Teleologic Blog: Science Archives

July 02, 2008

The "Brain's Best Guess" Theory of Perception

This from an article about (sort of) itching in the New Yorker... by Atul Gawande.

A new scientific understanding of perception has emerged in the past few decades, and it has overturned classical, centuries-long beliefs about how our brains work—though it has apparently not penetrated the medical world yet. The old understanding of perception is what neuroscientists call “the naïve view,” and it is the view that most people, in or out of medicine, still have. We’re inclined to think that people normally perceive things in the world directly. We believe that the hardness of a rock, the coldness of an ice cube, the itchiness of a sweater are picked up by our nerve endings, transmitted through the spinal cord like a message through a wire, and decoded by the brain.

In a 1710 “Treatise Concerning the Principles of Human Knowledge,” the Irish philosopher George Berkeley objected to this view. We do not know the world of objects, he argued; we know only our mental ideas of objects. “Light and colours, heat and cold, extension and figures—in a word, the things we see and feel—what are they but so many sensations, notions, ideas?” Indeed, he concluded, the objects of the world are likely just inventions of the mind, put in there by God. To which Samuel Johnson famously responded by kicking a large stone and declaring, “I refute it thus!”

Still, Berkeley had recognized some serious flaws in the direct-perception theory—in the notion that when we see, hear, or feel we are just taking in the sights, sounds, and textures of the world. For one thing, it cannot explain how we experience things that seem physically real but aren’t: sensations of itching that arise from nothing more than itchy thoughts; dreams that can seem indistinguishable from reality; phantom sensations that amputees have in their missing limbs. And, the more we examine the actual nerve transmissions we receive from the world outside, the more inadequate they seem.

Our assumption had been that the sensory data we receive from our eyes, ears, nose, fingers, and so on contain all the information that we need for perception, and that perception must work something like a radio. It’s hard to conceive that a Boston Symphony Orchestra concert is in a radio wave. But it is. So you might think that it’s the same with the signals we receive—that if you hooked up someone’s nerves to a monitor you could watch what the person is experiencing as if it were a television show.

Yet, as scientists set about analyzing the signals, they found them to be radically impoverished. Suppose someone is viewing a tree in a clearing. Given simply the transmissions along the optic nerve from the light entering the eye, one would not be able to reconstruct the three-dimensionality, or the distance, or the detail of the bark—attributes that we perceive instantly.

Or consider what neuroscientists call “the binding problem.” Tracking a dog as it runs behind a picket fence, all that your eyes receive is separated vertical images of the dog, with large slices missing. Yet somehow you perceive the mutt to be whole, an intact entity travelling through space. Put two dogs together behind the fence and you don’t think they’ve morphed into one. Your mind now configures the slices as two independent creatures.

The images in our mind are extraordinarily rich. We can tell if something is liquid or solid, heavy or light, dead or alive. But the information we work from is poor—a distorted, two-dimensional transmission with entire spots missing. So the mind fills in most of the picture. You can get a sense of this from brain-anatomy studies. If visual sensations were primarily received rather than constructed by the brain, you’d expect that most of the fibres going to the brain’s primary visual cortex would come from the retina. Instead, scientists have found that only twenty per cent do; eighty per cent come downward from regions of the brain governing functions like memory. Richard Gregory, a prominent British neuropsychologist, estimates that visual perception is more than ninety per cent memory and less than ten per cent sensory nerve signals. When Oaklander theorized that M.’s itch was endogenous, rather than generated by peripheral nerve signals, she was onto something important.

The fallacy of reducing perception to reception is especially clear when it comes to phantom limbs. Doctors have often explained such sensations as a matter of inflamed or frayed nerve endings in the stump sending aberrant signals to the brain. But this explanation should long ago have been suspect. Efforts by surgeons to cut back on the nerve typically produce the same results that M. had when they cut the sensory nerve to her forehead: a brief period of relief followed by a return of the sensation.

Moreover, the feelings people experience in their phantom limbs are far too varied and rich to be explained by the random firings of a bruised nerve. People report not just pain but also sensations of sweatiness, heat, texture, and movement in a missing limb. There is no experience people have with real limbs that they do not experience with phantom limbs. They feel their phantom leg swinging, water trickling down a phantom arm, a phantom ring becoming too tight for a phantom digit. Children have used phantom fingers to count and solve arithmetic problems. V. S. Ramachandran, an eminent neuroscientist at the University of California, San Diego, has written up the case of a woman who was born with only stumps at her shoulders, and yet, as far back as she could remember, felt herself to have arms and hands; she even feels herself gesticulating when she speaks. And phantoms do not occur just in limbs. Around half of women who have undergone a mastectomy experience a phantom breast, with the nipple being the most vivid part. You’ve likely had an experience of phantom sensation yourself. When the dentist gives you a local anesthetic, and your lip goes numb, the nerves go dead. Yet you don’t feel your lip disappear. Quite the opposite: it feels larger and plumper than normal, even though you can see in a mirror that the size hasn’t changed.

The account of perception that’s starting to emerge is what we might call the “brain’s best guess” theory of perception: perception is the brain’s best guess about what is happening in the outside world. The mind integrates scattered, weak, rudimentary signals from a variety of sensory channels, information from past experiences, and hard-wired processes, and produces a sensory experience full of brain-provided color, sound, texture, and meaning. We see a friendly yellow Labrador bounding behind a picket fence not because that is the transmission we receive but because this is the perception our weaver-brain assembles as its best hypothesis of what is out there from the slivers of information we get. Perception is inference.

The theory—and a theory is all it is right now—has begun to make sense of some bewildering phenomena. Among them is an experiment that Ramachandran performed with volunteers who had phantom pain in an amputated arm. They put their surviving arm through a hole in the side of a box with a mirror inside, so that, peering through the open top, they would see their arm and its mirror image, as if they had two arms. Ramachandran then asked them to move both their intact arm and, in their mind, their phantom arm—to pretend that they were conducting an orchestra, say. The patients had the sense that they had two arms again. Even though they knew it was an illusion, it provided immediate relief. People who for years had been unable to unclench their phantom fist suddenly felt their hand open; phantom arms in painfully contorted positions could relax. With daily use of the mirror box over weeks, patients sensed their phantom limbs actually shrink into their stumps and, in several instances, completely vanish. Researchers at Walter Reed Army Medical Center recently published the results of a randomized trial of mirror therapy for soldiers with phantom-limb pain, showing dramatic success.

A lot about this phenomenon remains murky, but here’s what the new theory suggests is going on: when your arm is amputated, nerve transmissions are shut off, and the brain’s best guess often seems to be that the arm is still there, but paralyzed, or clenched, or beginning to cramp up. Things can stay like this for years. The mirror box, however, provides the brain with new visual input—however illusory—suggesting motion in the absent arm. The brain has to incorporate the new information into its sensory map of what’s happening. Therefore, it guesses again, and the pain goes away.

The rest of the article is about itching...

Posted by rakhier at 02:03 PM | Comments (0)

June 18, 2008

Bacterial Evolution in the Lab

This is a good story from the New Scientist magazine (June 9, 2008)

A major evolutionary innovation has unfurled right in front of researchers' eyes. It's the first time evolution has been caught in the act of making such a rare and complex new trait.

And because the species in question is a bacterium, scientists have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events.

Twenty years ago, evolutionary biologist Richard Lenski of Michigan State University in East Lansing, US, took a single Escherichia coli bacterium and used its descendants to found 12 laboratory populations.

The 12 have been growing ever since, gradually accumulating mutations and evolving for more than 44,000 generations, while Lenski watches what happens.
Profound change

Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity.

"It's the most profound change we have seen during the experiment. This was clearly something quite different for them, and it's outside what was normally considered the bounds of E. coli as a species, which makes it especially interesting," says Lenski.
Rare mutation?

By this time, Lenski calculated, enough bacterial cells had lived and died that all simple mutations must already have occurred several times over.

That meant the "citrate-plus" trait must have been something special – either it was a single mutation of an unusually improbable sort, a rare chromosome inversion, say, or else gaining the ability to use citrate required the accumulation of several mutations in sequence.

To find out which, Lenski turned to his freezer, where he had saved samples of each population every 500 generations. These allowed him to replay history from any starting point he chose, by reviving the bacteria and letting evolution "replay" again.

Would the same population evolve Cit+ again, he wondered, or would any of the 12 be equally likely to hit the jackpot?
Evidence of evolution

The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

In the meantime, the experiment stands as proof that evolution does not always lead to the best possible outcome. Instead, a chance event can sometimes open evolutionary doors for one population that remain forever closed to other populations with different histories.

Lenski's experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. "The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events," he says. "That's just what creationists say can't happen."

Journal reference: Proceedings of the National Academy of Sciences (DOI: 10.1073/pnas.0803151105)

No rational person disputes that evolution takes place. The still unresolved problem is: how did life itself evolve? As I see it there are two things that must happen at the same time in the same "generation"

1) Proto-life must figure out how to harness external energy to "do things".

2) Proto-life must figure out how to make perfect copies of itself.

Its impossible for me to imagine proto-life forms sitting around and then one day, changing so that they start to harness energy from the sun so they can do things (like: move, store energy, grow in size, etc.).

Its equally impossible for me to imagine how, this same primitive life form not only "figured out" how to harness energy but also, before it died, figured out how to reproduce an exact copy of itself. So I'm completely unconvinced that there is a natural explanation for the origin of life. But as to evolution, no question. Its real.

Posted by rakhier at 10:32 PM | Comments (0)

June 17, 2008

Who are the Aggressive Drivers?

A study done by University of Colorado researchers has concluded: its the people with bumper stickers.

Watch out for cars with bumper stickers. (Shankar Vedantam, Washington Post, Monday, June 16, 2008)

That's the surprising conclusion of a recent study by Colorado State University social psychologist William Szlemko. Drivers of cars with bumper stickers, window decals, personalized license plates and other "territorial markers" not only get mad when someone cuts in their lane or is slow to respond to a changed traffic light, but they are far more likely than those who do not personalize their cars to use their vehicles to express rage -- by honking, tailgating and other aggressive behavior.

It does not seem to matter whether the messages on the stickers are about peace and love -- "Visualize World Peace," "My Kid Is an Honor Student" -- or angry and in your face -- "Don't Mess With Texas," "My Kid Beat Up Your Honor Student."

Szlemko and his colleagues at Fort Collins found that people who personalize their cars acknowledge that they are aggressive drivers, but usually do not realize that they are reporting much higher levels of aggression than people whose cars do not have visible markers on their vehicles.

Drivers who do not personalize their cars get angry, too, Szlemko and his colleagues concluded in a paper they recently published in the Journal of Applied Social Psychology, but they don't act out their anger. They fume, mentally call the other driver a jerk, and move on.

"The more markers a car has, the more aggressively the person tends to drive when provoked," Szlemko said. "Just the presence of territory markers predicts the tendency to be an aggressive driver."

The key to the phenomenon apparently lies in the idea of territoriality. Drivers with road rage tend to think of public streets and highways as "my street" and "my lane" -- in other words, they think they "own the road."

Why would bumper stickers predict which people are likely to view public roadways as private property?

Social scientists such as Szlemko say that people carry around three kinds of territorial spaces in their heads. One is personal territory -- like a home, or a bedroom. The second kind involves space that is temporarily yours -- an office cubicle or a gym locker. The third kind is public territory: park benches, walking trails -- and roads.

Previous research has shown that these different territorial spaces evoke distinct emotional responses. People are willing to physically defend private territory in ways they would never do with public territory. And people personalize private territory with various kinds of markers -- in their homes, for example, they hang paintings, alter the decor and carry out renovations.

"Territoriality is hard-wired into our ancestors from tens of thousands of years ago," said Paul Bell, a co-author of the study at Colorado State. "Animals are territorial because it had survival value. If you could keep others away from your hunting groups, you had more game to spear . . . it becomes part of the biology."

Drivers who individualize their cars using bumper stickers, window decals and personalized license plates, the researchers hypothesized, see their cars in the same way as they see their homes and bedrooms -- as deeply personal space, or primary territory.

Unlike any environment our evolutionary ancestors might have confronted, driving a car simultaneously places people in both private territory -- their cars -- and public territory -- the road. Drivers who personalize their cars with bumper stickers and other markers of private territory, the researchers argue, forget when they are on the road that they are in public territory because the immediate cues surrounding them tell them that they are in a deeply private space.

"If you are in a vehicle that you identify as a primary territory, you would defend that against other people whom you perceive as being disrespectful of your space," Bell added. "What you ignore is that you are on a public roadway -- you lose sight of the fact you are in a public area and you don't own the road."

Szlemko said that, in an as-yet-unpublished experiment, he conducted tests of road rage in actual traffic. He had one researcher sit in a car in a left-turn lane. When the light turned green, the researcher simply stayed still, blocking the car behind.

Another researcher, meanwhile, examined whether the blocked car had bumper stickers and other markers of territoriality. The experimental question was how long it would take for the driver of the blocked car to honk in frustration.

Szlemko said that drivers of cars with decals, bumper stickers and personalized license plates honked at the offending vehicle nearly two full seconds faster than drivers of cars without any territorial markers.

Ah the joys of modern science.

Posted by rakhier at 08:49 AM | Comments (0)

September 01, 2006

Why Global Warming Does Not Worry Me

Global Warming doesn't worry me.

Let me explain why. Using facts, at least as we understand them.

It is a fact, well accepted in the scientific comunity of paleo-climatology that the Earth's average temperature (on land) has been much hotter than the present day average. Not a bit hoter but much hotter. "Our present-day Arctic Ocean is about 10-15°C cooler than it was at the time of the dinosaurs for almost all of the time from about 2 to at least 200 million years ago". It is a well established fact that for most of the last 500 million years there was no ice on our planet's poles. No ice. Antarctica was fully forested as recently as 45 million years ago. Take a look at this chart if you don't believe me.
It is a fact that all the major species of life which we see today were alive and well back through the time when the Earth was "hot".
It is a fact that right now (2006) in the midst of the "hottest years of the last 100 years" that we are still no where close to even the average Earth temperature of the last 500 million years. The Earth has been "cold" for the last two million years, frequently colder than now but still, "cold". It has yet to warm up to the average temperature of the planet from even five million years ago.
There have been many (and by many I mean more 15) different periods of glaciation on the Earth over the last 2 million years. Glaciers, by and large, destroy life. It is a fact that almost no life can live on solid ice. Glaciers and glaciation are, by my definition, bad.
With a rise in average global temperatures there is a rise in the amount of water vapor in the atmosphere (higher temperature = more evaporation from the Earth's oceans). There is a direct connection between the amount of water vapor in the atmosphere and the amount of rainfall. In other words, higher temperatures = more evaporation from the ocean = more rainfall. As you can see from this map showing the world climate of 50 million years ago, there is a lot less desert (arid terrain) than there is today. Desert is complicated so I can't state for a fact that higher temperatures equals less desert but that certainly seems like a reasonable historic assumption (Compare this map from 14 million years ago to today's map).
Life, as we know it, will survive quite well on a hotter Earth. This is a fact. Individual species will be effected, some will go extinct, others will flourish but as a whole, global warming is not a problem for life on this Earth. Species have been going extinct since the begining of life. This is normal. Change is normal.
It is a fact that we do not know why the Earth's average temperature has changed in the past. Clearly we can see the Earth has changed. Clearly it was hotter 50 million years ago and has cooled fairly steadily since then. No one knows why the Earth has been in a glacial period in the last two million years. No rational person argues that the temperature fluctuations we see in the past were due to human activity. Is the warming trend we have observed in the last 100 years due to human activity? We don't know. It is possible, even likely, in my opinion but quite clearly, the Earth has warmed up before, many times, without any human activity. I fail to see why this time, it is certainly human activity which is causing the warming while the other times, it wasn't.

Isn't it likely that the same processes which caused warming in the past are at work today? Given that we can't explain prior warming episodes, it seems rather unscientific to argue that we do know the cause of this warming trend.
Life for some humans, perhaps many humans, will get harder in the future if the warming trend continues. This is a fact. Humans have built cities next to oceans, which are going to rise as more ice on or near the poles turns to water. Humans have built farms in areas which get rain now, but may get less rain (or too much rain) in the future. Some countries (island nations) may actually be drowned by the ocean. Other regions may become uninhabitable.

Conversly, some areas which are uninhabitable now are going to become habitable with a rise in global temperatures. With changes in rainfall, some areas which are arid now are likely to become farmable in the future.

To all this I say: change is coming. We humans don't live on a static, unchanging world. 5,000 years ago most of Iraq was the best agracultural farmland in the world. Now it isn't. This is just one of thousands of changes that have occured just in the last 5,000 years of human history. Changes happened before then, and changes were going to happen to our world no matter what we did, or didn't do.

Some people seem to think that if we just "left the Earth alone" then the world wouldn't change. This is a delusion. The Earth is a dynamic system, vastly more complex than we understand and subject to forces and processes about which we know little and can predict little.
Some people have argued that the world's major industrial nations need to reduce their "greenhouse gas emissions". The Kyoto Protocol was an attempt to formalize this idea. I have many objections to the Kyoto Protocol but I will list just one: China.

China over the last decade has been growing economically at a rate of above 8% per year. It has the world's largest population and it is burning coal to power its cities and it is burning oil to power its fleet of cars. According to the Economist, China will surpass the U.S. in the production of "greenhouse gases" by the year 2030. China is a major world power, ruled by a small "party" of around six million people. Its government is not subject to the will of the people nor is it subject to international law or world pressure. There is, in my opinion, no chance that China will change its policies from its current policy of "nationalistic self interest". China has followed this policy for the last 2,000 years, it won't change in my lifetime. Unless it can be shown that it is in China's self interest to reduce "greenhouse gas" emissions, it won't happen.

No power on Earth can (or will) control China. Either the Chinese will do it themselves, or it won't be done. Given the massive growth in China's emissions, no possible reduction by other industrial nations can make up for the increase coming out of China. So, the chances that the world will, as a whole, stablize the global emissions of "greenhouse gases" are, in my opinion, just about zero. Baring a radical change in the Chinese goverment (or energy production technology), Chinese (and by extension the world's) emissions will continue to grow for the next 50 to 100 years.

The bottom line is: there will be more carbon-dioxide in the Earth's atmosphere in the future. Period.

Based on the above analysis, I do not view this as a disaster. The Earth has been much warmer before now and life was fine. Humans may have problems and we may have to spend a great deal of money solving those problems but, change was invevitable. Perhaps colder, perhaps hotter, but it wasn't going to stay the same. Look at the temperature graphs. They do not show long periods of no change.

I do not see the increase in global average temperature as remotely threatening human life on Earth. I futher think that if human civilization is going to be destroyed, the odds of the destruction resulting from the stress caused by global warming is low. Human civilization is under threat from many directions, spending hundreds of billions of dollars on trying to prevent the Earth from warming up a few degrees is, in my analysis, a giant waste of resources.

This is why I'm not worried about global warming.

Posted by rakhier at 02:13 PM | Comments (0)

May 06, 2006

Why is Soil Brown?

I learned a great deal from this answer. The Q&A is found on the SciAm web site.

Why is most ground brown? Steven Allison, an ecology researcher at the University of California, Irvine, provides this answer.

Many soils are brown in color because they contain large amounts of carbon. In particular, carbon-containing polymers called humic compounds absorb most visible wavelengths of light and give soils a dark brown appearance. Often the majority of soil carbon is present as humic compounds, which means they have a large impact on soil chemistry and fertility

What is most surprising about humic compounds, and indeed all soil carbon, is that there is so much of it. Many species of bacteria, fungi and other invertebrates decompose and consume soil carbon as a food source, yet soils hold somewhere between 1,500 and 2,300 petagrams--or as much as two quintillion grams--of carbon globally; this is two to three times the amount of carbon present in all the plants in the world. A large fraction of this soil carbon is ancient--hundreds to thousands of years old--meaning that it has escaped conversion into carbon dioxide by soil decomposers. These escape mechanisms are ultimately what cause the ground to be brown.

Ecologists have long wondered how plants avoid being eaten by herbivores, that is: Why is the world green? Yet few have asked the analogous question about carbon in the soil. It turns out that chemistry explains why herbivores don’t eat some plants and why so much soil carbon escapes decomposition. The chemical challenges are especially acute for decomposers, because so many of them are microorganisms that cannot take up their food directly. Instead, they secrete enzymes to break down organic compounds into small molecules that they can take up. If these enzymes are intercepted or destroyed in the soil environment, then decomposition slows down.

Even when microbial enzymes persist in the soil, they are not capable of degrading all forms of soil carbon. Soils represent the final destination for carbon fixed by plants during photosynthesis. After plants die, decomposers consume the dead plant carbon and assimilate some of it while respiring the remainder as carbon dioxide. When the decomposers die, their assimilated carbon can be consumed and respired by other decomposers. Over time, this recycling process returns most of the carbon to the atmosphere as carbon dioxide, but a small fraction is transformed into chemically resistant forms that accumulate in the soil. These compounds no longer resemble plant material at all but rather are the chemical leftovers of decomposition. Many are humic compounds and their complicated chemical structures prevent enzymes from efficiently attacking them. Along with chemically similar compounds called polyphenols, humic compounds act as a true dead end for soil carbon because they can also bind to and inactivate the very enzymes that could potentially degrade them.

Other environmental factors also diminish the efficiency of microbial enzymes. If soils are nitrogen poor, then microbes may not have the nutrients available to build enzymes. Some enzymes require oxygen as a substrate, thus anoxic conditions often cause soil carbon to accumulate; this occurs in many bogs and peatlands because of their waterlogged soils. Also, many soil minerals adsorb enzymes and soil carbon, including humic compounds. This process blocks the enzymes from achieving the correct orientation to attack their carbon substrates.

Not all ground is brown, of course: soil minerals, when not covered in carbon compounds, often give soils a red, yellow or gray hue. In some ecosystems, we see the colors of the underlying minerals instead of brown ground, because carbon inputs to the soil are low due to erosion or a lack of plant growth, as in the iron-rich red soils of certain deserts. Yet, ultimately, the majority of ground is brown because the majority of soils remain carbon-rich.

Answer posted on May 01, 2006

I must say, I never considered why all the carbon in the soil wasn't turned into carbon dioxide. Also, the reason why the soil of Hawaii is so red is because it is such young soil and still shows the minerals.

Posted by rakhier at 01:39 PM | Comments (0)

December 01, 2005

A Vaccine against Nicotine

This is quite surprising. FuturePundit has a story about a vaccine trial which shows promise in reducing people's desire for nicotine.

Dorothy Hatsukami, Ph.D., director of the University of Minnesota Cancer Center's Transdisciplinary Tobacco Use Research Center (TTURC), is the lead author on this study. The 38-week study included 68 active smokers who were randomly assigned to receive one of three different doses of the vaccine or a placebo. The findings are published in the current issue of the journal Clinical Pharmacology and Therapeutics.

"The vaccine works by producing antibodies that specifically bind to nicotine and thereby prevent much of the nicotine from entering the brain," Hatsukami said. "This process potentially reduces the pleasurable effects from smoking and reduces the addiction to nicotine."

This would be a wonderful development as smoking is a terrible habit and nicotine is a utterly worthless drug.

Posted by rakhier at 02:23 PM | Comments (0)

Twins have a lower than expected IQ...

A very thorough study has shown that twins have a lower than expected IQ when you account for lots of the other factors:

Researchers studied 9,832 single-born children and 236 twins born in Aberdeen, Scotland between 1950 and 1956, using a previous child development survey as a base. They also gathered further information on mother's age at delivery, birth weight, at what stage of the child's gestation they were born, their father's occupational social class, and information on other siblings.

They found that at age seven, the average IQ score for twins was 5.3 points lower than that for single-born children of the same family, and 6.0 points lower at age nine.

The study also showed that taking into account factors such as the child's sex, mother's age, and number of older siblings made little difference to the IQ gap.

Despite advances in recent years in obstetric practice and neonatal care, the authors argue that the likely explanation is because some twins have a shorter length of time in the womb than other children and are prone to impaired fetal growth.

As FuturePundit says, this result makes sense. He also says something that I've long belived "I also wonder if the use of drugs to prolong pregnancy could raise average IQ. If pregnancies could be stretched out a few extra weeks would the resulting babies grow up to be smarter?"

Sadly, the number of twins being born is going up, due to several factors, amoung them: increasing age of having a first child and use of fertility drugs by older women. I also think twins are real nightmare to raise, the parents are constantly frazzeled in the first year or two of the twins life.

Posted by rakhier at 02:18 PM | Comments (0)

November 29, 2005

News on the Cancer Front...

We have learned something new about cancer: the Immune System ought to be fighting it but doesn't. From the New York Times science section:

The old idea, Dr. Pardoll said, was that cancers arise every day but the immune system destroys them. Anything that weakens the immune system - stress, for example - could hinder this surveillance. The result would be a cancer that grows large enough to resist the body's effort to heal itself. "Nobody believes that anymore," Dr. Pardoll said.

Dr. Fred Applebaum, director of the clinical research division at the Fred Hutchinson Center, said that he and most other cancer experts believed the theory. But then they looked at mice that were genetically engineered to have no functioning immune systems. "They really don't show a huge increase in the incidence of cancer," Dr. Applebaum said.

For example, researchers looked at people whose immune systems were suppressed because they were taking drugs to prevent rejection of a transplanted organ or because they had AIDS.

"There are small increases in certain types of cancers," Dr. Applebaum said, but those tend to be cancers that are associated with infections - like stomach cancer, associated with ulcer-causing Helicobacter pylori; liver cancer, associated with hepatitis B and hepatitis C infections; Kaposi's sarcoma, associated with herpesvirus 8 infections; lymphoma, associated with Epstein-Barr virus; and cervical cancer, associated with human papillomavirus. "The common types of cancer, the ones that cause the huge burden of suffering in humans, really aren't increased," he said.

What happens to the immune system in cancer patients? It should be protecting them. Every tissue of the body is larded with white blood cells, and cancers are no exception. In fact, Dr. Pardoll said, in some tumors, including melanomas and kidney cancers, white blood cells make up 50 percent of the cancer's weight.

And cancer cells are clearly foreign tissue. Their surfaces are studded with proteins that look very different from the proteins on normal cells. The T cells of the immune system, which should start the attack, are perfectly capable of recognizing the foreignness of the cancer cells. But for some reason, they do not.

Why not? The answer, Dr. Pardoll, Dr. Allison and others have found, is that proteins on the surface of cancer cells turn off the immune system's attack. At the same time, the tumor is excreting molecules that recruit immune system cells to help it metastasize, spreading through tissues and organs.

"We knew very little about what regulated these immune responses to tumors until very recently," Dr. Pardoll said. "We now are in a position to totally rewrite the book."

One immediate consequence of this line of thinking is a new idea for treatment: scientists could seal off the cancer cells' proteins that block the immune system and enable white blood cells to kill the tumor. Or they could make the immune system more aggressive. To do that, they can block a molecule on the surface of T cells, CTLA-4, that tends to dampen the immune response.

The first strategy is only starting to be investigated because the discoveries are so new. But the second strategy is well under way.

In mice, said James Allison, chairman of the immunology program at Sloan-Kettering, some cancers went away after just a single injection of an antibody to CTLA-4. Other cancers required a vaccine, as well, to bolster the newly unleashed immune attack. But then, Dr. Allison found, even the most intractable tumors in mice were destroyed.

Dr. Allison licensed the technique to Bristol-Myers Squibb, which is working with Medarex to see if the method will work in humans.

This is huge news. The immune system should be killing cancer cells but it doesn't. Mice without functioning immune systems don't get cancer at a higher rate than normal mice. Minor tweaks to the immune system MIGHT get the white blood cells kill cancer cells. Wow.

Posted by rakhier at 08:08 PM | Comments (0)

Gingseng Seems to Help Fight the Common Cold...

This news story made some waves.

The study shows that patients taking ginseng during the four-month winter period experienced fewer colds, and those that did develop one experienced a less-intense version of the virus.

In the study, researchers, from the University of Alberta in Canada, administered either a common ginseng extract or placebo to a study group of 278 patients. Each patient possessed a clean bill of health yet admitted to having a susceptibility to colds, as they experienced at least two of them during last winter.

Sixty-four percent of the placebo group and 55 percent of the ginseng group contracted colds over the the study period. 23 percent of the placebo group experienced two or more colds during the winter, while only 10 percent of ginseng patients suffered similar circumstances.

On average, the length of cold for the ginseng group was 8.7 days, compared to 11.1 in placebo subjects.

This is a good scientific study (double-blind) and it should significant positive results. Combine this with the long-standing belief and use of gingseng in Chinese medicine and I think we have a winner. Certainly, gingseng won't hurt you, unlike other herbal medicines I can think of.

I went out and bought some the next day.

Posted by rakhier at 07:59 PM | Comments (0)

November 14, 2005

Getting cold gives you a cold!

A recently published study by Cardiff's Common Cold Center (in Wales) shows that getting cold does make it far more likely that you will "come down with a cold". This notion had been dismissed as impossible for the last 20 years but Cardiff researchers have proved it.

The other 90 in tests during the common cold "season" sat with their feet in an empty bowl.

During the next four or five days, almost a third (29 percent) of the chilled volunteers developed cold symptoms -- compared to just 9 percent in the control group, the scientists said.

Why might this be true?

If they become chilled this causes a pronounced constriction of the blood vessels in the nose and shuts off the warm blood that supplies the white cells that fight infection.

The reduced defences in the nose allow the virus to get stronger and common cold symptoms develop.

Although the chilled subject believes they have 'caught a cold' what has in fact happened is that the dormant infection has taken hold.

Like many people, this study confirms long-held beliefs. Its nice to see that the belief is true.

Posted by rakhier at 09:14 AM | Comments (0)

October 03, 2005

Peruvian Ants Kill All But One Type of Tree...

This small article from the New York Times talks about an unusual behavior found in ant colonies in Peru. The ants have been shown to kill all but one type of tree around their colony.

Many other ant species use this chemical to kill off parasites or attackers. But M. schumanni, Ms. Frederickson said, is the first known to use the acid as an herbicide.

"They actually attack plants in the same way that other ants in this family would attack another insect," she said. "They grab the tissue with their mandibles, make a hole in it, stick their abdomen in and release a couple of drops."

Her experiments, described in the journal Nature, show that the saplings lose most of their leaves within five days and die within several weeks. Ms. Frederickson said it appeared that the ants used chemical cues to determine which species to attack.

The behavior benefits both the D. hirsuta and M. schumanni. With no competing species, the trees get more light, nutrients and water. And as more of the trees grow and the devil's garden expands, the ants get more places to live.

M. schumanni colonies can be extremely large, with a million or more workers and as many as 15,000 queens. Colonies can exist for centuries, as Ms. Frederickson discovered when she analyzed the growth rates of the 26 plots in her study. The largest one, with 351 trees, had been tended by the same ant colony for more than 800 years.

So, not only do some ants farm (leafcutter ants farm a fungus and have been doing so for at least 100 million years) but some ants quite deliberately change the vegitation in their area to better suit their life.

Posted by rakhier at 12:41 PM | Comments (0)

Food Doesn't Effect Cancer...

This very large article from the New York Times talks about recent serious studies which show that what you eat does not seem to effect your chances of getting cancer.

Beta carotene was of special interest. People who ate lots of fruits and vegetables had more beta carotene in their blood, and the more beta carotene in the blood, the lower the cancer risk.

But a four-year study that asked whether beta carotene, with or without vitamins C and E, could protect against colon polyps, from which most colon cancers start, found no effect. People who took either beta carotene, vitamin C, vitamin E or all three had virtually identical rates of new polyps compared to participants taking dummy pills.

Another study, of 22,000 doctors randomly assigned to take beta carotene or a placebo, looked for an effect on any and all cancers. It found nothing. Two more, involving current and former smokers, found that those taking beta carotene actually had slightly higher lung cancer rates than those taking placebos...

The fiber hypothesis had enormous appeal. Carcinogens from food can end up in stool. But when people eat a lot of fiber, their stool is bulkier and so carcinogens would be diluted. Bulkier stool is also excreted faster, reducing the time that the colon is in contact with cancer-causing substances.

Fiber also binds bile acids in the bowel, substances that can damage the colon and, possibly, result in cancer. And the intestines metabolize fiber into short-chain fatty acids that seemed protective against cancer.

Adding to the case for fiber was the fact that when researchers fed rodents carcinogens, the animals were protected against colon cancer if they also ate a lot of fiber.

Based on these indications, the cancer institute financed two studies on high-fiber diets and colon polyps. In one, 2,079 people were randomly assigned to eat low-fat high-fiber diets or to follow their usual diets. In the other, 1,429 people were assigned to eat high-fiber bran cereals or wheat bran fiber or to eat cereal and bars that looked and tasted the same but that were low on fiber. Fiber, the studies found, had no effect.

"We had high expectations and good rationale," Dr. Schatzkin said. But, he said, "we got absolutely null results."

These new studies which show null results are good studies. Randomized. Carefully followed. People don't know what they are eating. And the results have been uniformly negative.

This is big news. It throws doubt on all the talk we have been hearing for the last 20 years about how a good diet was going to substantially reduce our chances of getting various types of cancer. At this point we are now pretty much back where we started. Strangely high levels of some cancers in the U.S. vs. some other countries and no clue why.

Posted by rakhier at 12:28 PM | Comments (0)

August 30, 2005

Harder than Diamond

A new version of carbon has been created which is harder than diamond.

The hardness of a material is measured by its isothermal bulk modulus. Aggregated diamond nanorods have a modulus of 491 gigapascals (GPa), compared with 442 GPa for conventional diamond. Dubrovinskaia and two of her co-workers - Leonid Dubrovinky and Falko Langenhorst - have patented the process used to make the new material.

Diamond derives its hardness from the fact that each carbon atom is connected to four other atoms by strong covalent bonds. The new material is different in that it is made of tiny interlocking diamond rods. Each rod is a crystal that has a diameter of between 5 and 20 nanometres and a length of about 1 micron.

The group created the ADNRs by compressing the carbon-60 molecules to 20 GPa, which is nearly 200 times atmospheric pressure, while simultaneously heating to 2500 Kelvin. "The synthesis was possible due to a unique 5000-tonne multianvil press at Bayerisches Geoinstitut in Bayreuth that is capable of reaching pressures of 25 GPa and temperatures of 2700 K at the same time," Dubrovinskaia told PhysicsWeb.

The Bayreuth team measured the properties of the samples with a diamond anvil cell at the European Synchrotron Radiation Facility at Grenoble in France. These measurements indicated that ADNRs are about 0.3% denser than diamond, and that the new material has the lowest compressibility of any known material.

In addition to working out why the new material is so hard, the Bayreuth team also hope to exploit its industrial potential. "We have developed a concept for innovative technology to produce the novel material in industrial-scale quantities and now we are looking for partners in order to realize our ideas," said Dubrovinskaia.

While nice, I doubt anything really important will come from this. Its not that much better than normal diamond.

Posted by rakhier at 08:46 AM | Comments (0)

August 19, 2005

New super-fast way to make carbon nano-tube material..

The ribbons are transparent, flexible, and conduct electricity. Weight for weight, they are stronger than steel sheets, yet a square kilometre of the material would weigh only 30 kilograms. "This is basically a new material," says Baughman.

Article at News@Nature.com

Posted by rakhier at 02:56 PM | Comments (0)

July 14, 2005

Research about why women might not be naturally monogamous...

I think this article by FuturePundit speaks for itself. The implications are obvious. BTW: one study done in one part of an ordinary town in Britain found fully 25% of the children in the population tested were genetically NOT related to the man listed who was listed on the child's birth certificate.

Posted by rakhier at 08:11 PM | Comments (0)

May 04, 2005

Say Goodbye to Genetic Privacy...

Give up on the idea that your genetic sequence will remain private information 30 years from now. So argues FuturePundit in this essay.

Consider that identity theft is a rapidly growing problem. Most cases of identity theft are discovered when someone gets a bill for a product or service they didn't buy. But identity theft for the purpose of getting DNA tested would necessarily eventually result in the victim ever benig notified that someone else temporarily masqueraded as them. Why? Because when the DNA sample is submitted it would not have to be submitted with the real name of the person the DNA sample was stolen from.

As he argues, there is no plasible regulatory method for keeping your DNA private. Better hope you have good genes in the future because prospective mates ARE going to check you out before committing to having a child with you.

Posted by rakhier at 11:05 AM | Comments (0)

Where does Natural Gas Come From? Archaic Bacteria!

This is going to shake up our understanding of life on Earth (again). FuturePundit has an essay in which he describes the results of research into bacteria which eats oil and turns it into methane.

It has been a mystery as to where oil fields come from. The old explaination that it was organic material once on the Earth's surface and then "subducted" and compressed and heated and turned to oil only explained a small amount of the world's oil fields. Where did the rest of the oil come from? Leaving that mystery aside, I have never heard an explaination for why natural gas was almost always found at the same time as oil deposits.

But now we know at least part of the answer: there are methane-generating microorganisms in at least one oil field.

Luca scientists have also begun to isolate and identify particular members of the Monument Butte microbial consortium. Through partial DNA sequence analysis, the company has identified Clostridia and Thermatoga as two of the key members of this consortium. Clostridia form a broad genus of bacteria known for their diverse metabolic pathways. Clostridia frequently thrive in anaerobic environments and many species are known for their heat tolerance. Thermatoga microorganisms are known to play a role in the anaerobic oxidation of hydrocarbons to alcohols, organic acids and carbon dioxide. Thermatoga also thrive in high temperature environments, such as those found in sub-surface oil wells.

This is significant news. Could previously unknown microorganisms be responsible for most of the world's natural gas? Imagine these creatures, eating oil, expelling methane as a waste product. These things could be found throughout the Earth's crust.

Because oil is a liquid, it is likely to be an easier substrate for the microbial consortia to contact, biodegrade, and convert to methane compared to solid-phase substrates such as coal and the kerogen in shale. Biodegradation is carried out by the consortia, and it has been shown that a mixed group of microorganisms is more effective at biodegrading organic compounds than any of the component strains acting alone. These microorganisms utilize the hydrocarbons as both a carbon and energy source, and the process most likely takes place at the oil/water interface (13). The enzymatic diversity within these microorganisms required to carry out the myriad of metabolic steps involved in methanogenesis is extensive. The ability to influence and control these microbial reactions in situ has major economic implications.

It is now known that there is a lot of living things far below the surface of the Earth.

Bottom line: introducing colonies of these microbes into depleted oil fields could transform useless oil fields into the long term sources of natural gas.

Posted by rakhier at 10:51 AM | Comments (0)

The End of the MRI Scan - Hello HUTT

FuturePundit has an article which talks about the development of the successor to the MRI Scanner: the HUTT - High-resolution Ultrasonic Transmission Tomography. HUTT is much better than MRI, it is essentially a super UltraSound scanner. No radiation. No giant super-conductors. Just sound waves that travel through the body and then are analyzed by computer programs. Read about it here.

Posted by rakhier at 10:48 AM | Comments (0)

March 29, 2005

A new twist in eco-systems: introducing a preditor kills the grass...

This is from the NYTimes Science section today. It is new to me, a case where the ecosystem is so fragile that introduction of a bird eating carnivor is able to destroy the grass on an island.

---

Foxes may not graze, but a new scientific study describes how their arrival on Aleutian islands destroyed rich grasslands and left only sparse tundra. The authors of the report, which appeared in Science last week, say this transformation shows how an entire ecosystem may go into a tailspin if just one new top carnivore shows up.

The inadvertent experiment began in the late 1700's and continued into the early 20th century as fur traders looking to expand their supply released nonnative arctic foxes and, in some cases, red foxes on more than 400 Alaskan islands. Some died out, but many populations survived.

The new habitats included much of the Aleutian archipelago that curves west toward Asia. Except for the occasional polar bear rafting in on winter ice, the windswept islands had few predators before.

The botanical impoverishment that has resulted is the reverse of what usually happens when a new meat-eater comes along.

"Traditionally, the predator eats the grazer; the grazer no longer eats the green stuff; and the habitat gets more green," said Dr. Donald Croll, a professor of biology at the University of California, Santa Cruz, and the lead author of the report.

An example of the more usual routine is in Yellowstone National Park, where returning wolves, preying on sapling-browsing elk and confining the wary survivors to areas where they can see wolves coming, have touched off a resurgence of willow, aspen and other vegetation.

The contrary effect in the Aleutians, once sorted out, has a simple explanation.

The grazers on these islands were grass- and seed-eating Aleutian geese, which are smaller cousins of Canada geese. The foxes drove the geese near extinction, which would have been a boon for grasses except that the foxes also feasted on the eggs and hatchlings of puffins, auklets and other ocean-feeding seabirds they found brooding in vast numbers almost everywhere.

Some islands lost almost all birds except for cliff-nesting species. And as ground-nesting birds faded, so did their nutrient-rich excrement, or guano, which had been a natural fertilizer.

The research team concluded that islands with no foxes received an average 361.9 grams per square meter yearly. Fox-infested islands get just 5.7 grams per square meter of guano per year.

"You ever smell one of those rookeries?" Dr. Croll asked. "That is the odor of ammonia, like in fertilizer. Even the wind scatters it around." Without the regular subsidy of nitrogen and potassium-rich nutrients winged in from the sea, grasses lost their competitive edge over tundra shrubs and herbaceous plants...

Posted by rakhier at 04:50 PM | Comments (0)

March 02, 2005

A theoretical invisibility device...

This article says that two scientists Mr. Alù and Mr. Engheta of the University of Pennsylvania have come up with a theoretical method of making an object invisible. ---

Plasmons are waves of electron density, caused when the electrons on the surface of a metallic material move in rhythm. The researchers say that a shell of plasmonic material will scatter light negligibly if the light's frequency is close to the resonant frequency of the plasmons. The scattering from the shell effectively cancels out the scattering from the object.

OK, the current problems: 1) They haven't made this yet. 2) It only works on a narrow band of light (such as invisible to green light but visible on red light) 3) only tiny objects can be hidden from visible light through this method.

Still, what was once only a theory can sometimes become very powerful reality (like lasers).

Posted by rakhier at 12:06 PM | Comments (0)