Wednesday, February 24, 2010

And Now...Another Metaphor

The Brain's Dark Energy

Brain regions active when our minds wander may hold a key to understanding neurological disorders and even consciousness itself

By Marcus E. Raichle

Imagine you are almost dozing in a lounge chair outside, with a magazine on your lap. Suddenly, a fly lands on your arm. You grab the magazine and swat at the insect. What was going on in your brain after the fly landed? And what was going on just before? Many neuroscientists have long assumed that much of the neural activity inside your head when at rest matches your subdued, somnolent mood. In this view, the activity in the resting brain represents nothing more than random noise, akin to the snowy pattern on the television screen when a station is not broadcasting. Then, when the fly alights on your forearm, the brain focuses on the conscious task of squashing the bug. But recent analysis produced by neuroimaging technologies has revealed something quite remarkable: a great deal of meaningful activity is occurring in the brain when a person is sitting back and doing nothing at all.

It turns out that when your mind is at rest—when you are daydreaming quietly in a chair, say, asleep in a bed or anesthetized for surgery—dispersed brain areas are chattering away to one another. And the energy consumed by this ever active messaging, known as the brain’s default mode, is about 20 times that used by the brain when it responds consciously to a pesky fly or another outside stimulus. Indeed, most things we do consciously, be it sitting down to eat dinner or making a speech, mark a departure from the baseline activity of the brain default mode.

My Comment: This is only part of the entire article, but the key is that the author is using a computer science metaphor combined with another metaphor from physics—dark energy (a metaphor disguised as a noun) to describe our consciousness. And both of these are light years ahead of conventional psychology when it comes to gathering information about why we are the way we are, and the possibilities of how we can be. I mean, if we get the right operating system in our minds, second minds (see previous post), hearts, and souls…conceivable high levels of goodness here.

But of Course!

Think Twice: How the Gut's "Second Brain" Influences Mood and Well-Being

The emerging and surprising view of how the enteric nervous system in our bellies goes far beyond just processing the food we eat

By Adam Hadhazy

As Olympians go for the gold in Vancouver, even the steeliest are likely to experience that familiar feeling of "butterflies" in the stomach. Underlying this sensation is an often-overlooked network of neurons lining our guts that is so extensive some scientists have nicknamed it our "second brain".

A deeper understanding of this mass of neural tissue, filled with important neurotransmitters, is revealing that it does much more than merely handle digestion or inflict the occasional nervous pang. The little brain in our innards, in connection with the big one in our skulls, partly determines our mental state and plays key roles in certain diseases throughout the body.

Although its influence is far-reaching, the second brain is not the seat of any conscious thoughts or decision-making.

"The second brain doesn't help with the great thought processes…religion, philosophy and poetry is left to the brain in the head," says Michael Gershon, chairman of the Department of Anatomy and Cell Biology at New York–Presbyterian Hospital/Columbia University Medical Center, an expert in the nascent field of neurogastroenterology and author of the 1998 book The Second Brain (HarperCollins).

Technically known as the enteric nervous system, the second brain consists of sheaths of neurons embedded in the walls of the long tube of our gut, or alimentary canal, which measures about nine meters end to end from the esophagus to the anus. The second brain contains some 100 million neurons, more than in either the spinal cord or the peripheral nervous system, Gershon says.

This multitude of neurons in the enteric nervous system enables us to "feel" the inner world of our gut and its contents. Much of this neural firepower comes to bear in the elaborate daily grind of digestion. Breaking down food, absorbing nutrients, and expelling of waste requires chemical processing, mechanical mixing and rhythmic muscle contractions that move everything on down the line.

Thus equipped with its own reflexes and senses, the second brain can control gut behavior independently of the brain, Gershon says. We likely evolved this intricate web of nerves to perform digestion and excretion "on site," rather than remotely from our brains through the middleman of the spinal cord. "The brain in the head doesn't need to get its hands dirty with the messy business of digestion, which is delegated to the brain in the gut," Gershon says. He and other researchers explain, however, that the second brain's complexity likely cannot be interpreted through this process alone.

"The system is way too complicated to have evolved only to make sure things move out of your colon," says Emeran Mayer, professor of physiology, psychiatry and biobehavioral sciences at the David Geffen School of Medicine at the University of California, Los Angeles (U.C.L.A.). For example, scientists were shocked to learn that about 90 percent of the fibers in the primary visceral nerve, the vagus, carry information from the gut to the brain and not the other way around. "Some of that info is decidedly unpleasant," Gershon says.

The second brain informs our state of mind in other more obscure ways, as well. "A big part of our emotions are probably influenced by the nerves in our gut," Mayer says. Butterflies in the stomach—signaling in the gut as part of our physiological stress response, Gershon says—is but one example. Although gastrointestinal (GI) turmoil can sour one's moods, everyday emotional well-being may rely on messages from the brain below to the brain above. For example, electrical stimulation of the vagus nerve—a useful treatment for depression—may mimic these signals, Gershon says.

Given the two brains' commonalities, other depression treatments that target the mind can unintentionally impact the gut. The enteric nervous system uses more than 30 neurotransmitters, just like the brain, and in fact 95 percent of the body's serotonin is found in the bowels. Because antidepressant medications called selective serotonin reuptake inhibitors (SSRIs) increase serotonin levels, it's little wonder that meds meant to cause chemical changes in the mind often provoke GI issues as a side effect. Irritable bowel syndrome—which afflicts more than two million Americans—also arises in part from too much serotonin in our entrails, and could perhaps be regarded as a "mental illness" of the second brain.

Scientists are learning that the serotonin made by the enteric nervous system might also play a role in more surprising diseases: In a new Nature Medicine study published online February 7, a drug that inhibited the release of serotonin from the gut counteracted the bone-deteriorating disease osteoporosis in postmenopausal rodents. (Scientific American is part of Nature Publishing Group.) "It was totally unexpected that the gut would regulate bone mass to the extent that one could use this regulation to cure—at least in rodents—osteoporosis," says Gerard Karsenty, lead author of the study and chair of the Department of Genetics and Development at Columbia University Medical Center.

Serotonin seeping from the second brain might even play some part in autism, the developmental disorder often first noticed in early childhood. Gershon has discovered that the same genes involved in synapse formation between neurons in the brain are involved in the alimentary synapse formation. "If these genes are affected in autism," he says, "it could explain why so many kids with autism have GI motor abnormalities" in addition to elevated levels of gut-produced serotonin in their blood.

Down the road, the blossoming field of neurogastroenterology will likely offer some new insight into the workings of the second brain—and its impact on the body and mind. "We have never systematically looked at [the enteric nervous system] in relating lesions in it to diseases like they have for the" central nervous system, Gershon says. One day, perhaps there will be well-known connections between diseases and lesions in the gut's nervous system as some in the brain and spinal cord today indicate multiple sclerosis.

Cutting-edge research is currently investigating how the second brain mediates the body's immune response; after all, at least 70 percent of our immune system is aimed at the gut to expel and kill foreign invaders.

U.C.L.A.'s Mayer is doing work on how the trillions of bacteria in the gut "communicate" with enteric nervous system cells (which they greatly outnumber). His work with the gut's nervous system has led him to think that in coming years psychiatry will need to expand to treat the second brain in addition to the one atop the shoulders.

So for those physically skilled and mentally strong enough to compete in the Olympic Games—as well as those watching at home—it may well behoove us all to pay more heed to our so-called "gut feelings" in the future.

My Comment: 1) And now we have a greater understanding why the Buddha’s an extra large—that’s wisdom in his belly. (Still, I’m sure he still wishes he could fit into his Levi's with the 32 waist. 2) We also have a greater understanding why there are laws of Kashrut. Given the fact of the second brain, that's the only circumstance of which I can think where such laws are logical and a matter of common sense. 3) And I suspect that’s how to approach all of the laws of the Torah—continually asking ourselves: under what physical circumstances are these laws a matter of common sense logic? This action, this question, forces us to regularly question our understanding of the universe. Not terribly different than scientists, no?

Tuesday, February 23, 2010

Religious Gold

The Hottest Science Experiment on the Planet

by Calla Cofield

Rocking the thermometer at 4 trillion degrees Celsius, a subatomic soup that might reflect the state of matter shortly after the Big Bang has set a new world record: It's the hottest substance ever created in a lab. The previous record, recorded at Sandia National Lab in 2006, was a balmy 2 billion degrees Celsius. The core of the sun burns at a chill 15 million degrees.

The uber-hot brew is created at Brookhaven National Laboratory on Long Island. The lab's Relativistic Heavy Ion Collider, RHIC, accelerates gold particles to nearly the speed of light before slamming them together to see what they're made of. When the energy of the colliding gold particles is transferred into heat, the temperature soars. Scientists with the Pioneering High Energy Nuclear Interaction eXperiment, PHENIX, who took the temperature measurement, announced a value of 4 trillion, but that's only an average over the lifetime of the substance. At its hottest stage, the infusion may reach 7 trillion degrees Celsius.

"Matter as we know it shouldn't exist at that temperature," says PHENIX Spokesperson Barbara Jacak. And from what they can tell, it doesn't really. The protons and neutrons making up the gold nuclei appear to melt in the intense heat, and leave behind porridge made of the subatomic particles quarks and gluons. Jacak describes the resulting substance as "a liquid-like plasma."

But those words can't really describe the nature of the soupy mess. Nothing can, yet. Particle physicists, cosmologists, and even string theorists are all trying to understand why quarks and gluons, the building blocks of protons and neutrons (which in turn build atoms), behave this way at such high temperatures. Why doesn't the mixture turn into a gas, like water turns to steam at 100 degrees Celsius? How hot would it have to be to vaporize? And if the universe was filled with this liquid goop shortly after the Big Bang, how did it eventually turn into stars, planets, and people?

"We get giant discussions and even some vociferous arguments," says Jacak. "The big question for us is what is going on inside [this substance] and how does it work. On the experimental side we're trying to measure its properties, and one of the first properties you could measure is its temperature."

It sounds simple enough, but PHENIX scientists have been working on this task since the construction of the experiment ten years ago. Taking the temperature of a subatomic plasma that lives in the wreckage of a gold particle collision turns out to be extremely difficult (which is why Jacak says it's possible that other experiments have created even hotter substances, but might have no way to measure them).

Potters know that in the belly of a kiln, a piece of clay will change color as it heats up: First it's a warm red, then a brilliant yellow, and finally a blinding white. It's the photons coming off the clay that reveal the temperature, and PHENIX scientists relied on the same principle to measure the temperature of the plasma. The problem is, those photons (which are too high-energy to be seen by human eyes) are lost in the shower of photons created by the gold particle collision. The task was not so much like pulling a needle out of a haystack as it is like finding a single non-descript piece of hay in the entire barn. PHENIX's breakthrough analysis not only represents a new world record, but new possibilities for understanding the universe.

Long Island residents might be wondering how PHENIX doesn't burn a hole in the Earth with their flaming concoction, or if the group could harness the heat to run a generator. But the substance only exists for one trillionth of a trillionth of a second, and is smaller than a single atom. Nonetheless, trying to conceive of just how hot that tiny drizzle of particle goulash gets is enough to fry your brain.

My Comment: It’s possible that weird things in Judaism are different than weird things in other religions. I say that it’s possible because I know so little about other religions. Everything could be the same. By weird things I refer to items that don’t seem to fit our understanding. In Judaism such things mean ‘dig here’, ‘X’ marks the spot, knowledge underneath. Many Jews don’t take the weirdness that far, many think it just means that there are some things that can’t be understood. I don’t buy that there are so many things beyond our comprehension. I do buy that some answers may take a long time to find.

For instance, did anyone ever wonder what the Creator of the Universe wants with gold? Living in the Western world, we think it’s a symbol, more than a symbol, it IS wealth. But what does Gd want with wealth? Makes no sense. Until this experiment. Gold is related to high energy situations. In this case we can see it from a collision. We cannot see all of the energy around us, and whether we live in a low energy world or high energy world. And we’re not talking about electricity. We are talking about a type of energy, and the levels of which have not yet been discovered. Although, because of the principle of Tikkun Olam it’s a good guess that things aren’t the way they are supposed to be.

Science, though, has made the first connection between why so much gold is mentioned in scriptures. Energy, high energy.

This is simply a hypothesis. But it’s better than the dominant conclusion many have already reached. Such is a life of inquiry and uncertainty, which, like it or not, is life of the seriously religious. Lots of uncertainty.

Sunday, February 21, 2010

Physics Seminars Turn Religious

04 December 2008 by Amanda Gefter

Must we all choose between believing in a multiverse or believing in God?

WHAT would you rather believe in, God or the multiverse? It sounds like an instance of cosmic apples and oranges, but increasingly we are being told it's a choice we must make. Take the dialogue earlier this year between Richard Dawkins and physicist Steven Weinberg in Austin, Texas. Discussing the fact that the universe appears fine-tuned for our existence, Weinberg told Dawkins: "If you discovered a really impressive fine-tuning... I think you'd really be left with only two explanations: a benevolent designer or a multiverse."

Weinberg went on to clarify that invoking a benevolent designer does not count as a genuine explanation, but I was intrigued by his either/or scenario. Is that really our only choice? Supernatural creator or parallel worlds?

It is according to an article in this month's Discover magazine. "Short of invoking a benevolent creator, many physicists see only one possible explanation," writes journalist Tim Folger. "Our universe may be but one of perhaps infinitely many universes in an inconceivably vast multiverse." Folger quotes cosmologist Bernard Carr: "If you don't want God, you'd better have a multiverse."

There are plenty of reasons to take the multiverse seriously. Three key theories - quantum mechanics, cosmic inflation and string theory - all converge on the idea. But the reason physicists talk about the multiverse as an alternative to God is because it helps explain why the universe is so bio-friendly. From the strength of gravity to the mass of a proton, it's as if the universe were designed just for us. If, however, there are an infinite number of universes - with physical constants that vary from one to the next - our cosy neighbourhood isn't only possible, it's inevitable.

But to suggest that if this theory doesn't pan out our only other option is a supernatural one is to abandon science itself. Not only is it an unfounded leap of logic, it suggests intelligent design offers as valid an explanation as a cosmological theory does, and lends credence to creationists' mistaken claim that the multiverse was invented to serve as science's get-out-of-God-free card. Indeed, Folger's article was immediately referenced on creationist websites, including the Access Research Network, an intelligent-design hub, and Uncommon Descent, the blog of the Seattle-based Discovery Institute's William Dembski.

To make matters worse, physicists are also dragging morality into the picture. In a recent show about the multiverse that aired on the History Channel, physicist Michio Kaku asked: "Why should I obey the law knowing that in some universe if I commit a crime I'm going to get away with it?" The ID community has already tried to draw lines from Darwin to the Holocaust in their attempt to paint rational people as Satan's minions. Are physicists really suggesting that the multiverse gives us licence to commit evil? It's an absurd notion, which moral philosophers have already killed off in other guises.

Pitting the multiverse against religion presents a false dichotomy. Science never boils down to a choice between two alternative explanations. It is always plausible that both are wrong and a third or fourth or fifth will turn out to be correct.

Science never boils down to a straight choice between two explanations.

What might a third option look like here? Physicist John Wheeler once offered a suggestion: maybe we should approach cosmic fine-tuning not as a problem but as a clue. Perhaps it is evidence that we somehow endow the universe with certain features by the mere act of observation. It's an idea that Stephen Hawking has been thinking about, too. Hawking advocates what he calls top-down cosmology, in which observers are creating the universe and its entire history right now. If we in some sense create the universe, it is not surprising that the universe is well suited to us.

That's speculative, but at least it's science.

My Comment:
So the discussion is taking place in scientific forums, with the understanding that if you factor out the Intelligent Design community, you will get some very interesting scientific discussions which also happen to be intelligent religious discussions. Starting with the observation upon which everyone seems to agree, that human consciousness is a force in the universe just like gravity. And then it wouldn’t be long before the question arises, is each individual consciousness like a universe unto itself, or is it part of some greater consciousness, like the leaf is part of a tree?

Wednesday, February 17, 2010

One Picture is Worth an Infinite Amount of Words

Take a look at this.

My Comment: Just go down the list of religions and philosophies with which you're even vaguely familiar. Isn't this picture a cornerstone of each one? In Judaism, saving one person is like saving the entire world. In Chinese philosophy, you can learn everything about the universe and never leave your own backyard. It's endless. Way back when, this was foundation of all common sense. And here it is empirically. Finally. The universe is fractal. Describe it mathematically, poetically, religiously, philosophically--it all gets down to this one picture.

Tuesday, February 16, 2010

Antikythera Mechanism: Scientists Crack Secrets Of 2,000-Year-Old Astronomical Computer

ScienceDaily (July 31, 2008) — Cardiff University experts have led an international team in unravelling the secrets of a 2,000-year-old computer which could transform the way we think about the ancient world.

Professor Mike Edmunds of the School of Physics and Astronomy and mathematician Dr Tony Freeth first heard of the Antikythera Mechanism, a clock-like astronomical calculator dating from the second century BC, several years ago. Now they believe they have cracked the centuries-old mystery of how it actually works.

Remnants of a broken wooden and bronze case containing more than 30 gears was found by divers exploring a shipwreck off the island of Antikythera at the turn of the 20th century. Scientists have been trying to reconstruct it ever since. The new research suggests it is more sophisticated than anyone previously thought.

Detailed work on the gears in the mechanism showed it was able to track astronomical movements with remarkable precision. The calculator was able to follow the movements of the moon and the sun through the Zodiac, predict eclipses and even recreate the irregular orbit of the moon. The team believe it may also have predicted the positions of the planets.

The findings suggest that Greek technology was far more advanced than previously thought. No other civilisation is known to have created anything as complicated for another thousand years.

Professor Edmunds said: "This device is just extraordinary, the only thing of its kind. The design is beautiful, the astronomy is exactly right. The way the mechanics are designed just makes your jaw drop. Whoever has done this has done it extremely carefully."

The team was made up of researchers from Cardiff, the National Archeological Museum of Athens and the Universities of Athens and Thessaloniki, supported by a substantial grant from the Leverhulme Trust. The researchers were greatly aided by Hertfordshire firm X-Tek, who developed powerful X-Ray computer technology to help with the study of corroded fragments of the machine. Computer giant Hewlett-Packard provided imaging technology to enhance the surface details of the machine.

The mechanism is in 70 pieces and stored in precisely controlled conditions in Athens where it cannot be touched. Recreating its workings was a difficult, painstaking process, involving astronomers, mathematicians, computer experts, script analysts and conservation experts.

After unveiling their full findings at a two-day international conference in Athens and in the journal Nature, the researchers are now hoping to create a computer model of how the machine worked, and, in time, a full working replica. It is still uncertain what the ancient Greeks used the mechanism for, or how widespread this technology was.

Professor Edmunds said: "It does raise the question what else were they making at the time. In term of historic and scarcity value, I have to regard this mechanism as being more valuable than the Mona Lisa."

My Comment: Let’s hope this is one more item that will lay to waste the myth that ancient cultures weren’t precise in their thinking, that they believed only in superstition, and that scientific observation , that is, clear understanding of the material world, was beyond them. Let’s also hope that the thought becomes plausible, that in many ways they may have been more advanced than we are today.

Distribution Of Creatures Great And Small Can Be Predicted Mathematically

ScienceDaily (July 19, 2008) — In studying how animals change size as they evolve, biologists have unearthed several interesting patterns. For instance, most species are small, but the largest members of a taxonomic group -- such as the great white shark, the Komodo dragon, or the African elephant -- are often thousands or millions of times bigger than the typical species.

Now for the first time two SFI researchers explain these patterns within an elegant statistical framework.

"The agreement between our model and real-world data is surprisingly close," says SFI Postdoctoral Fellow Aaron Clauset, who, along with SFI Professor Douglas Erwin, presented the findings in a July 18 Science paper.

In Clauset and Erwin's model, descendant species are close in size to their ancestors, but with some amount of random variation. But, this variation is constrained, first by a hard limit on how small a species can become, due to physiological constraints, and second by a soft limit on how large a species can become before becoming extinct. After millions of virtual years of new species evolving and old species becoming extinct, the model reaches an equilibrium in which the tendency of species to grow larger is offset by their tendency to become extinct more quickly.

By using fossil data on extinct mammals from up to 60 million years ago to specify the form of the model, the researchers showed that this evolutionary process accurately reproduces the diversity of 4,000 mammal species from the last 50,000 years.

"The model is remarkably compact, " says Aaron. "It also omits many traditional ideas from evolution and ecology, such as population dynamics or species interactions, yet makes very accurate predictions."

Because species size is fundamentally related to so many other characteristics like metabolism, life span and habitat, the researchers' simple evolutionary model offers support to idea that some aspects of evolutionary and ecological theory can be unified.

My Comment: This is simply thought provoking—the thought being, is mathematics just a way of measuring what is, or a way of determining where an object will be given all of its different momentums—or, and this is cool, does nature follow mathematical patterns as if the math itself is what causes nature to look and behave the way it does? This is particularly interesting in Judaism where the letters of words are also numbers, which means that each word is also an equation. The problem is that we Jews don’t know the mathematical operations between each letter. Lots of room for research there.

Monday, February 15, 2010

Re-engineering the Human Immune System

(Found here.)Swine Flu. Spanish Flu. SARS. Almost every year, it seems, there is a new virus to watch out for. Roughly thirty thousand Americans die annually from a new flu strain — meaning roughly one flu fatality for every two victims of car accidents — and there is always the possibility that we will do battle with a much deadlier strain of flu virus, such as the one (cousin to the current swine flu) that killed 50 million people in 1918.

Currently, our bodies’ responses are, almost literally, catch as can. The immune system has two major components. Innate immunity responds first, but its responses are generic, its repertoire built-in and its memory nonexistent. On its own, it would not be enough. To deal with chronic infection and to develop responses targeted to specific pathogens the body also relies on a second “acquired immune system” that regulates and amplifies the responses of the inbuilt system, but also allows the body to cope with new challenges. Much of its action turns on production of antibodies, each of which is individually tailored to the physical chemistry of a particular alien invader. In the best case, the immune system creates an antibody that is a perfect match to some potential threat, and, more than that, the acquired immune system maintains a memory of that antibody, better preparing the body for future invasions from the same pathogen. Ideally, the antibody in question will bind to — and ultimately neutralize or even kill — the potentially threatening organisms.

Alas, at least for now, the process of manufacturing potent antibodies depends heavily on chance, and a type of lymphocyte known as B cells. In principle, B cells have the capacity to recombine to form a nearly infinite variety of antibodies: roughly 65 different “V regions” in the genome can combine with roughly 25 “D regions” and 6 “J regions,” which further undergo random mutations. In practice, getting the right antibody depends on getting the right combination at the right time. Which combinations emerge at any given moment in any given individual is a function of two things: the repertoire of antibody molecules a given organism has already generated, and a random interplay of combination and mutation that is much like natural selection itself — new B cells that are effective in locking onto enemy pathogens persist and spread; those that do a poor job tend to die off.

Unfortunately, there is no guarantee that this system will work. In any given individual there may be no extant antibody that is sufficiently close. If there is a hole in a given individual’s repertoire, that individual may never develop an adequate antibody. Even if there is an adequate starting point, the immune system still may fail to generate a proper antibody. The most useful mutations may or may not emerge, in part because the whole system is governed by a second type of immune cell known as the T cell. The job of T cells is to recognize small fragments of viral proteins as peptides and then help the B cells produce antibodies. Like B cells, T cells also have a recombinative system, generating billions of different receptors, only a few of which will recognize a given viral antigen. In effect, two separate systems must independently identify the same pathogen in order for the whole thing to work. At its best, the system is remarkably powerful — a single exposure to a pathogen can elicit a protective antibody that lasts a lifetime; people who were exposed to Spanish flu in 1918 still retain relevant antibodies today, 91 years later. (See Resources) But the system can be hit-or-miss. That same Spanish flu claimed 50 million lives, and there is no assurance that any given person will be able to generate the antibodies they need, even if they are vaccinated.

For now, the best way to supplement the body’s own defenses is through vaccines, but vaccines are far from a panacea. Each vaccine must be prepared in advance, few vaccines provide full protection to everybody, and despite popular misconception, even fewer last a lifetime. For example, smallpox vaccinations were lifelong, but tetanus vaccines generally last 5-10 years. There is still no vaccine for HIV infection. And when it comes to bacteria like tuberculosis, current vaccines are almost entirely ineffective. What’s more, the whole process is achingly indirect. Vaccines work by first stimulating B cells and T cells in order to induce production of antibodies. They don’t directly produce the needed antibodies. Rather, they try (not always successfully) to get the body to generate its own antibodies. In turn, stimulation of T cells requires yet another set of cells — called dendritic cells — and the presence of a diverse set of molecules called the major histocompatibility complex, creating still further complexity in generating an immune response.

Our best hope may be to cut out the middleman. Rather than merely hoping that the vaccine will indirectly lead to the antibody an individual needs, imagine if we could genetically engineer these antibodies and make them available as needed. Call it immunity-on-demand.

At first blush, the idea might seem farfetched. But there’s a good chance this system, or something like it, will actually be in place within decades. For starters, as mentioned above, every T cell and B cell expresses a unique receptor that recognizes a very small piece of a foreign structure from viruses or bacteria, such as proteins. Advances in recent genetic technology have made it possible to reprogram B cells, directly or through stem cells, to produce antibodies against parts of viral or bacterial proteins. Similarly, a new clonal army of T cells that are genetically engineered to recognize parts of a virus or bacteria would help the B cells produce potent antibodies against soft spots of these viruses and other pathogens that would otherwise neutralize or kill them.

Already scientists at Caltech, headed by Nobel laureate David Baltimore, have engineered stem cells that can be programmed into B cells, which produce potent antibodies against HIV. Meanwhile, cancer researcher Steven Rosenberg at NIH has been engineering clonal T cells capable of recognizing tumors and transferring these cells to patients with a skin cancer called melanoma. His work has shown promising results in clinical trials. Together, these results could lay the groundwork for a new future, in which relevant antibodies and T cell receptors are directly downloaded, rather than indirectly induced.

Of course, many challenges remain. The first is to be able to better understand the pathogens themselves: each has an Achilles’ heel, but we’ve yet to find a fully systematic way of finding any given pathogen’s weakness, a prerequisite for any system of immunity on demand. It will also be important to develop structural models to artificially create the antibodies and T cell receptors that can recognize these regions. Eventually, as computational power continues to grow and as our structural biology knowledge increases, we may be able to design artificial vaccines completely in silico. For now, this is more dream than reality.

The real obstacle, however, is not the creation or the manufacture of protective antibodies against pathogens, but the delivery of those antibodies or cells into the body. Currently the only way to deliver antibodies into the body is difficult and unreliable. One needs to isolate stem or immune cells (B and T cells) from each individual patient and then custom-tailor the receptors for their genetic backgrounds, a process that is far too expensive to implement on a mass scale. Stem cells, nonetheless, do offer real promise. Already it seems plausible that in the future, bioengineers could create new stem cells from your blood cells and freeze them until needed. If there were to be a deadly new virus, bioprogrammers could design the potential immune receptors and genetically engineer and introduce them into your stored stem cells, which can then be injected into your blood. Eventually it may even be possible to deliver the immune receptor genes directly into your body, where they would target the stem cells and reprogram them.

At first blush, the idea of immunity-on-demand might seem farfetched.

All this is, of course, a delicate proposition. In some ways, an overactive immune system is as much of a risk as an underactive one: more than a million people worldwide a year die from collateral damage, like septic shock after bacterial infection, and inflammations that may ultimately induce chronic illness such as heart disease and perhaps even cancer. Coping with the immune system’s excesses will require advances in understanding the precise mechanisms of immune regulation. This fine-tuning of the immune response could also have the bonus effect of preventing autoimmune diseases.

We are not sure when this will all happen, but there’s a good chance it will, and perhaps the only question is when. There was a great leap forward in medicine when sterilization techniques were first implemented. Here’s to the hope that the fruits of information technology can underwrite a second, even bigger leap.

My Comment: Paraphrasing the worlds of Crocodile Dundee—that’s not a leap, this is a leap. I’m referring to the upside, the potiential of neuropeptides, which are almost completely under our control, can change faster than scientific research, and can do all of the above if not more—and here’s the kicker—if we humans just knew how to change our present recipe of neuropeptides to a recipe that will in fact heal us from all disease. That possibility is well within the implications of that discovery years ago. But the bulk of that research cannot come from scientific laboratories. The stuff of neuropeptides comes from our own thoughts, beliefs, experiences, choices—all that comprises the human experience.

And that means we have to get up every day and begin searching for the right recipe of daily life, the right outlook, the right paradigm, the things that can transform us, that give life meaning for us and for future generations.

It’s been on the religious front burner for thousands of years and those of us who are religious still haven’t gotten it right, and those who aren’t religious have yet to accidentally stumble upon it.

Underneath all of this is the fact that we can become better at being human today that we were yesterday.

Thursday, February 11, 2010

Scientific Research Reveals Possibility of Reincarnation

Physicists Prove Teleportation of Energy Is Possible

Over five years ago, scientists succeeded in teleporting information. Unfortunately, the advance failed to bring us any closer to the Star Trek future we all dream of. Now, researchers in Japan have used the same principles to prove that energy can be teleported in the same fashion as information. Rather than just hastening the dawn of quantum computing, this development could lead to practical, significant changes in energy distribution.

According to the theory, developed by Masahiro Hotta of Tohoku University, Japan, a series of entangled particles could be stretched across an infinite amount of space. By inducing an energy change in one of the particles, the other entangled particles would change as well. Eventually, to preserve conservation of energy, the original particle would be destroyed, with its energy passing to the final particle in the chain. Thus, the energy has been teleported from one particle to another.

Naturally, Hotta doesn't present any blueprint for replacing power lines with teleporting energy, concentrating instead on the implications for studying quantum mechanics. However, with a concept this profound, the implications beyond theory are nearly endless.

My Comment: If the particles stretch across time, then we’ve got some physicists who have just proved the possibility of reincarnation. Who knew? And, we all thank you.

Joke Science

ScienceDaily (Feb. 5, 2010) — Important new research about the effects of acupuncture on the brain may provide an understanding of the complex mechanisms of acupuncture and could lead to a wider acceptability of the treatment.

The study, by researchers at the University of York and the Hull York Medical School published in Brain Research, indicates that acupuncture has a significant effect on specific neural structures. When a patient receives acupuncture treatment, a sensation called deqi can be obtained; scientific analysis shows that this deactivates areas within the brain that are associated with the processing of pain.

Dr Hugh MacPherson, of the Complementary Medicine Research Group in the University's Department of Health Sciences, says: "These results provide objective scientific evidence that acupuncture has specific effects within the brain which hopefully will lead to a better understanding of how acupuncture works."

Neuroscientist Dr Aziz Asghar, of the York Neuroimaging Centre and the Hull York Medical School, adds: "The results are fascinating. Whether such brain deactivations constitute a mechanism which underlies or contributes to the therapeutic effect of acupuncture is an intriguing possibility which requires further research."

Last summer, following research conducted in York, acupuncture was recommended for the first time by the National Institute for Health and Clinical Excellence (NICE) as a treatment option for NHS patients with lower back pain. NICE guidelines now state that GPs should 'consider offering a course of acupuncture comprising a maximum of 10 sessions over a period of up to 12 weeks' for patients with this common condition.

Current clinical trials at the University of York are investigating the effectiveness and cost-effectiveness of acupuncture for Irritable Bowel Syndrome (IBS) and for depression. Recent studies in the US have also shown that acupuncture can be an effective treatment for migraines and osteoarthritis of the knee.
The York team believe that the new research could help to clear the way for acupuncture to be more broadly accepted as a treatment option on the NHS for a number of medical conditions.

My Comment: Studies on acupuncture tend to bring out the worst qualities in science, which can be corrected only by each individual. Not each individual scientist. Each regular, normal, lay person. All we need to do is buy a book about acupuncture, such as The Web that has No Weaver, and read it. Or, we can make an appointment with an acupuncturist and ask them what they do and why it works. Or we can make a phone call to an acupuncturist and ask the same questions. These are steps scientists will not take. And that’s because Chinese medicine works on another paradigm, and one thing we know about Western institutions, they will not tinker with the paradigm unless they absolutely have to. Biologists must describe everything biologically or chemically. They don’t describe things energetically, like the physicists, unless, again, they absolutely have to. So here is another in a long list of studies saying that acupuncture is effective, and explained in chemical terms. It’s just narrow minded science. It’s like the old joke about a guy looking for something on the ground of a lighted parking lot. What are you looking for, some other guy asks. My car keys, is the reply. Where’d you lose them? Over there on that dark vacant lot. Then why are you looking here? The light is better over here.

Wednesday, February 10, 2010

Think of the Implications

ScienceDaily(Jan. 19, 2010) — It's not thinking in the way humans, dogs or even birds think, but new findings from researchers at the University of Tennessee, Knoxville, show that bacteria are more capable of complex decision-making than previously known.

The discovery sets a landmark in research to understand the way bacteria are able to respond and adapt to changes in their environment, a trait shared by nearly all living things, and it could lead to innovations in fields from medicine to agriculture.

In the long-term, the researchers think that scientists will be able to take the findings, published in the Proceedings of the National Academy of Sciences, and use them to tailor medicines in new ways to fight harmful bacteria or to find enhanced ways to use bacteria in agricultural or other applications.

Biology typically looks at the common bacteria Escherichia coli as the model for bacteria's ability to move actively and independently, but Gladys Alexandre, an associate professor of biochemistry, cellular and molecular biology at UT Knoxville, decided to look at the more complex soil bacterium, Azospirillum brasilense.

"As bacteria's ability to make decisions goes, E. coli is kind of dumb, which makes it easy for researchers to study sensing and information processing -- essentially, decision making -- in this bacterium," says Alexandre.

It helps to understand the way that bacteria "think." Their cells contain a number of receptors, and each one affects a certain behavior or trait in the bacteria, for example where to move, how to function, even whether to become virulent. The advent of genetic sequencing means we know more about how many receptors bacteria have, and the more receptors, the more ways a bacterium has to sense its surroundings.

E. coli has only five receptors that direct its decision-making process about movement, while Azospirillum brasilense has 48, making it comparatively much "smarter" in its ability to detect changes in its environments and as a result, to make complex decisions regarding where to move.

What scientists have not known and have been unable to study until now is how the individual receptors, by sensing their environment, directly affect the bacteria's behavior and ability to adapt to their environment. Alexandre's study is one of the first to isolate and study a receptor in this way.

She and her colleagues focused on a receptor they suspected was related to the way bacteria convert nitrogen gas from the atmosphere into a form -- ammonium -- that can be used by all organisms. This ability is called nitrogen fixation and while it is uniquely found in bacteria, it is critically important to all living organisms, as it is the only way nitrogen can eventually be incorporated into building blocks of cells.

The process is carried out by an enzyme which is damaged in the presence of high concentrations of oxygen, which presents a dilemma for the bacterium, as the energy needed for the process is usually acquired in the presence of oxygen.

When Alexandre and her team created mutant versions of the bacteria without the receptor, the mutant bacteria were unable to detect where the right position in oxygen concentration was, affecting the nitrogen fixation reaction. In other words, the mutant bacteria were somewhat "blind" and could not detect the right position, showing them their hunch was correct about the receptor's purpose. But their curiosity expanded: if they were able to uncover the receptor's purpose, would they be able to out exactly how it functioned?

For that, they enlisted the help of UT-Oak Ridge National Laboratory distinguished scientist Igor Jouline, an expert in carrying out complex computations of biological systems, such as the one governing the receptor at the heart of Alexandre's research. Working with Alexandre's data, Jouline was able to generate a model of the receptor's structure and compare it to other structures on a nearly atom-by-atom basis.

This enabled them to predict which one of the more than 100 amino acids in the sensory part of the receptor is responsible for sensing the precise oxygen concentration that this bacterium needs for nitrogen fixation. It's a process that, using normal genetic techniques, would have taken a substantial commitment of hours and resources, but was made simpler and less labor-intensive by using computing.

Alexandre hopes that other scientists and researchers can use a similar technique to look at receptor sites on other bacteria of interest. She noted that the ability to work with Jouline and with the resources available through UT Knoxville's partnership with ORNL was key to her discovery.

"Partnering with Igor provided us great insight," said Alexandre. "We would not have been able to fully understand how this receptor works without him."
Alexandre says there's good long-term potential for the knowledge gained in the study.

"We see now that bacteria are, in their way, big thinkers, and by knowing how they 'feel' about the environment around them, we can look at new and different ways to work with them."

My Comment: Well, let’s see what questions arise. How about—What is consciousness? And—How far does consciousness extend? Not to mention—How is this possible? These are the questions that will slap you in the face, questions that are not encouraged in science classes. These are religious questions. Unless you are a scientist of such note that you get complete freedom of thought. Like Roger Penrose. If there is a difference between his theory of panpsychism and the first cornerstone of religion, I’d like to know what that might be.

Monday, February 8, 2010

The Brain Dictionary

ScienceDaily (Jan. 13, 2010) — Two hundred years ago, archaeologists used the Rosetta Stone to understand the ancient Egyptian scrolls. Now, a team of Carnegie Mellon University scientists has discovered the beginnings of a neural Rosetta Stone. By combining brain imaging and machine learning techniques, neuroscientists Marcel Just and Vladimir Cherkassky and computer scientists Tom Mitchell and Sandesh Aryal determined how the brain arranges noun representations. Understanding how the brain codes nouns is important for treating psychiatric and neurological illnesses.

"In effect, we discovered how the brain's dictionary is organized," said Just, the D.O. Hebb Professor of Psychology and director of the Center for Cognitive Brain Imaging. "It isn't alphabetical or ordered by the sizes of objects or their colors. It's through the three basic features that the brain uses to define common nouns like apartment, hammer and carrot."

As the researchers report January 12 in the journal PLoS One, the three codes or factors concern basic human fundamentals: you physically interact with the object (how you hold it, kick it, twist it, etc.); it is related to eating (biting, sipping, tasting, swallowing); and it is related to shelter or enclosure.

The three factors, each coded in three to five different locations in the brain, were found by a computer algorithm that searched for commonalities among brain areas in how participants responded to 60 different nouns describing physical objects. For example, the word apartment evoked high activation in the five areas that code shelter-related words.

In the case of hammer, the motor cortex was the brain area activated to code the physical interaction. "To the brain, a key part of the meaning of hammer is how you hold it, and it is the sensory-motor cortex that represents 'hammer holding,'" said Cherkassky, who has a background in both computer science and neuroscience.

The research also showed that the noun meanings were coded similarly in all of the participants' brains. "This result demonstrates that when two people think about the word 'hammer' or 'house,' their brain activation patterns are very similar. But beyond that, our results show that these three discovered brain codes capture key building blocks also shared across people," said Mitchell, head of the Machine Learning Department in the School of Computer Science.

This study marked the first time that the thoughts stimulated by words alone were accurately identified using brain imaging, in contrast to earlier studies that used picture stimuli or pictures together with words. The programs were able to identify the thought without benefit of a picture representation in the visual area of the brain, focusing instead on the semantic or conceptual representation of the objects.

Additionally, the team was able to predict where the activation would be for a previously unseen noun. A computer program assigned a score to each word for each of the three dimensions, and that score predicted how much brain activation there would be in each of 12 specified brain locations. The theory generated a prediction of the activation for apartment based only on the patterns derived from the other 59 words. As one slice of the observed brain image from a human participant (left) and the theory (right) shows, the theory makes precise predictions, particularly about the two shelter-related coding areas in this slice (circled), where brighter red indicates more activation.

To test the theory, the team used the word scores to identify which word a participant was thinking about, just by analyzing the person's brain activation patterns for that word. The program was able to tell which of the 60 words a participant was thinking about, with a rank accuracy as high as 84 percent for two of the participants, and an average rank accuracy of 72 percent across all 10 participants (where pure guessing would be accurate 50 percent of the time).

One absent code in the study that is essential for the human species concerns sex or love or reproduction. "Our vocabulary of 60 test nouns lacked any words related to the missing dimension, such as 'spouse' or 'boyfriend' or even 'person,'" Just said. "We certainly expect some human dimension to be part of the brain's coding of nouns, in addition to the three dimensions we found."

"With psychiatric and neurological illnesses, the meanings of certain concepts are sometimes distorted," Just said. "These new techniques make it possible to measure those distortions and point toward a way to 'undistort' them. For example, a person with agoraphobia, the fear of open spaces, might have an exaggerated coding of the shelter dimension. A person with autism might have a weaker coding of social contact."

Another implication is in developing and testing domain expertise at the neural level. "We teach to the mind but we are shaping the brain, and now we can give the brain a test of how well it has learned a concept," says Just. "If an instructor knows how an advanced concept is represented in the brains of experts in that area, she will be able to teach to the brain test. We can do it for hammers and carrots right now. In the near future isotope and telomere may soon be on some brain researcher's agenda."

My Comment: These findings also tell us why Jewish education has been such a colossal failure. Key words are left undefined, abstract, and therefore do not cause the brain to react in any way. Words such as holiness, humility, nefesh, ruach, neshumah, cleanliness, sin, redemption, repentance, forgiveness, and so many others are left in ghostlike limbo that Jews, both young and old cannot connect to, like it or not, the core of who we are. I believe that an application of scientific notions of empiricism, clarity, and the historical quest to make visible what in the past was invisible is what is needed. And frequently, as I’ve shown, with non-Western concepts like life force, chi, nefesh—a simple daily scan of the science section can go a long way towards greater religious and personal understanding.