a guess (e. g. z=3), plug it in, and then vary z until you come close to what you wanted.

If you can't quite recall what all the terminology means, Wright even has a very good tutorial on the whole subject of cosmology. Or perhaps instead, or in addition, you might look at my cosmology turorial.

And if you're really serious about cosmology and would like to know in excruciating detail what the mathematics are behind the calculations, take a look at Wright's paper at the arXiv: [astro-ph/0609593] A Cosmology Calculator for the World Wide Web

Oh, and if you're not quite sure why anyone in their right mind might care about this sort of thing, there's a nice Scientific American article by Abraham Loeb that was just published: The Dark Ages of the Universe. It deals with the period of time from when matter and energy decoupled – the time of the cosmic microwave background – up until the first very bright stars began to shine. The times correspond to a redshift around z=10. The article explains what's so interesting about this period.

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Researchers Find Smallest Cellular Genome

Here's another thing to remember in case you're at a party and running our of conversational ideas. The living creature (other than viruses) with the smallest number of genes is the bacterium Carsonella ruddii – just 182 genes and 159,662 base-pairs of DNA.

Researchers Find Smallest Cellular Genome
The bacteria Carsonella ruddii has the fewest genes of any cell. The bacteria's newly sequenced genome, the complete set of DNA for the organism, is only one-third the size of the previously reported "smallest" cellular genome.

"It's the smallest genome -- not by a bit but by a long way," said co-author Nancy A. Moran, UA Regents' Professor of ecology and evolutionary biology and a member of the National Academy of Sciences. "It's very surprising. It's unbelievable, really. We would not have predicted such a small size. It's believed that more genes are required for a cell to work."

Carsonella ruddii has only 159,662 base-pairs of DNA, which translates to only 182 protein-coding genes, reports a team of scientists from The University of Arizona in Tucson and from Japan.

Of course, C. ruddii is cheating a little. It lives only in certain specialized cells of a sap-eating insect (Pachypsylla venusta). The bacterium has no genes needed for certain enzymes (required for replication) and nutrients such as folic acid, so it must rely on its host for these. Consequently, C. ruddii is not a good guide for identifying a minumum set of genes needed for a free-living organism.

If you want to sound really well-informed about this, here are some other things to read:

Bacteria boast the 'tiniest genomes' to date – New Scientist

Tiny Genome May Reflect Organelle in the Making – Scientific American

Smallest Genome of Living Creature Discovered – LiveScience

The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella and The Bacterial World Gets Smaller – Science [subscription rqd. for full access]


Fertile women dress to impress

Sunday, October 15, 2006

And as long as I'm writing about aspects of gender and sexuality, this is interesting:

Fertile women dress to impress, U.S. study finds
Women dress to impress when they are at their most fertile, U.S. researchers said on Tuesday in a study they say shows that signs of human ovulation may not be as mysterious as some scientists believe.

A study of young college women showed they frequently wore more fashionable or flashier clothing and jewelery when they were ovulating, as assessed by a panel of men and women looking at their photographs.

Some will say, "Nothing surprising about that." Others will say, "It's just a stereotype."

We report. You decide.

The point is that, even though human females have an estrous cycle like most other placental mammals do, it has been believed that they do not exhibit outward signs during the most receptive part of the cycle. According to the Wikipedia article,
Humans, unlike some other species, do not have any external signs to signal receptivity at ovulation. Research has shown however, that women tend to have more sexual thoughts and are most prone to sexual activity right before ovulation.

The new research is saying that lack of external signs is another gender myth, although the signs are subtle:
"They tend to put on skirts instead of pants, show more skin and generally dress more fashionably," said Martie Haselton, a communication studies and psychology expert at the University of California Los Angeles who led the study.

Writing in the journal Hormones and Behavior, Haselton and colleagues said their findings disproved the conventional wisdom that women are unique among animals in concealing, even from themselves, when they are most fertile.

It's interesting that, apparently, this is only a behavioral change, and that there are still no outward physiological signs of peak fertility.

Hormones are still at work. It's just that in humans their effect is on the brain only, rather than on the epidermis.

More detailed report: Forget Basal Body Temperature -- Check Out Her Clothes; Signs Of Ovulation May Be More Obvious Than Supposed

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Women become sexually aroused as quickly as men

Let's hear it for gender equality...

And let it not be said that most scientific research has little practical application. The following might be very useful to know in "real life" situations...

Women become sexually aroused as quickly as men
Women may have a reputation for demanding lengthy foreplay, but they become sexually aroused as quickly as men, according to a new study that used thermal imaging to measure increased blood flow to genital regions.

While watching pornography, both sexes reach peak arousal within 10 minutes, on average, researchers report.

The new finding is based on the use of infrared imaging technology to measure skin temperature from a distance. This is not only more sensitive to temperature differences, but also does not require uncomfortable instruments in contact with the subjects' genitals.
In the new study, 28 men and 30 women first watched a video of the Canadian countryside in a room on their own, so that researchers could establish each individual’s baseline temperatures.

Subjects were naked from the waist down and positioned themselves such that their genital area was exposed and readable by the thermal imaging device. The participants next watched another video with the same subject matter, or one featuring pornography, horror or comedic clips from the Best Bits of Mr Bean.

The computer only registered a spike in genital temperatures while subjects watched pornography, and not the other films. In those viewing porn, these temperatures increased by about 2°C, on average.

Moreover, men reached peak sexual arousal in 665 seconds – about 10 minutes – while women arrived at maximal arousal in 743 seconds.

Other reports of the research: here, here, here.

However, Vaughan at Mind Hacks raises some questions about this research. For example, it seems that only physical arousal was measured, assuming skin temperature is a good indicator of that. But psychological arousal may be different between men and women.
Why there is such a marked difference in feeling sexy and being aroused in women is still a mystery, but it is something that needs to be borne in mind when interpreting any study (and particularly, any news story) that talks about 'sexual arousal' as a single type of experience.

Unfortunately, Kukkonen and colleagues' study seems to have been widely and uncritically reported as suggesting that women get 'hot' in about the same time as men do, when in fact, the picture is far more complex.

Another interesting question is raised if you take a look at information on some of the grad students in the lab that did the study, in particular, Tuuli Kukkonen, who was involved in this research project. Is the fact that these are young, attractive females relevant? Would this have had any differential effect on the male subjects vs. the females? Just wondering.

But suppose that there is some validity to the research findings. The next question would be, why is there a "gender gap myth" that men are more easily aroused sexually than women? Is it possible this is something women want men to believe, perhaps in order to justify longer foreplay? Do women want their men to "work harder" at sexual intimacy, to create a sense of higher perceived "value" in some economic sense? Evolutionary psychology might suggest this is something that happens without being a conscious intention on anyone's part.

Questions, questions.

Other blog articles: Pure Pedantry, Sciencebase,
Health Logics.

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NASA Performs Headcount of Local Black Holes

Saturday, October 14, 2006

File this one under interesting facts to mention if you run out of things to say at a cocktail party:

NASA Performs Headcount of Local Black Holes
Nearly every massive galaxy seems to have a supermassive black hole, but only a few percent appear to be active. Our galaxy's central black hole is dormant, and this and similar black holes are not included in the Swift census. All black holes were likely once active, and why some remain active and others are dormant in the modern, local universe is a mystery.

"You can't understand the universe without understanding black holes," said Richard Mushotzky of Goddard, a census team leader. "Perhaps as much as 20 percent of all of the radiated energy in the universe---most X-rays, large fractions of ultraviolet and infrared light, and a good deal of radio waves---arise in one way or another from AGN activity." [Emphasis added.]

By the way, an "AGN", or "active galactic nucleus" is a supermassive black hole surrounded by and interacting with a large quantity of gas at the center of a large galaxy:
AGN have a mass of millions to billions of suns, which are confined within a region about the size of our solar system. The term "active" refers to the process of actively pulling in gas and whole stars and generating copious amounts of energy from a tiny galactic core in the process. Examples include quasars and Seyfert galaxies.

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We just mentioned caffeine here, in relation to the mood-enhancing effects of fast thinking.

So along comes a little more information about the connections.

Probing Question: Is caffeine harmful to your health?

The basic answer seems to be "no", when the stuff is used in moderation. Just as interesting are the details of how it works:
How does caffeine achieve its most sought-after effect of counteracting fatigue? To understand that, we first have to understand the chemistry of fatigue itself. Like all cells in the body, brain cells access fuel through an energy-storage nucleotide called ATP. ATP -- adenosine triphosphate -- loses one of its three phosphate molecules with each burst of energy it releases, eventually becoming a single adenosine molecule. The longer a person is awake, the more adenosine will accumulate on special adenosine receptors in the brain, signaling it to slow its activity.

Enter caffeine. Acting as a wolf in sheep's clothing, caffeine is molecularly similar enough to adenosine to fit into its receptors, blocking adenosine from getting through -- yet it is distinct enough not to be "read" by the brain as instructions to take a nap.

Without adenosine's calming effect, the brain's neurons fire more rapidly and the body reads this increased activity as an emergency requiring the release of the "flight or fight" chemical: adrenalin [AKA: epinephrine]. The result? You feel excited, alert, mentally quick, ready for anything.

Of course, if there actually is a lot of adenosine in the brain, that's a sign it may be running on a nearly empty tank. Probably not a good idea to continue this too long without replenishing the fuel supply.

Another thing to watch out for: If you take caffeine while pulling an all-nighter to finish that important assignment, you may not be able to come back and have a good nap after the work is turned in:

Negative Effects Of Caffeine Are Stronger On Daytime Sleep Than On Nocturnal Sleep
A new study at the Université de Montréal has concluded that people drinking coffee to get through a night shift or a night of studying will strongly hurt their recovery sleep the next day.


Philosophia Naturalis #2 is published

Thursday, October 12, 2006

The second edition of Philosophia Naturalis is now up at Nonoscience. Happy reading!

And thanks to Arunn for putting it all together.

Science blog trek

I need to get out more. There's so much interesting stuff out there. Here are some finds from a recent trek around the science blogosphere:

Sex in an MRI Machine
This piece from Stuart Coleman at Daily Irreverence is to get your attention so you keep reading. Don't show it to your maiden aunt Bertha. It has sexually explicit stuff in it, like penises and vaginas. But perhaps not the way they're seen in porn flicks. The title explains it all. This is actual, bona fide research. Wish I could read the grant proposal for this... so I could plagiarize it.

Omega-3 oils & marijuana may stave off Alzheimer’s
Here's one that may be of more interest to Bertha, courtesy of the Neurophilosopher. And it isn't just about fish oil, either. "In recent months, various studies have provided evidence that apple juice, a Mediterranean diet, cabernet sauvignon and curry can either reduce the likelehood of developing Alzheminer’s or reverse the cognitive impairment which is symptomatic of the disease. To that list we can now add omega-3 oils. And marijuana."

Origins of Gene Structure
Dan Rhoads at Migrations tackles some difficult questions in evolutionary theory. Specifically, how can we explain the evolution of the intricate gene expression process in eukaryotic cells? Do we need to resort to models of "genetic drift" as opposed to "adaptive selection"?

Conditions for the Emergence of Life
This is another one from Dan. He likes to deal with difficult, fundamental issues in molecular evolution, and nothing is more fundamental than the question of how life got started. This article just sketches some of the questions about how life could arise from a self-organizing chemical system.

DarkSyde's Open Science Thread for 10/7/06
DarkSyde, who also blogs (sometimes) at Unscrewing the Inscrutable, is a regular contributor at Kos's place, on both politics and science. He posts a regular article on Fridays, and short link fests like this one from time to time. This particular fest has an item about quantum teleportation. Maybe I'll write more about that later. But what was really interesting was the following item from Sean Carroll.

The Cell Is Like Tron
For biologists, I should note that this Sean Carroll is Sean M. Carroll, the cosmologist, not Sean B. Carroll, the evo-devo biologist. Anyhow, the item here is actually mostly for biologists -- a spectacular computer animation of the internal structures of a cell. But it will impress, if not astonish, just about anyone. Do not fail to take a look at it. If you want to know what's going on, there's some explanation here, where you'll also find a high-res version. (A faster/smoother high res version is here.) This thing was originally mentioned at Pharyngula. As a free bonus, Sean also throws in a couple of links for physicists.

Asymmetry of the cosmic microwave background

Wednesday, October 11, 2006

One of these days I need to do a series of posts on the cosmic microwave background (CMB). It's seriously interesting stuff. If you're not into astrophysics that much, you've still heard of it recently, because it helped a couple of guys win this year's Nobel Prize in Physics. (More good reporting on this here, here, here, here, here.)

And that's not the first Nobel Prize it's responsible for. Back in 1978, two other guys got a Nobel Prize for "discovering" the CMB. (I used the scare quotes, because the discovery was rather serendipitous, and at first the discoverers thought they had found nothing more interesting than a little guano.)

But even the current Nobel was based on work done more than 10 years ago. Quite a lot has happened in the meantime. (See this good article for a quick summary.) And now, some very recent research has found that the universe isn't quite as isotropic (the same in all directions) on the large scale, as cosmologists have always assumed. The CMB is an ellipsoid rather than a perfect sphere:

Ellipsoidal Universe
One remaining oddity about the WMAP results, however, concerns the way in which portions of the sky contribute to the overall map of cosmic microwaves; samples of the sky smaller than one degree across, or at the degree level, or tens of degrees seem to be contributing radiation at expected levels. Only the largest possible scale, that on the order of the whole sky itself (the technical term is quadrupole moment), seems to be under-represented.

Now Leonardo Campanelli of the University of Ferrara and his colleagues Paolo Cea and Luigi Tedesco at the University of Bari (all in Italy) have studied what happens to the quadrupole anomaly if one supposes that the shell from which the cosmic microwaves come toward earth is an ellipsoid and not a sphere.

This is probably not going to invalidate all of what we think we know about the early universe, but it does certainly call for an explanation. The authors of the research article suggest that "a uniform magnetic field pervading the cosmos, or a defect in the fabric of spacetime, could bring about a non-zero eccentricity."

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Scientists and Engineers for America

Tuesday, October 10, 2006

This seems like a great idea to me. If you think that science is being distorted or misrepresented politically in the U. S., this is something you ought to look into.

Scientists and Engineers for America

Today a group of scientists and concerned citizens launch a new organization, Scientists and Engineers for America, dedicated to electing public officials who respect evidence and understand the importance of using scientific and engineering advice in making public policy.

The principal role of the science and technology community is to advance human understanding. But there are times when this is not enough. Scientists and engineers have a right, indeed an obligation, to enter the political debate when the nation’s leaders systematically ignore scientific evidence and analysis, put ideological interests ahead of scientific truths, suppress valid scientific evidence and harass and threaten scientists for speaking honestly about their research.

How fast thinking makes us happy, energized and self-confident

Sunday, October 8, 2006

Recent psychological research claims to have found evidence for what the title of this piece says: merely speeding up our thought processes is enough to make us feel better mentally.

I don't know about you, but I don't find this very surprising. I feel a lot more like a tortise than a hare before I've had my first dose of caffeine for the day. But I generally get into a higher gear right after that, and my mood becomes a whole lot better too.

It's hard to deny the mood-enhancing effects of caffeine when you look at the stock price of a company like Starbucks. According to Wikipedia,
By the time of its initial public offering on the stock market in 1992, Starbucks had grown to 165 outlets. In April 2003, Starbucks added nearly that many new outlets in a single day by completing the purchase of Seattle's Best Coffee and Torrefazione Italia from AFC Enterprises, bringing the total number of Starbucks-operated locations worldwide to more than 6,400.

The company probably wouldn't have enjoyed such success, even at the prices they charge, if they didn't make a whole lot of people feel good.

But psychologists can reproduce the effect in the lab, without any chemical additives:

Study explores 'manic' thinking
How fast thinking makes us happy, energized and self-confident

Fast thinking, or "racing thoughts," is most commonly known as a symptom of the clinical psychiatric disorder of mania (and of the manic part of bipolar disorder or "manic-depression"). But, according to Princeton University psychologist Emily Pronin, most healthy people also have experienced racing thoughts at some point in time--perhaps when they are excited about a new idea they have just learned, or when they are brainstorming with a group of people, or even when they lie in bed unable to fall asleep. Pronin and her Harvard colleague Daniel Wegner decided to explore whether inducing people to think fast might lead them to feel some of the other experiences also associated with the manic experience.

It would be most intresting to know a lot more about the neurochemistry involved here. No doubt it's related to "runner's high", endorphins, higher levels of epinephrine (which is closely related to the neurotransmitter norepinephrine), and that sort of thing.


At all events, in times like these, it's always good to have some happy news.


No Extra Gravity for Dark Matter

Considering that there's no way to actually "see" dark matter directly, it's impressive that more is being learned about it all the time. Now we've found that it experiences the force of gravity to the same degree as ordinary matter, with an error of no more than 10%:

No Extra Gravity for Dark Matter
The Milky Way is gradually pulling apart a smaller orbiting neighbor known as the Sagittarius dwarf spheroidal galaxy. Just as gravity from the moon causes Earth's oceans to bulge, so too does the gravity of the Milky Way create enormous tides that deform Sagittarius. These are so strong that they rip stars out of the galaxy, producing two long streams of stars, one stretching ahead of Sagittarius and one lagging behind. By observing the stars streaming out in both directions, the researchers conclude that the dark matter and ordinary matter within the smaller galaxy feel the same pull from the Milky Way.

Update (10/11/06): This observation is quite analogous to the (probably apocryphal) story of Galileo dropping objects of different materials and densities from the tower of Pisa. Since the objects take the same time (neglecting air resistance) to fall, this shows that gravity exerts the same force regardless of the type of matter it is acting on.

Additional information:

How Fast Does Dark Matter Fall?

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Self-resurrecting bacteria

Friday, October 6, 2006

Who said resurrection is impossible? One species of bacterium, Deinococcus radiodurans, can do it — but it's the only case known.

Cheating DNA Death: How an Extremophile Repairs Shattered Chromosomes
Fifty years ago, scientists uncovered a microbe capable of withstanding radiation in canned meat that had been bombarded with gamma rays. Named Deinococcus radiodurans — or "strange berry that withstands radiation" — the microorganism can survive doses of radiation up to 500 times that which would kill a human. These doses shatter D. radiodurans's DNA — just as they would in a human — but the microbe can repair its broken DNA and spring back to life within hours, depending on the dose. Researchers in France have finally determined how the most durable of extremophiles manages this trick. "We have discovered the mechanism by which a clinically dead cell resurrects back to life," explains Miroslav Radman of INSERM, France's public biomedical research institution. "This extreme radiation resistance is but a by-product of its selection for resistance to desiccation."

It's taken microbiologists 50 years, but the details of how D. radiodurans accomplishes the feat of resurrection have finally been figured out. Well, almost all the details.

When any type of cell is exposed to enough toxic chemicals, oxidative damage, high levels of ionizing radiation, or dehydration, what kills the cell is the fragmentation of its DNA. Without intact DNA, a cell can't manufacture proteins required to sustain its life. What D. radiodurans seems uniquely capable of doing is putting all of its fragmented DNA back together, and in just the right order. Something that all the king's horses and all the king's men could not do for Humpty Dumpty.

It turns out there are two stages to this process. In the first stage, the short fragments of (single-stranded) DNA are gradually reassembled into longer and longer pieces, until they are complete again. This is possible at all only because of the unique structure of DNA — DNA segments will stick together only when they have precisely matching base sequences in common. The process is facilitated in bacterial DNA by an enzyme called DNA polymerase I. The enzyme is encoded by a gene known as polA, which is present in all prokaryotes. However, the DNA polymerase I found in D. radiodurans apparently performs its job much more efficiently than its analogue in other bacteria. This natural process is similar to the laboratory process known as polymerase chain reaction (PCR), which also uses a polymerase enzyme.

But it's the second stage that is really special in D. radiodurans, and which has just been elucidated in the latest research:
... single long strands of DNA do little to resurrect the microorganism until the second stage of the newly discovered process kicks in: the simple pairing discovered by Watson and Crick decades ago — adenine (A) bonds with thymine (T), and cytosine (C) bonds with guanine (G). By inserting a special version of the nucleotide thymine that only binds to single strands of DNA — known as 5-bromodeoxyuridine — the researchers could observe as the single strands bonded with complementary strands to form complete chromosomes. "Once the chromosome is functional, the synthesis of all cellular components starts, and the cellular life is back," Radman says.

Interesting questions remain unanswered. An obvious one is how this unique capability of D. radiodurans evolved. Of course, it's obvious that the capability is highly advantageous to the survival of any microbe that inhabits an extreme environment. But there are few, if any, environments on Earth that have the level of ionizing radiation in which D. radiodurans can survive. So there must have been some other extreme feature of the environment, like toxic chemicals or frequent dessication. But then, why don't many other kinds of bacteria have the same abilities as D. radiodurans? Perhaps something even stranger happened, and D. radiodurans evolved in an environment outside Earth, with much more radiation — like Mars — and later migrated to Earth on a meteorite.

Another important question is: what makes the form of DNA polymerase in D. radiodurans so special and efficient? Knowing this could be very useful, for instance if we wanted to endow other bacteria with the same kind of survivability in extreme environments. We might want to do that to create bacteria that could detoxify toxic wastes.

Eukaryotic cells (found in "higher" animals than bacteria) use a different type of DNA polymerase than what prokaryotes use, and they are much more complex in general than bacteria. But yet another interesting question is whether it is possible to endow eukaryotic cells with a more effective DNA repair capability.


Further information:

Microbe probe -- announcement of earlier (2001) research on D. radiodurans

Radiation-resistant organism reveals its defense strategies -- announcement of earlier (2003) research on D. radiodurans

Deinococcus radiodurans -- History and summary of research on D. radiodurans

D. radiodurans -- links to more information on D. radiodurans


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