Mathematics a Natural Force? Part II

Nature by Numbers from Cristóbal Vila on Vimeo.

My Comment: It would be interesting to see what would happen if someone began to substitute the Hebrew numeric system for the Hindu/Arabic/Greek numeric system. By the way, this is a Fibonacci sequence treated as a function. That is, they let it catch wind and soar.

Could Facebook Make You Happy? Mmmm....Could be.

Meaningful talks can make you happier

by Samia Sehgal - March 7, 2010

Happiness doesn’t come from shallow socializing alone, it comes from engaging in deep and relevant talks.

Your talk influences how you feel, suggests a new study. Scientists have found while meaningful conversation can boost your cheerfulness, trivial talks can make you miserable.

Psychologists at the University of Arizona investigated the difference between happy and unhappy people on the basis of the conversations they had. It was found that a person is likely to be happier if he indulges less in petty talks and more in purposeful conversations.

“Profound conversations have the potential to make people happier,” said Matthias Mehl, an assistant professor of psychology at the University of Arizona and co-author of the study.

Connecting happiness to daily conversations

Participants of the study were assessed for their personality and well-being to gauge their level of happiness. 79 college men and women were then asked to wear unobtrusive recording devices over four days to monitor the talks they had with the people around them.

After listening to all the conversations, the researchers divided them into trivial small talks and deep, meaningful talks.

It was found that the happiest people had a lesser tendency to spend time alone; they spent 70 per cent more time talking as compared to those who were least happy.

Deep conversations make happy individuals

The study, published in ‘Psychological Science’ journal, reveals that “the happiest participants had twice as many deep and meaningful conversations and engaged in one third as much small talk as the unhappiest participants”.

The type of conversations you have indicates how you interact with your people.
“Just as self-disclosure can instill a sense of intimacy in a relationship, deep conversations may instill a sense of meaning in interaction with partners,” Mehl said.

The study authors do not rule out the importance of small talk; “For smooth social functioning, we need small talk,” said Mehl, but “What really connects you to people is substantive, meaningful conversation rather than small talk.”

More for men?

Another interesting finding of the study was related to gender. While women are known to share their feelings and deeper thoughts easier then men, the study authors found that the effects of having significant conversations were slightly greater for men. However, they did not discuss the reason behind this difference.
Happier people are known to be more social. But the study says happiness doesn’t come from shallow socializing alone, it comes from engaging in deep and relevant talks with your people.

According to Mehl, the study suggests that “happy life is social and conversationally deep rather than solitary and superficial”.

My Comment: The article pretty much speaks for itself.

Again We Meet at the Corner of Religion and Science

Bugging bugs: Learning to speak microbe

05 March 2010


by Hayley Birch

DEEP in your lungs, there's a battle raging. It's a warm, moist environment where the ever-opportunistic bacterium Pseudomonas aeruginosa has taken up residence. If your lungs are healthy, chances are the invader will be quickly dispatched. But in the mucus-clogged lungs of people with cystic fibrosis, the bacterium finds an ideal habitat. First, the microbes quietly multiply and then they suddenly switch their behaviour. A host of biochemical changes sticks the population of cells together, forming a gluey biofilm that even a potent cocktail of antibiotics struggles to shift.

Microbes like P. aeruginosa were once thought of as disorganised renegades, each cell working alone. Microbiologists like Thomas Bjarnsholt, who is battling to understand how P. aeruginosa causes chronic infection in people with cystic fibrosis, now know otherwise. They are up against a highly organised army, using a sophisticated communication system to coordinate its behaviour.

But it's Bjarnsholt's latest discovery that reveals microbes' gift for language: the bacteria aren't just talking amongst themselves, but also quietly listening in on signals sent by their human host. So when a cavalry of white blood cells arrives to repel the invading bacteria, the entrenched biofilm senses their presence, and launches a coordinated counterattack (Microbiology, vol 155, p 3500). The microbes release deadly compounds called rhamnolipids, which burst the white blood cells, killing them before they can even take aim, says Bjarnsholt, who is at the University of Copenhagen in Denmark.

Examples like this belie the notion that bacteria are simple, silent loners. Over recent decades, many species of bacteria have been shown to be in constant communication with each other. But now an even more sophisticated picture is emerging, one in which bacteria not only receive signals from each other, but also intercept them from the cells of their plant or animal hosts, including us.

Bacteria don't just listen in on each other, but also on their plant or animal hosts - including us.

These communication skills seem to offer invading bacteria quite an advantage on the battlefield. But they are also drawing the attention of researchers looking for new ways to fight microbes. If these "cross-kingdom" signals are indeed widespread, then intercepting or subverting them would offer a whole new way of tackling infection, not only in cystic fibrosis, but also in a wide range of other diseases. Such an approach would simply block the signals prompting the bacterial army to mobilise, rather than trying to wipe it out as antibiotics do. Bacteria would then no longer be forced to evolve drug resistance to survive, potentially bringing to an end the scourge of the superbug.

If cross-kingdom signals are widespread, then intercepting them would offer a whole new way of tackling infection

Bacteria communicate using chemical signals, releasing and receiving signalling molecules in a process known as quorum sensing. In its simplest form, bacteria use quorum sensing to keep track of their neighbours. Some bioluminescent bacteria, for example, light up when their population exceeds a threshold size (Journal of Bacteriology, vol 104, p 313).

Studies of the phenomenon in 1970 discovered that bioluminescent bacteria were using molecules called N-acyl homoserine lactones (ALHs) to coordinate this behaviour - an early hint that bacteria are a talkative bunch. But it wasn't until the early 1990s, with the discovery that ALHs are produced by many species of microbe, that it started becoming clear that quorum sensing was common throughout the bacterial kingdom. And this signalling isn't all friendly chatter, some bacteria intercept and break down the signals from other species, or even release signals to trick others into changing their behaviour.

But in a research review published in August 2009, Steve Atkinson and Paul Williams, microbiologists at the University of Nottingham in the UK, brought home just how widespread these signalling networks are: they reach far beyond the humble bacteria into other kingdoms, including plants, fungi, and our own (Journal of the Royal Society Interface, vol 6, p 959). As Atkinson puts it, "There's a war going on out there."

Take Candida albicans, the yeast that causes thrush infections. This organism likes the same warm, moist habitats as P. aeruginosa and the two battle it out in a bid to colonise their human hosts, deploying quorum-sensing signals as weapons against each other. The yeast fires off signals that trick the bacterium into slashing production of one of its armaments - a reactive chemical called pyocyanin, which makes life particularly uncomfortable for the yeast. The bacterium, meanwhile, produces signals that keep the yeast's growth in check, preventing it from transforming itself from a single-celled yeast into a branching, multicellular fungus.

Then there's our own immune system's battle to prevent P. aeruginosa making itself at home in our lungs. Bjarnsholt is hunting for the signal P. aeruginosa uses to "listen out" for white blood cells, and ways to block it. He doesn't think of the bacteria as being physically aware of their hosts. To them, the signals they detect are just foreign compounds they have to fend off. But it's certainly a far more sophisticated take on the host-pathogen relationship than we're used to, notes Atkinson. "Rather than the pathogen just piling into the host cell and taking over its DNA, it's about signal production, interception - and maybe even coercion of the host to do something that it wouldn't normally do."

Microbe management

This coercion might even extend to including bacteria that can modify the way our bodies work, says Vanessa Sperandio, a microbiologist working on quorum sensing at the University of Texas Southwestern Medical Center in Dallas. "It's a little out there," she admits, "but there are some good examples. Kids who have certain bacterial infections can be very compulsive about touching their mouths, which helps the spread. I think we're going to start seeing lots of examples like that."

Many of the early examples of cross-kingdom communication that Atkinson and Williams catalogued are less than congenial, but there is also good evidence for cooperative interaction between bacteria and their hosts, says Atkinson - particularly between ourselves and our microbiome, the huge population of bacteria that live in us and on us.

These days we're all well acquainted with the millions of microbes lining our insides. Yogurt adverts have taught us nothing if not to love the friendly bacteria which line our guts, helping to keep nastier bugs at bay. Microbes don't just make themselves at home in the intestines, however. They're in your mouth, up your nose, and covering your skin, all the while releasing a cacophony of quorum-sensing signals.

Atkinson thinks our own cells exploit this same signalling system to monitor and cajole our personal population of microbes, just as they eavesdrop on and manipulate us. In other words, we don't passively host this bacterial colony, but actively engage it in conversation. We've evolved together, he says. "We have to consider that we're intrinsically linked."

Sperandio, who is studying how bacteria sense and respond to human stress hormones like adrenalin, agrees. "I think that if you consider how much we interact with microbes, it's not surprising that you're going to have some chemical signalling. Just consider in your intestine, you have 10 times more bacterial cells than you have your own."

Picking out these chemical signals from the maelstrom of molecules that swirl in our gut is proving to be a battle, but that's exactly where some of these cooperative signals have been spotted. Take those friendly gut bacteria, for example, and in particular one that goes by the name of Bacillus subtilis. Not a natural gut bacterium, B. subtilis has long been used as a probiotic agent in food. Though its health-boosting properties were not well understood, some have suggested it gently stimulates the immune system, priming it for action against less friendly bugs.

Then in 2007 a team led by Eugene Chang at the University of Chicago suggested a route by which these bacteria could influence the health of intestinal cells - a route involving quorum-sensing molecules. The team discovered that a certain B. subtilis signalling molecule, known as competence and sporulation factor (CSF), is detected by human gut cells (Cell Host & Microbe, vol 1, p 299). Chang thinks of this signal detection as a kind of "bacteriostat" mechanism: our cells are monitoring CSF as a way of detecting and adapting to important changes in the gut flora.

Cracking the code

"The idea is that when quorum sensing molecules are secreted, it usually signals some change in the balance of the bacterial population," says Chang. So by listening for signals, our cells can adjust to these changes. In this case, the detection of CSF causes our cells to fire up the production of molecules called heat shock proteins, protective molecules known to help cells maintain crucial machinery during times of stress - from temperature extremes to toxins.

Perhaps the most intriguing evidence for the importance of monitoring our microbiome comes from the gut's CSF receptor itself. This receptor was previously thought to be a simple nutrient transporter, despite being found in even the furthermost reaches of the intestine, where most nutrients would already have been absorbed. Its blueprint is encoded in a region of the human genome in which mutations are associated with inflammatory bowel disease. This suggests that without these receptors, we're unable to maintain a normal, healthy gut.

Such examples suggest cross-kingdom signalling has medical implications far beyond infectious diseases. Several other illnesses, including Crohn's disease and some cancers, have been linked to imbalances in the species of bacteria that live in our guts. Sperandio suggests that any number of illnesses could be associated with your balance of bacteria, and that these illness might be tackled using signal interference.

But with so many bacteria - hundreds of different species can inhabit your skin alone - how can we begin to master this chemical language to examine its medical potential? Is there a better way to spot these signals than to pick them out one by one? Pieter Dorrestein and his team at the University of California, San Diego, and Paul Straight at Texas A&M University in College Station, have been developing a tool that could accelerate efforts to crack the code of microbial communication.

The team is using an imaging system based on mass spectrometry to detect swathes of signals at the same time. They grow their bacteria on a stainless steel plate, and use a laser to vaporise their signalling molecules, feeding these into a mass spectrometer to catalogue the molecules present.

As proof of principle, Dorrestein and Straight have mapped the interactions between two species of soil-dwelling bacteria (Nature Chemical Biology, vol 5, p 885). Even in this simple case, the instrument detected as many as 100 different signalling molecules fired off by the two bacteria, only 10 of which the team managed to match to known molecules. Despite the huge scale of the problem, the team is already starting to translate their work into inter-kingdom studies, probing the interactions between bacteria and cells of the human immune system. By imaging cross-talk between different species, they even hope to identify inhibitors for Staphylococcus aureus, the hospital superbug that has evolved to defend itself against whole groups of our most effective antibiotics.

The method should provide food for thought for Bjarnsholt, who has yet to find any serious candidate compounds for signal-blocking in P. aeruginosa infections in people with cystic fibrosis. His best bet for a drug lead is an extract of garlic, although the active component that interferes with the signal remains unknown. He thinks it will be a few years yet before quorum sensing inhibitors come into their own. "I don't think it's just around the corner - there's got to be a lot more research," he says. But when it comes to fighting drug resistance, the more targets we go after the better, he adds. We need to target signalling, biofilm formation and classical biological processes like bacteria cell wall formation, all at once.

Whatever the potential for medical advancement, the growing recognition of cross-kingdom signalling has a more immediate philosophical implication: we're going to have to start changing the way we think about microbes. Bacteria aren't just isolated cells, or even isolated populations, but multi-species communities that communicate with each other and, crucially, us. We are, almost certainly, more intimately connected with the bacteria that inhabit us than we ever would have believed. "We'd be naive to believe that we exist in splendid isolation from all other organisms," says Atkinson. "We've thought that way for too long."

My Comment: I wonder if grammar can be considered scientific. For instance, after reading this article, define “I”. First person pronoun, refers to....not such a simple answer anymore. "I think therefore I am" appears a bit naive now, doesn't it? This also happens to be one of the foundational quests of religion, the search for "I". These findings definitely once again shed light on the questions of self, consciousness, and the fractal nature of Judaism, if not all religions. Just saying.

Previously Suspected By Whom

Genetics in the Gut: Intestinal Microbes Could Drive Obesity and Other Health Issues

The diversity of germs in the human gut suggests microbiota play a greater role in health than previously thought, even driving obesity and other metabolic conditions.

By Katherine Harmon

Outnumbering our human cells by about 10 to one, the many minuscule microbes that live in and on our bodies are a big part of crucial everyday functions. The lion's share live in the intestinal tract, where they help fend off bad bacteria and aid in digesting our dinners. But as scientists use genetics to uncover what microbes are actually present and what they're doing in there, they are discovering that the bugs play an even larger role in human health than previously suspected—and perhaps at times exerting more influence than human genes themselves.

One team of researchers recently completed a catalogue of some 3.3 million human gut microbe genes. Their work, led by Junjie Qin of BGI–Shenzhen (formerly the Beijing Genomics Institute) and published in the March 4 edition of Nature, adds to the expanding—but nowhere near complete—census of species that reside in the intestinal tract. (Scientific American is part of Nature Publishing Group.)

Another group turned its attention to a particular host gene that seems to impact these inhabitants of the intestines. They found that in mice, a loss of one key gene led to a shift in microbiota communities and an increase in insulin resistance, obesity and other symptoms of metabolic syndrome (a cluster of these conditions). Their results were published online March 4 in Science.

The field of gut microbe study has bloomed in the past few years after decades in the shadows. As the authors of the Science report noted, "The inability to culture most gut bacteria makes assessment of their causal role in health and disease technically challenging." But the advance of genetic sequencing has enabled researchers to make steady progress in getting to the bottom of these beasties and their role in health. And in addition to being a quick way to assess these microbial populations, genomics can also help to elucidate how the two systems—human and microbe—interact.

Stomach survey
The number of microbes in the human gut was known to be vast, but the 3.3 million microbial genes located in it were a good deal "more than what we originally expected," says Jun Wang, of BGI and co-author of the Nature study. The number was especially surprising given that the microbiota tended to be very similar across the 124 individuals they sampled in Denmark and Spain.

Previous work had scanned for these microbial genes in the past. The largest had created about three gigabases (billion base pairs) of microbial sequences that was trumped by Wang's team, which assembled more than 576 gigabases.

The hefty catalogue is a "big advance" in the field, says Andrew Gewirtz of the Department of Pathology and Laboratory Medicine at Emory University who was not involved in this study. "It really sets in place a framework for defining—in detail—the microbiome," he says. And as Wang and his colleagues noted in their study, "To understand and exploit the impact of the gut microbes on human health and well-being it is necessary to decipher the content, diversity and functioning of the microbial gut community."

More than 99 percent of the genes the group found were from bacteria. "These bacteria have functions, which are essential to our health: They synthesize vitamins, break down certain compounds—which cannot be assimilated by our body—[and] play an important role in our immune system," Wang points out.

Wang's group, which is part of the European Commission–funded MetaHIT (Metagenomics of the Human Intestinal Tract) consortium, relied on fecal samples from the 124 individuals. Despite the presumed vastness of gut-microbe diversity, the researchers found that about 70 percent of the genetic material in their European sample overlapped with that from previous studies that examined U.S. and Japanese subjects, suggesting that, in fact, "the prevalent human microbiome is of a finite and not overly large size," the researchers concluded.

It is "a very important paper for paving the way for future studies," Gewirtz says. "Once you define the baseline you can start looking in detail at disease."

Wang and his colleagues already had this next step in mind. The samples for the genetic catalogue came from two groups of obese individuals: those with inflammatory bowel disease, and a healthy group. The genetic analysis of the microbial inhabitants of the respective guts "clearly separates patients from healthy individuals," the researchers concluded in their paper, suggesting new possibilities for diagnosis and eventually treatment.

Inflammatory mutations
As the prevalence of metabolic diseases continues to increase across the U.S. and many other countries, a growing body of research has suggested that some of these physiological changes might have their roots deep in the gut—not in the human cells but some of the many microbes there.

Emory's Gewirtz and his team tracked the gut microbiota in mice as the rodents experienced different kinds of metabolic disorders, such as obesity and insulin resistance. They bred mice with a genetic deficiency (specifically, the absence of Toll-like receptor 5, or TLR5, which has a hand in immune response) to see how it might change their microbial gut communities and metabolic health—and try to understand the order in which the changes were happening. "It's very much appreciated that obesity is associated with insulin resistance and type 2 diabetes," Gewirtz says. But "which comes first is not entirely clear."

They found that their mice without the TLR5 gene—even when put on restricted diets—still showed insulin resistance, suggesting that insulin resistance might lead to obesity rather than the other way around. But if these mice were allowed to eat as they pleased, they ate 10 percent more than their peers and, by 20 weeks old, had body mass indexes that were 20 percent higher. Many researchers and public health officials have blamed the availability (and content) of contemporary foods, increasingly sedentary lifestyles and human genetics for more metabolic syndrome cases. But the mouse study suggests that there might be more to the picture. "The tendency to overeat may be underlain by changes that are more likely physiological than genetic," Gewirtz says.

Gewirtz and others propose that inflammation—in conjunction with changes in the gut microbiome—might be driving the cycle. Inflammation can change the character of the gut microbes, in some cases allowing more calories to be extracted from food. But, Gewirtz says, "We do not know which is coming first" if inflammation is changing the microbiota or vice versa. It is likely, he notes, that whatever kicks off the process, it will start a sort of feedback loop, where one will increase accelerates the other.

How much of their findings in mice are likely to translate to humans? The stomach bacteria in mice are not found in people. But Gewirtz and his team noted that analogous species live in the human stomach. "We think it's very plausible" that the findings will carry over to humans, especially because they "fit with a lot of the ideas" currently circulating in the research community about insulin resistance and inflammation, Gewirtz says. His group has already started a new investigation comparing the human genes and microbial profiles of people with metabolic syndrome to healthy controls to see if some of the same correlations in mice appear in humans.

Next genetic steps
Although a fuller grasp of microbial genetics promises to boost wellness even further, plenty of big unknowns remain. Scientists are still unsure just how and when these communities of microbes establish themselves in each person's gut. "Everyone is born sterile," Gewirtz says, noting that colonization starts during birth but that they do not know when it reaches relative stability. Regardless of timing, it means that, "the environment is a big, big factor in determining what someone's microbiota will be like," he adds.

If gut microbiota do play a large role in diseases such as obesity and metabolic syndrome, then a recent past change in these communities might help to explain the expansion of patients—and waistlines—in developed countries. "The genetics of humans have not changed appreciably in the last several hundred years," Gewirtz says. "But several changes in the environment have made it so that the gut microbiota is likely considerably different than it was 50 years ago."

Wang and his colleagues are already attempting to track the composition of human gut microbiota back in time to see if this might be the case. But they have their sights set on even bigger collections of genetic data. "Our dream is to build a library" of reference genomes, Wang notes. He hopes to have 10,000 genomes for bacteria within two years. And, he estimated, as soon as more definitive data about these gut genetics emerge, microbial-targeted therapeutics will likely be quick to follow.

My Comment: All I’ll say is that most traditional cuisines, based in ancient civilizations, have very effective foods and means for controlling all of this flora. In fact, I would say that these cuisines are based around notions of ingesting healthy flora and ridding the body of harmful bacteria. How, oh how, could they have known about this possibly 5-10,000 years ago, depending upon which archaeologist you read.

The Latest in Psychology That Has Nothing to Do with Psychology

Bacterial Balance Keeps Us Healthy: Microbial Genes in Gut Outnumber Genes in Human Body

ScienceDaily (Mar. 4, 2010) — The thousands of bacteria, fungi and other microbes that live in our gut are essential contributors to our good health. They break down toxins, manufacture some vitamins and essential amino acids, and form a barrier against invaders. A study published in Nature shows that, at 3.3 million, microbial genes in our gut outnumber previous estimates for the whole of the human body.

Scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, working within the European project MetaHIT and in collaboration with colleagues at the Beijing Genomics Institute at Shenzhen, China, established a reference gene set for the human gut microbiome -- a catalogue of the microbe genes present in the human gut. Their work proves that high-throughput techniques can be used to sequence environmental samples, and brings us closer to an understanding of how to maintain the microbial balance that keeps us healthy.

"Knowing which combination of genes is necessary for the right balance of microbes to thrive within our gut may allow us to use stool samples, which are non-invasive, as a measure of health," says Peer Bork, whose group at EMBL took part in the analysis. "One day, we may even be able to treat certain health problems simply by eating a yoghurt with the right bacteria in it."

This catalogue of the microbial genes harboured by the human gut will also be useful as a reference for future studies aiming to investigate the connections between bacterial genetic make-up and particular diseases or aspects of people's lifestyles, such as diet.

To gain a comprehensive picture of the microbial genes present in the human gut, Bork and colleagues turned to the emerging field of metagenomics, in which researchers take samples from the environment they wish to study and sequence all the genetic material contained therein. They were the first to employ a high-throughput method called Illumina sequencing to metagenomics, dispelling previous doubts over the feasibility of using this method for such studies.

From a bacterium's point of view, the human gut is not the best place to set up home, with low pH and little oxygen or light. Thus, bacteria have had to evolve means of surviving in this challenging environment, which this study now begins to unveil. The scientists identified the genes that each individual bacterium needs to survive in the human gut, as well as those that have to be present for the community to thrive, but not necessarily in all individuals, since if one species produces a necessary compound, others may not have to. This could explain another of the scientists' findings, namely that the gut microbiomes of individual humans are more similar than previously thought: there appears to be a common set of genes which are present in different humans, probably because they ensure that crucial functions are carried out. In the future, the scientists would like to investigate whether the same or different species of bacteria contribute those genes in different humans.

The research was conducted within the European project MetaHIT, coordinated by Dusko Ehrlich at the Institut National de la Recherche Agronomique, in France, with genetic sequencing carried out by Jun Wang's team at the Beijing Genomics Institute at Shenzhen, China.

My Comment: There will be quite a bit more research findings pertaining to this, as it opens new ideas in diet, food, and therefore culture. But it also has significance in the field of psychology—and by now, if you steadily follow this blog, it should be clear that the field of psychology greatly lacks behind the fields of physics, biology, biochemistry, genetics, just about every other field—on the very subject of psychology and consciousness. Heck, if you redefine psychology and the study of consciousness, then the field of psychology even lags behind the ancient religions, in terms of valuable knowledge.

Is Quantum Mechanics Controlling Your Thoughts?

01.13.2009

Science's weirdest realm may be responsible for photosynthesis, our sense of smell, and even consciousness itself.

by Mark Anderson

Graham Fleming sits down at an L-shaped lab bench, occupying a footprint about the size of two parking spaces. Alongside him, a couple of off-the-shelf lasers spit out pulses of light just millionths of a billionth of a second long. After snaking through a jagged path of mirrors and lenses, these minus¬cule flashes disappear into a smoky black box containing proteins from green sulfur bacteria, which ordinarily obtain their energy and nourishment from the sun. Inside the black box, optics manufactured to billionths-of-a-meter precision detect something extraordinary: Within the bacterial proteins, dancing electrons make seemingly impossible leaps and appear to inhabit multiple places at once.

Peering deep into these proteins, Fleming and his colleagues at the University of California at Berkeley and at Washington University in St. Louis have discovered the driving engine of a key step in photosynthesis, the process by which plants and some microorganisms convert water, carbon dioxide, and sunlight into oxygen and carbohydrates. More efficient by far in its ability to convert energy than any operation devised by man, this cascade helps drive almost all life on earth. Remarkably, photosynthesis appears to derive its ferocious efficiency not from the familiar physical laws that govern the visible world but from the seemingly exotic rules of quantum mechanics, the physics of the subatomic world. Somehow, in every green plant or photosynthetic bacterium, the two disparate realms of physics not only meet but mesh harmoniously. Welcome to the strange new world of quantum biology.

On the face of things, quantum mechanics and the biological sciences do not mix. Biology focuses on larger-scale processes, from molecular interactions between proteins and DNA up to the behavior of organisms as a whole; quantum mechanics describes the often-strange nature of electrons, protons, muons, and quarks—the smallest of the small. Many events in biology are considered straightforward, with one reaction begetting another in a linear, predictable way. By contrast, quantum mechanics is fuzzy because when the world is observed at the subatomic scale, it is apparent that particles are also waves: A dancing electron is both a tangible nugget and an oscillation of energy. (Larger objects also exist in particle and wave form, but the effect is not noticeable in the macroscopic world.)

Quantum mechanics holds that any given particle has a chance of being in a whole range of locations and, in a sense, occupies all those places at once. Physicists describe quantum reality in an equation they call the wave function, which reflects all the potential ways a system can evolve. Until a scientist measures the system, a particle exists in its multitude of locations. But at the time of measurement, the particle has to “choose” just a single spot. At that point, quantum physicists say, probability narrows to a single outcome and the wave function “collapses,” sending ripples of certainty through space-time. Imposing certainty on one particle could alter the characteristics of any others it has been connected with, even if those particles are now light-years away. (This process of influence at a distance is what physicists call entanglement.) As in a game of dominoes, alteration of one particle affects the next one, and so on.

The implications of all this are mind-bending. In the macro world, a ball never spontaneously shoots itself over a wall. In the quantum world, though, an electron in one biomolecule might hop to a second biomolecule, even though classical laws of physics hold that the electrons are too tightly bound to leave. The phenomenon of hopping across seemingly forbidden gaps is called quantum tunneling.

From tunneling to entanglement, the special properties of the quantum realm allow events to unfold at speeds and efficiencies that would be unachievable with classical physics alone. Could quantum mechanisms be driving some of the most elegant and inexplicable processes of life? For years experts doubted it: Quantum phenomena typically reveal themselves only in lab settings, in vacuum chambers chilled to near absolute zero. Biological systems are warm and wet. Most researchers thought the thermal noise of life would drown out any quantum weirdness that might rear its head.

Yet new experiments keep finding quantum processes at play in biological systems, says Christopher Altman, a researcher at the Kavli Institute of Nanoscience in the Netherlands. With the advent of powerful new tools like femtosecond (10-15 second) lasers and nanoscale-precision positioning, life’s quantum dance is finally coming into view.

INTO THE LIGHT

One of the most significant quantum observations in the life sciences comes from Fleming and his collaborators. Their study of photosynthesis in green sulfur bacteria, published in 2007 in Nature [subscription required], tracked the detailed chemical steps that allow plants to harness sunlight and use it to convert simple raw materials into the oxygen we breathe and the carbohydrates we eat. Specifically, the team examined the protein scaffold connecting the bacteria’s external solar collectors, called the chlorosome, to reaction centers deep inside the cells. Unlike electric power lines, which lose as much as 20 percent of energy in transmission, these bacteria transmit energy at a staggering efficiency rate of 95 percent or better.

The secret, Fleming and his colleagues found, is quantum physics.
To unearth the bacteria’s inner workings, the researchers zapped the connective proteins with multiple ultrafast laser pulses. Over a span of femto¬seconds, they followed the light energy through the scaffolding to the cellular reaction centers where energy conversion takes place.

Then came the revelation: Instead of haphazardly moving from one connective channel to the next, as might be seen in classical physics, energy traveled in several directions at the same time. The researchers theorized that only when the energy had reached the end of the series of connections could an efficient pathway retroactively be found. At that point, the quantum process collapsed, and the electrons’ energy followed that single, most effective path.

Electrons moving through a leaf or a green sulfur bacterial bloom are effectively performing a quantum “random walk”—a sort of primitive quantum computation—to seek out the optimum transmission route for the solar energy they carry. “We have shown that this quantum random-walk stuff really exists,” Fleming says. “Have we absolutely demonstrated that it improves the efficiency? Not yet. But that’s our conjecture. And a lot of people agree with it.”

Elated by the finding, researchers are looking to mimic nature’s quantum ability to build solar energy collectors that work with near-photosynthetic efficiency. Alán Aspuru-Guzik, an assistant professor of chemistry and chemical biology at Harvard University, heads a team that is researching ways to incorporate the quantum lessons of photosynthesis into organic photovoltaic solar cells. This research is in only the earliest stages, but Aspuru-Guzik believes that Fleming’s work will be applicable in the race to manufacture cheap, efficient solar power cells out of organic molecules.

TUNNELING FOR SMELL

Quantum physics may explain the mysterious biological process of smell, too, says biophysicist Luca Turin, who first published his controversial hypothesis in 1996 while teaching at University College London. Then, as now, the prevailing notion was that the sensation of different smells is triggered when molecules called odorants fit into receptors in our nostrils like three-dimensional puzzle pieces snapping into place. The glitch here, for Turin, was that molecules with similar shapes do not necessarily smell anything like one another. Pinanethiol [C10H18S] has a strong grapefruit odor, for instance, while its near-twin pinanol [C10H18O] smells of pine needles. Smell must be triggered, he concluded, by some criteria other than an odorant’s shape alone.

What is really happening, Turin posited, is that the approximately 350 types of human smell receptors perform an act of quantum tunneling when a new odorant enters the nostril and reaches the olfactory nerve. After the odorant attaches to one of the nerve’s receptors, electrons from that receptor tunnel through the odorant, jiggling it back and forth. In this view, the odorant’s unique pattern of vibration is what makes a rose smell rosy and a wet dog smell wet-doggy.

In the quantum world, an electron from one biomolecule might hop to another, though classical laws of physics forbid it.

In 2007 Turin (who is now chief technical officer of the odorant-designing company Flexitral in Chantilly, Virginia) and his hypothesis received support from a paper by four physicists at University College London. That work, published in the journal Physical Review Letters [subscription required], showed how the smell-tunneling process may operate. As an odorant approaches, electrons released from one side of a receptor quantum-mechanically tunnel through the odorant to the opposite side of the receptor. Exposed to this electric current, the heavier pinanethiol would vibrate differently from the lighter but similarly shaped pinanol.
“I call it the ‘swipe-card model,’?” says coauthor A. Marshall Stoneham, an emeritus professor of physics. “The card’s got to be a good enough shape to swipe through one of the receptors.” But it is the frequency of vibration, not the shape, that determines the scent of a molecule.

THE GREEN TEA PARTY

Even green tea may tie into subtle subatomic processes. In 2007 four biochemists from the Auton¬omous University of Barcelona announced that the secret to green tea’s effectiveness as an anti-oxidant—a substance that neutralizes the harmful free radicals that can damage cells—may also be quantum mechanical. Publishing their findings in the Journal of the American Chemical Society [subscription required], the group reported that antioxidants called catechins act like fishing trollers in the human body. (Catechins are among the chief organic compounds found in tea, wine, and some fruits and vegetables.)

Free radical molecules, by-products of the body’s breakdown of food or environmental toxins, have a spare electron. That extra electron makes free radicals reactive, and hence dangerous as they travel through the bloodstream. But an electron from the catechin can make use of quantum mechanics to tunnel across the gap to the free radical. Suddenly the catechin has chemically bound up the free radical, preventing it from interacting with and damaging cells in the body.
Quantum tunneling has also been observed in enzymes, the proteins that facilitate molecular reactions within cells. Two studies, one published in Science in 2006 and the other in Biophysical Journal in 2007, have found that some enzymes appear to lack the energy to complete the reactions they ultimately propel; the enzyme’s success, it now seems, could be explained only through quantum means.

QUANTUM TO THE CORE

Stuart Hameroff, an anesthesiologist and director of the Center for Consciousness Studies at the University of Arizona, argues that the highest function of life—consciousness—is likely a quantum phenomenon too. This is illustrated, he says, through anesthetics. The brain of a patient under anesthesia continues to operate actively, but without a conscious mind at work. What enables anesthetics such as xenon or isoflurane gas to switch off the conscious mind?

Hameroff speculates that anesthetics “interrupt a delicate quantum process” within the neurons of the brain. Each neuron contains hundreds of long, cylindrical protein structures, called microtubules, that serve as scaffolding. Anesthetics, Hameroff says, dissolve inside tiny oily regions of the microtubules, affecting how some electrons inside these regions behave.

He speculates that the action unfolds like this: When certain key electrons are in one “place,” call it to the “left,” part of the microtubule is squashed; when the electrons fall to the “right,” the section is elongated. But the laws of quantum mechanics allow for electrons to be both “left” and “right” at the same time, and thus for the micro¬tubules to be both elongated and squashed at once. Each section of the constantly shifting system has an impact on other sections, potentially via quantum entanglement, leading to a dynamic quantum-mechanical dance.

It is in this faster-than-light subatomic communication, Hameroff says, that consciousness is born. Anesthetics get in the way of the dancing electrons and stop the gyration at its quantum-mechanical core; that is how they are able to switch consciousness off.

It is still a long way from Hameroff’s hypothetical (and experimentally unproven) quantum neurons to a sentient, conscious human brain. But many human experiences, Hameroff says, from dreams to subconscious emotions to fuzzy memory, seem closer to the Alice in Wonderland rules governing the quantum world than to the cut-and-dried reality that classical physics suggests. Discovering a quantum portal within every neuron in your head might be the ultimate trip through the looking glass.

My Comment: This is important on so many levels. One is that we are mostly unaware of the degree to which we compartmentalize knowledge and consciousness. This fragmentation is definitely something we have to overcome in order to experience the oneness for which so many religions implore us to strive. The second is that this is one more item we should confront making us either choose or add a quantum paradigm to our sense of cause and effect. Now, I’ve noticed that many religious laws and teachings don’t make much sense in a Newtonian universe, but these same teachings and laws make a great deal more sense in a quantum universe or an Einsteinian universe—the greatest of which is the religious experience itself.

Contradictions

Astrophysicists Map Milky Way's Four Spiral Arms

ScienceDaily (Jan. 9, 2009) — A research team that has developed the first complete map of the Milky Way galaxy's spiral arms. The map shows the inner part of the Milky Way has two prominent, symmetric spiral arms, which extend into the outer galaxy where they branch into four spiral arms.

"For the first time these arms are mapped over the entire Milky Way," said Iowa State University's Martin Pohl, an associate professor of physics and astronomy. "The branching of two of the arms may explain why previous studies -- using mainly the inner or mainly the outer galaxy -- have found conflicting numbers of spiral arms."

The new map was developed by Pohl, Peter Englmaier of the University of Zurich in Switzerland and Nicolai Bissantz of Ruhr-University in Bochum, Germany.

As the sun and other stars revolve around the center of the Milky Way, researchers cannot see the spiral arms directly, but have to rely on indirect evidence to find them. In the visible light, the Milky Way appears as an irregular, densely populated strip of stars. Dark clouds of dust obscure the galaxy's central region so it cannot be observed in visible light.

The National Aeronautics and Space Administration's Cosmic Background Explorer satellite was able to map the Milky Way in infrared light using an instrument called the Diffuse IR Background Experiment. The infrared light makes the dust clouds almost fully transparent.

Englmaier and Bissantz used the infrared data from the satellite to develop a kinematic model of gas flow in the inner galaxy. Pohl used the model to reconstruct the distribution of molecular gas in the galaxy. And that led to the researchers' map of the galaxy's spiral arms.

The Milky Way is the best studied galaxy in the universe because other galaxies are too far away for detailed observations. And so studies of the galaxy are an important reference point for the interpretation of other galaxies.

Astrophysicists know that the stars in the Milky Way are distributed as a disk with a central bulge dominated by a long bar-shaped arrangement of stars. Outside this central area, stars are located along spiral arms.

In addition to the two main spiral arms in the inner galaxy, two weaker arms exist. These arms end about 10,000 light-years from the galaxy's center. (The sun is located about 25,000 light-years from the galactic center.) One of these arms has been known for a long time, but has always been a mystery because of its large deviation from circular motion. The new model explains the deviation as a result of alternations to its orbit caused by the bar's gravitational pull. The other, symmetric arm on the far side of the galaxy was recently found in gas data.

The discovery of this second arm was a great relief for Englmaier: "Finally it is clear that our model assumption of symmetry was correct and the inner galaxy is indeed quite symmetric in structure."

Other scientific groups are already interested in using the new map for their research. A group from France, for example, hopes to use it in their search for dark matter.

My Comment: By now it should be clear that one just can’t look out of the window and see the laws and structures of the universe. Except that you can do exactly that, if you know what you’re seeing. What you’re seeing is a fractal structure. The same can be said about books that are considered holy, that you can’t just pick them up, read the words, and understand what you’re reading. Except that you can, if you know that you are reading about a description of a fractal structure—the universe. It takes some serious thought and study to see that the Torah is describing a fractal universe, beginning with the four rivers of Eden. And because of the time needed to get from the illusion that you’re reading about a garden and only a garden—to understanding that you’re really beginning to read about something quite a bit bigger and quite a bit smaller than that garden, as well as that garden, I can only comment on the Torah. There just isn’t enough time to begin to talk about the Vedas, or Lao Tzu, or any other book or writings by a sage. That’s for others. But since there is so much controversy today about the first several sections of Genesis—I’ll weigh in that it may mean what is says, but that it’s hard to know what it means.

Factoring Out Intelligent Design

Evolution Of 'Irreducible Complexity' Explained

ScienceDaily (Apr. 6, 2006) — Using new techniques for resurrecting ancient genes, scientists have for the first time reconstructed the Darwinian evolution of an apparently "irreducibly complex" molecular system.

The research was led by Joe Thornton, assistant professor of biology at the University of Oregon's Center for Ecology and Evolutionary Biology, and will be published in the April 7 issue of SCIENCE.

How natural selection can drive the evolution of complex molecular systems -- those in which the function of each part depends on its interactions with the other parts--has been an unsolved issue in evolutionary biology. Advocates of Intelligent Design argue that such systems are "irreducibly complex" and thus incompatible with gradual evolution by natural selection.

"Our work demonstrates a fundamental error in the current challenges to Darwinism," said Thornton. "New techniques allowed us to see how ancient genes and their functions evolved hundreds of millions of years ago. We found that complexity evolved piecemeal through a process of Molecular Exploitation -- old genes, constrained by selection for entirely different functions, have been recruited by evolution to participate in new interactions and new functions."

The scientists used state-of-the-art statistical and molecular methods to unravel the evolution of an elegant example of molecular complexity -- the specific partnership of the hormone aldosterone, which regulates behavior and kidney function, along with the receptor protein that allows the body's cells to respond to the hormone. They resurrected the ancestral receptor gene -- which existed more than 450 million years ago, before the first animals with bones appeared on Earth -- and characterized its molecular functions. The experiments showed that the receptor had the capacity to be activated by aldosterone long before the hormone actually evolved.

Thornton's group then showed that the ancestral receptor also responded to a far more ancient hormone with a similar structure; this made it "preadapated" to be recruited into a new functional partnership when aldosterone later evolved. By recapitulating the evolution of the receptor's DNA sequence, the scientists showed that only two mutations were required to evolve the receptor's present-day functions in humans.

"The stepwise process we were able to reconstruct is entirely consistent with Darwinian evolution," Thornton said. "So-called irreducible complexity was just a reflection of a limited ability to see how evolution works. By reaching back to the ancestral forms of genes, we were able to show just how this crucial hormone-receptor pair evolved."

The study's other researchers include Jamie T. Bridgham, postdoctorate research associate in evolutionary biology and Sean M. Carroll, graduate research fellow in biology. The work was funded by National Science Foundation and National Institutes of Health grants and an Alfred P. Sloan Research Fellowship recently awarded to Thornton.

My Comment:This may challenge Intelligent Design as its advocates state their case, but you've got to admit that this finding is pretty darned cool. And that's because it challenges everyone's notion of sequential time--whether or not you are religious. But rethinking notions of time, like it or not, is a religious activity.