the extended phenotype: indirect genetic effects on ecosystems

thescientist |  The relationship between an individual’s phenotype and genotype has been fundamental to the genetic analysis of traits and to models of evolutionary change for decades. Of course, scientists have long recognized that phenotype responds to nongenetic factors, such as environmental variation in nutrient availability or the presence of other, competing species. But by assuming that the genetic component of a particular trait is confined to your genes and only yours, scientists overlooked another important input: the genes of your neighbors.

Take field crickets as an example. To identify potential mates, female crickets listen with ears on their forelegs to the males’ songs, produced by the rubbing together of their forewings. Some males emit series of long, trill-like chirps, an advertisement of their fitness that females find very attractive. Songs dominated by short chirps have less pull. But female crickets don’t evaluate songs on their absolute merits; instead, their preferences are influenced by the songs they’ve heard in the past. Female crickets previously exposed only to songs with long chirps are less likely to respond to short-chirp songs than females that have been exposed to the songs of less-fit males already. The insects appear to be retaining information about available males and then using that information to assess the attractiveness of suitors.¹

Choosing mates amidst competition is ubiquitous among animals, but the logistics of how such choice evolved is less straightforward: because male song type is largely determined by genetics, female mating behavior is under the influence of male genes. In other words, the females’ decision-making behaviors evolved based on the genetic composition of the entire social group. Such indirect genetic effects (IGEs), also called associative effects or extended phenotypes, are common and have profound implications for evolution. Beyond learning and behavior in social species, IGEs affect how organisms develop, how productive plants are, and whether individuals are attacked by predators, herbivores, and disease.

In some sense, examples of IGEs are intuitively obvious. No individual exists in a vacuum, isolated from the influences of others it encounters. Yet for decades, many prominent evolutionary theories assumed that all of the genetic influences on an individual’s phenotype came from genes within itself. What the field needs now is a clear framework that recognizes IGEs as additional factors in a population’s evolution, allowing for more-accurate predictions about how biological systems will change in the future. The genetic makeup of an individual not only influences phenotypes of individuals in its own species, but can have far-reaching effects on organisms at different trophic levels within its food web, impacting the dynamics of entire ecosystems. The role of commensal microbes in human health is a prime example of how IGEs can transcend species boundaries.

How IGEs affect evolutionary dynamics remains very much an open question. Recent theoretical strides in this area show how IGEs can greatly accelerate evolutionary change and hint at their hitherto unsuspected roles in such varied phenomena as animal mating rituals, the development of human agricultural systems, species range shifts in response to climate change, and even altruism. The influences of IGEs on diverse evolutionary processes are undoubtedly more complicated than most models can capture, and biologists must think creatively about new phenomena that IGEs may drive.

the body's ecosystem

thescientist |  The human body is teeming with microbes—trillions of them. The commensal bacteria and fungi that live on and inside us outnumber our own cells 10-to-1, and the viruses that teem inside those cells and ours may add another order of magnitude. Genetic analyses of samples from different body regions have revealed the diverse and dynamic communities of microbes that inhabit not just the gut and areas directly exposed to the outside world, but also parts of the body that were long assumed to be microbe-free, such as the placenta, which turns out to harbor bacteria most closely akin to those in the mouth. The mouth microbiome is also suspected of influencing bacterial communities in the lungs. Researchers are also examining the basic biology of the microbiomes of the penis, the vagina, and the skin.

“No tissue in the human body is sterile, including reproductive tissues and, for that matter, the unborn child,” Seth Bordenstein, a biologist at Vanderbilt University, says in an e-mail to The Scientist.

Altogether, the members of the human body’s microbial ecosystem make up anywhere from two to six pounds of a 200-pound adult’s total body weight, according to estimates from the Human Microbiome Project, launched in 2007 by the National Institutes of Health (NIH). The gastrointestinal tract is home to an overwhelming majority of these microbes, and, correspondingly, has attracted the most interest from the research community. But scientists are learning ever more about the microbiomes that inhabit parts of the body outside the gut, and they’re finding that these communities are likely just as important. Strong patterns, along with high diversity and variation across and within individuals, are recurring themes in microbiome research. While surveys of the body’s microbial communities continue, the field is also entering a second stage of inquiry: a quest to understand how the human microbiome promotes health or permits disease.

“None of us in the field—and this is true for the gut, this is true for the skin—none of us can actually tell how our experimental observations really relate to human disease, but we’re getting closer to mechanistic insights,” says immunologist Yasmine Belkaid, chief of mucosal immunology at the National Institute of Allergy and Infectious Disease.

cooperative social networking key to helping microbes spread...,

sciencedaily |  Fresh discoveries about how bacteria co-operate with each other when causing infection could help scientists identify animal diseases that might transmit to people.

Bugs that can co-operate best with each other are most likely to be able to jump to new species, including humans, a new study shows.

Bacteria interact by releasing molecules to help them adapt to their environment -- for example, when killing competing infections in their victim. They co-ordinate these actions by releasing tiny amounts of chemicals as signals.

Bacteria that can co-operate to create an environment in which they can thrive are potentially able to infect lots of different species, including humans. Discovering why some diseases are better equipped to infect more species than others -- and therefore could affect humans -- could be valuable in predicting and managing health threats.

Most new human infections arise from diseases that transmit from animals to humans. Many of these cause serious infections and are difficult to control, such as anthrax and the superbug MRSA.

Research led by the University of Edinburgh used a combination of mathematical models and scientific analysis of genetic code in almost 200 types of bacteria. They found that those bugs that carry lots of genes that help them to co-operate are best equipped to adapt to various environments.

Dr Luke McNally of the University of Edinburgh' School of Biological Sciences, who led the study, said: "Humans have been able to colonise almost all of their planet by collectively modifying the environment to suit themselves. Our study shows bugs try to do the same -- co-operation is important for the spread of bacteria to new species."

microbial colonization...,

thescientist |  Infants start out mostly microbe-free but quickly acquire gut bacteria, which take root in three successive groups. First, Bacilli dominate. Then Gammaproteobacteria surge, followed by Clostridia. But the pace at which these bacterial groups colonize the gastrointestinal tract depends on the time since the babies were conceived, not since when they were born. And time since conception appears to have more of an influence on the infant gut microbiome than other factors, such as exposure to antibiotics, whether babies were born vaginally or by cesarean section, and if they were breastfed. These are a few of the findings from a survey of 922 fecal samples collected from 58 premature babies, published today (August 11) in PNAS.

“It is an interesting study that provides useful data regarding temporal changes in microbial composition in the infant gut that can be mined further,” Shyamal Peddada, a biostatistician at the National Institute of Environmental Health Sciences who was not involved in the study, wrote in an e-mail to The Scientist.

“I think the paper does a nice job of showing that premature babies develop differently from full-term babies . . . it is not just a function of colonization after birth,” Rob Knight from the University of Colorado, Boulder, told The Scientist in an e-mail. “Differences in gut physiology or in the infant immune system could explain this pattern.”

Researchers at the Washington University School of Medicine in St. Louis embarked on this survey in an effort to better understand the role of the microbiota in the development of gut disorders common in premature infants, such as necrotizing enterocolitis. Without first defining the premature infant gut in the absence of gastrointestinal issues, the researchers struggled to identify potentially pathogenic bacterial patterns.

The researchers collected stool samples each time the babies defecated until they were thirty days old, and sampled every third elimination after that. They then sequenced 16S ribosomal RNA genes to identify the bacterial composition of each sample.

missing microbes: conspicuously obvious once the man points it out...,

martinblaser |   From Missing Microbes by Martin J. Blaser, MD. Blaser, former chair of medicine at NYU and president of the Infectious Diseases Society of America, is one of a growing number of medical practitioners and researchers who believe that we are experiencing a growing array of "modern plagues," and that the cause of these plagues is rooted in our "disappearing microbiota":

"Within the past few decades, amid all of [our] medical advances, something has gone terribly wrong. In many different ways we appear to be getting sicker. You can see the headlines every day. We are suffering from a mysterious array of what I call 'modern plagues': obesity, childhood diabetes, asthma, hay fever, food allergies, esophageal reflux and cancer, celiac disease, Crohn's disease, ulcerative colitis, autism, eczema. In all likelihood you or someone in your family or someone you know is afflicted. Unlike most lethal plagues of the past that struck relatively fast and hard, these are chronic conditions that diminish and degrade their victims' quality of life for decades. ...

"The autoimmune form of diabetes that begins in childhood and requires insulin injections (juvenile or Type I diabetes) has been doubling in incidence about every twenty years across the industrialized world. In Finland, where record keeping is meticulous, the incidence has risen 550 percent since 1950. ... But the disease itself has not changed; something in us has changed. Type I diabetes is also striking younger children. The average age of diagnosis used to be about nine. Now it is around six, and some children are becoming diabetic when they are three.

"The recent rise in asthma, a chronic inflammation of the airways, is similarly alarming. One in twelve people (about 25 million or 8 percent of the U.S. population) had asthma in 2009, compared with one in fourteen a decade earlier. Ten percent of American children suffer wheezing, breathlessness, chest tightness, and coughing; black children have it worst: one in six has the disease. Their rate increased by 50 percent from 2001 through 2009. But the rise in asthma has not spared any ethnicity: the rates were initially different in various groups, and all have been rising. ... No economic or social class has been spared.

"Food allergies are everywhere. A generation ago, peanut allergies were extremely rare. ... Ten percent of children suffer from hay fever. Eczema, a chronic skin inflammation, affects more than 15 percent of children and 2 percent of adults in the United States. In industrialized nations, the number of kids with eczema has tripled in the past thirty years. ...

"Why are all of these maladies rapidly rising at the same time across the developed world and spilling over into the developing world as it becomes more Westernized? Can it be a mere coincidenc

e? If there are ten of these modern plagues, are there ten separate causes? That seems unlikely.

"Or could there be one underlying cause fueling all these parallel increases? A single cause is easier to grasp; it is simpler, more parsimonious. But what cause could be grand enough to encompass asthma, obesity, esophageal reflux, juvenile diabetes, and allergies to specific foods, among all of the others? Eating too many calories could explain obesity but not asthma; many of the children who suffer from asthma are slim. Air pollution could explain asthma but not food allergies. ...

"The most popular explanation for the rise in childhood illness is the so-called hygiene hypothesis. The idea is that modern plagues are happening because we have made our world too clean. The result is that our children's immune systems have become quiescent and are therefore prone to false alarms and friendly fire. ...

"We need to look closely at the microorganisms that make a living in and on our bodies, massive assemblages of competing and cooperating microbes known collectively as the microbiome. ... Each of us hosts a ... diverse ecology of microbes that has coevolved with our species over millennia. They thrive in the mouth, gut, nasal passages, ear canal, and on the skin. In women, they coat the vagina. The microbes that constitute your microbiome are generally acquired early in life; surprisingly, by the age of three, the populations within children resemble those of adults. Together, they play a critical role in your immunity as well as your ability to combat disease. In short, it is your microbiome that keeps you healthy. And parts of it are disappearing.

"The reasons for this disaster are all around you, including overuse of antibiotics in humans and animals, Cesarean sections, and the widespread use of sanitizers and antiseptics, to name just a few. ...

"The loss of diversity within our microbiome is far more pernicious [than the overuse of antibiotics and resulting antibiotic resistance]. Its loss changes development itself, affecting our metabolism, immunity, and cognition.

"I have called this process the 'disappearing microbiota.' It's a funny term that does not immediately roll off your tongue, but I believe it is correct. For a number of reasons, we are losing our ancient microbes. This quandary is the central theme of this book. The loss of microbial diversity on and within our bodies is exacting a terrible price. I predict it will be worse in the future. Just as the internal combustion engine, the splitting of the atom, and pesticides all have had unanticipated effects, so too does the abuse of antibiotics and other medical or quasi-medical practices (e.g., sanitizer use).

"An even worse scenario is headed our way if we don't change our behavior. It is one so bleak, like a blizzard roaring over a frozen landscape, that I call it 'antibiotic winter.'"

the quantified microbiome visualization looks strangely like an appflow visualization...,

nationalgeographic |  Some of my friends are sporting wristbands these days that keep track of their bodies. Little computers nestled in these device inside record the steps they take each day, the beats of their heart, the length of their slumbers. At the end of each day, they can sit down at a computer and look at their data arrayed across a screen like a seismogram of flesh.

I got one of these devices as a gift recently. But as much as I enjoy wasting time with technology, I just didn’t care enough to put it on my wrist. I already know that I should run more, walk more, stand more, and avoid sitting in front of monitors more. I don’t need granular data to remind me of that.

But as I read the journal Genome Biology today, I decided that someday I might surrender to the Quantified Self movement. I’ll just have to wait till I can track my trillions of microbes from one day to the next.

Thanks to the falling cost of sequencing DNA, it’s now possible for us to survey the thousands of species that live in our bodies. A couple years ago, for example, I found out that I have 58 species in my bellybutton. But all I knew was that there were 58 species in my bellybutton at one point in time–that moment I swiped a Q-tip around my navel. But everything we know about bacteria tells us that our inner ecosystems can change swiftly. My bellybutton may be remarkably different today than it was when I put a Q-tip in it.

Eric Alm, a biologist at MIT, and a graduate student of his named Lawrence David decided to plumb this change by tracking a year in the life of their microbiomes. Each day, they saved some of their stool, and later, they extracted DNA from it to figure out which species of bacteria were living in their guts. David also spat some of his saliva into a tube each day so that he could compare how his microbiome changed in his gut compared to his mouth.

Even though their study only involved two people, it was still very much a Big Data project. And one of the major challenges of any Big Data project is to visualize the results in a useful way. A number on a wrist watch won’t cut it. Between Alm and David, they and their colleagues identified thousands of species of microbes. Most were rare, while a few hundred made up the majority of bugs in their bodies. Some species showed up briefly and vanished; others lingered all year.

Here’s one way to look at their microbiomes. It shows David’s saliva. Each band represents one of the dominant species (or operational taxonomic units). Species belonging to the same lineage (a phylum) have different shades of the same color.  Fist tap Dale.

genetic information transfer promotes cooperation in bacteria

pnas |  Many bacterial species are social, producing costly secreted “public good” molecules that enhance the growth of neighboring cells. The genes coding for these cooperative traits are often propagated via mobile genetic elements and can be virulence factors from a biomedical perspective. Here, we present an experimental framework that links genetic information exchange and the selection of cooperative traits. Using simulations and experiments based on a synthetic bacterial system to control public good secretion and plasmid conjugation, we demonstrate that horizontal gene transfer can favor cooperation. In a well-mixed environment, horizontal transfer brings a direct infectious advantage to any gene, regardless of its cooperation properties. However, in a structured population transfer selects specifically for cooperation by increasing the assortment among cooperative alleles. Conjugation allows cooperative alleles to overcome rarity thresholds and invade bacterial populations structured purely by stochastic dilution effects. Our results provide an explanation for the prevalence of cooperative genes on mobile elements, and suggest a previously unidentified benefit of horizontal gene transfer for bacteria. 

Bacteria often cooperate through the production of public goods that change their environment. These processes can affect human health by increasing virulence or antibiotic resistance. Public good production is costly, making cooperation susceptible to invasion by nonproducing “cheater” individuals. Bacteria also readily share genes, even among distinct species. Our experiments and models converge to show that when both cheating and cooperative genes are transferred, cooperators win against cheaters because transfer increases assortment among alleles, favoring cooperation. This can explain why genes for cooperation are often mobile, and suggests that, in addition to reducing antibiotic resistance spread, preventing gene mobility could reduce cooperative virulence.

microbial genes, brain & behaviour – epigenetic regulation of the gut–brain axis

wiley |  To date, there is rapidly increasing evidence for host–microbe interaction at virtually all levels of complexity, ranging from direct cell-to-cell communication to extensive systemic signalling, and involving various organs and organ systems, including the central nervous system. As such, the discovery that differential microbial composition is associated with alterations in behaviour and cognition has significantly contributed to establishing the microbiota–gut–brain axis as an extension of the well-accepted gut–brain axis concept. Many efforts have been focused on delineating a role for this axis in health and disease, ranging from stress-related disorders such as depression, anxiety and irritable bowel syndrome to neurodevelopmental disorders such as autism. There is also a growing appreciation of the role of epigenetic mechanisms in shaping brain and behaviour. However, the role of epigenetics in informing host–microbe interactions has received little attention to date. This is despite the fact that there are many plausible routes of interaction between epigenetic mechanisms and the host-microbiota dialogue. From this new perspective we put forward novel, yet testable, hypotheses. Firstly, we suggest that gut-microbial products can affect chromatin plasticity within their host's brain that in turn leads to changes in neuronal transcription and eventually alters host behaviour. Secondly, we argue that the microbiota is an important mediator of gene-environment interactions. Finally, we reason that the microbiota itself may be viewed as an epigenetic entity. In conclusion, the fields of (neuro)epigenetics and microbiology are converging at many levels and more interdisciplinary studies are necessary to unravel the full range of this interaction.

the human eusocial prime directive - cybernetic civilization

paulchefurka | Humanity appears to be in the grip of a global system - one that we originally created, but which is now shaping our lives independently of our wishes.

I've recently begun to suspect that humanity is at a point of endosymbiosis with our electronic communications and control technology, especially through the Internet. In a sense, we humans have incorporated ourselves as essential control elements of a planet-wide cybernetic super-organism. The precedent for something like this is the way that mitochondria migrated as bacteria into ancient prokaryotic cells to become essential components of the new eukaryotic cells that make up all modern organisms, including us.

To expand on the "super-organism" concept a bit, it looks to me as though what humanity has done over the last few centuries is built ourselves a global cybernetic exoskeleton. Although its development started back with the emergence of language and the taming of fire, it's most visible in the modern world, and especially in the last two decades.

Transportation systems act as its gut and bloodstream, carrying raw materials (the food of civilization) to the digestive organs of factories, and carrying the finished goods (the nutrients) to wherever they are needed. Engines and motors of all kinds are its muscles. The global electronic communication network is its nervous system. Electronic sensors of a million kinds are its organs of taste, touch, smell and sight. Legal systems, police and military make up its immune system.

Human beings have evolved culturally to the point where we now act largely as hyper-functional decision-making neurons within this super-organism, with endpoint devices like smart phones, PCs and their descendants acting as synapses, and network connections being analogous to nerve fibers.

Just as neurons cannot live outside the body, we have evolved a system that doesn't permit humans to live outside its boundaries. Not only is there very little "outside" left, but access to the necessities of life is now only possible though the auspices of the cybernetic system itself. (For example, consider living without a socially-approved job. It's barely possible for a few people, but essentially impossible for most of us.) As we have developed this system around us, we have had to relinquish more and more of our autonomy in favor of helping the machine continue functioning and growing.

While we can no longer survive outside our cybernetic exoskeleton, in return it can't exist without our input. I realized over the last month or so that this means the symbiosis has already occurred. If I had to put a "closure date" on it, the period where it transitioned to its current form was around 1990 (plus or minus a decade or so). We didn't even notice it happening - to us it just looked like our daily lives going on as usual.

I realize that I'm re-visiting an old, familiar science-fiction idea. In reality it seems to have happened through a quiet, "natural" process of coevolution driven by the mutual amplification effects of human ingenuity, electronic technology and large amounts of available energy - rather than through the drama of a Borg-like assimilation of humans into a hive mind, or Ray Kurzweil's eschatological vision of a Technological Singularity.

coopetition...,

wikipedia | Coopetition or Co-opetition (sometimes spelled "coopertition" or "co-opertition") is a neologism coined to describe cooperative competition. Coopetition is a portmanteau of cooperation and competition.

Basic principles of co-opetitive structures have been described in game theory, a scientific field that received more attention with the book Theory of Games and Economic Behavior in 1944 and the works of John Forbes Nash on non-cooperative games. It is also applied in the fields of political science and economics and even universally [works of V. Frank Asaro, J.D.: Universal Co-opetition,2011, and The Tortoise Shell Code, novel, 2012].

Coopetition occurs when companies interact with partial congruence of interests. They cooperate with each other to reach a higher value creation if compared to the value created without interaction, and struggle to achieve competitive advantage.

Often coopetition takes place when companies that are in the same market work together in the exploration of knowledge and research of new products, at the same time that they compete for market-share of their products and in the exploitation of the knowledge created. In this case, the interactions occur simultaneously and in different levels in the value chain. This is the case of the arrangement between PSA Peugeot Citroën and Toyota to share components for a new city car - simultaneously sold as the Peugeot 107, the Toyota Aygo, and the Citroën C1, where companies save money on shared costs while remaining fiercely competitive in other areas. Several advantages can be foreseen, as cost reductions, resources complementarity and technological transfer. Some difficulties also exist, as distribution of control, equity in risk, complementary needs and trust. Not only two companies can interact within a coopetitive environment, but several partnerships among competitors are possible.

human breath analysis and individual metabolic phenotypes

plosone | The metabolic phenotype varies widely due to external factors such as diet and gut microbiome composition, among others. Despite these temporal fluctuations, urine metabolite profiling studies have suggested that there are highly individual phenotypes that persist over extended periods of time. This hypothesis was tested by analyzing the exhaled breath of a group of subjects during nine days by mass spectrometry. Consistent with previous metabolomic studies based on urine, we conclude that individual signatures of breath composition exist. The confirmation of the existence of stable and specific breathprints may contribute to strengthen the inclusion of breath as a biofluid of choice in metabolomic studies. In addition, the fact that the method is rapid and totally non-invasive, yet individualized profiles can be tracked, makes it an appealing approach.

“lives in a pineapple under the sea... Absorbent and yellow and porous is he.”

NYTimes | It may be distressing to those committed to “autonomy,” but such manipulators have inherited the earth. Including us.

Take coughing, or sneezing. It may be beneficial for an infected person to cough up or sneeze out some of her tiny organismic invaders, although it isn’t so healthful for others nearby. But what if coughing and sneezing aren’t merely symptoms but also, even primarily, a manipulation of us, the “host,” by influenza viruses? Shades of zombie bees, fattened mice and grass-blade-besotted ants.

Just as Lenin urged us to ask “who, whom?” with regard to social interactions — who benefits at the expense of whom? — the new science of evolutionary medicine urges a similar question: who benefits when people show symptoms of a disease? Often, it’s the critters that are causing the disease in the first place.

But what about the daily, undiseased lives most of us experience? Voluntary actions are, we like to insist, ours and ours alone, not for the benefit of some parasitic or pathogenic occupying army. When we fall in love, we do so for ourselves, not at the behest of a romance-addled tapeworm. When we help a friend, we aren’t being manipulated by an altruistic bacterium. If we eat when hungry, sleep when tired, scratch an itch or write a poem, we aren’t knuckling under to the vices of our viruses.

But it isn’t that simple.

Think about having a child, and ask who — or rather, what — benefits from reproduction? It’s the genes. As modern biologists recognize, babies are our genes’ way of projecting themselves into the future.

Unlike the cases of parasites or pathogens, when genes manipulate “their” bodies, the situation seems less dire, if only because instead of foreign occupation it’s our genes, our selves. But those presumably personal genes aren’t any more hesitant about manipulating our bodies, and by extension our actions, than is a parasitic fly hijacking a honeybee.

Here, then, is heresy: maybe there is no one in charge — no independent, self-serving, order-issuing homunculus. Buddhists note that our skin doesn’t separate us from the environment, but joins us, just as biologists know that “we” are manipulated by, no less than manipulators of, the rest of life. Who is left after “you” are separated from your genes? Where does the rest of the world end, and each of us begin?

Let’s leave the last words to a modern icon of organic, oceanic wisdom: SpongeBob SquarePants. Mr. SquarePants, a cheerful, talkative — although admittedly, somewhat cartoonish — fellow of the phylum Porifera, “lives in a pineapple under the sea... Absorbent and yellow and porous is he.” I don’t know about the pineapple or the yellow, but absorbent and porous are we, too.

left in the dark: plant/human symbiosis and the fall of humanity

realitysandwich | “I believe that the lost secret of human emergence . . . the undefined catalyst that took a very bright monkey and turned that species into a self-reflecting dreamer . . . that catalyst has to be sought in these alkaloids in the food chain that were catalyzing higher states of intellectual activity.”
--Terence McKenna

Tony Wright and Graham Gynn are authors of Left In The Dark--the book that presents Tony’s research outlining a radical re-interpretation of the current data regarding human evolution and, they contend, our recent degenerated state we call “civilization”. You can read the book for free here. Despite such a young and extreme proposal positive reactions are growing and include such minds as Dennis McKenna, Stanislav Grof, Colin Groves, Michael Winkelman and many There are many mysterious anomalies about human evolution yet to be adequately explained. These include the human brains rapid expansion in size and complexity, why this accelerating expansion suddenly stalled roughly 200,000 years ago and our brains have been shrinking ever since, and why our rare glimpses of genius goes hand in hand with our species wide insanity.

The following is a discussion with Tony Wright on these anomalies and more, followed by some further information on his theory.

TS: After two decades of research and radical self-experimentation you’ve come to a synthesis between the ancient data and information coming out of modern science. Paradoxically this all seems to indicate a humongous problem, and simultaneously explains why we would be oblivious to it in the first place: we are all suffering from species wide neural retardation, and are now too deluded to even realize when faced with the mountain of evidence. Is this the general idea?

TW: Yes. It should be virtually impossible to find any supporting evidence for such a profound theory if there was no real problem with the development and structural integrity of our neural system in the first place. If there were only ancient accounts of the diagnosis, or any supporting biological data, or initial support from some of society’s sharpest minds, then it should at least ring alarm bells. That all those elements exist and in addition our collective behavior has long been thought by many to be insane indicates something really serious just doesn’t add up. If everything is fine then the theory would be a no-brainer to refute, and we should at least have no fear in thoroughly checking it out.

So during millions of years of evolution in the African tropical forest we developed a symbiosis with fruit, and your proposing that it is no coincidence the most complex tissue in the known universe evolved during a symbiosis with perhaps dozens of species of the most complex chemical factories on the planet. How did this occur?

I’m proposing that the accelerating expansion of the neo-cortex was due to a runaway feedback mechanism driven by our own hormone system in combination with the complex plant bio-chemistry provided by our diet. What has been overlooked is the profound effects of flooding our brains 24/7 for thousands of generations with this highly advanced molecular engineering formula. Fruit is essentially a womb-like developmental environment for the seeds and has very unique, highly complex hormonally active chemistry. Our early development is dictated by the transcription process whereby changes in how the DNA is read dictate the type of structures that develop. Steroids like testosterone are the key players here, but by incorporating more and more of these DNA-reading plant chemicals into our diet we basically shifted from a typical mammalian developmental environment to more of a plant developmental environment.

Along with regulating gene transcription many of these molecules increase brain activity, modulate the endocrine system including the pineal gland, inhibit mono amine oxidase (MAO inhibitors), are antioxidants and also inhibit the activity of our own hormones such as testosterone and oestrogens. Just altering the activity of these two hormones has a dramatic affect on many aspects of our development, physiology and neural structure. For example, decreasing they’re activity extends juvenility and the window for brain development by delaying the onset of sexual maturity.

All this coming together would have many interconnected affects and, being that this bio-chemistry would be present in the developmental environment it would dramatically impact what develops at this most sensitive and rapid stage of brain/endocrine system growth in the uterus.

This carried on after birth through breastfeeding, and then afterwards through directly ingesting this highly advanced molecular engineering cocktail we call fruit. Each generation would pass down a progressively modified neuro-endocrine system as a result. So after millions of years of ever more entangled co-evolution nearly all of the transcription chemicals present during our early development and on through life that were essential to our optimal design/functioning were lost and replaced by progressively worse substitutes irrelevant to our evolution . . . all the way until we reach today’s ‘junk’ food. Ironically much of this actually has the opposite effect of fruit bio-chemistry on our hormones, causing the unique process to reverse.

All of this sounds complex but at its foundation it’s just really basic engineering principles: If you change the design (transcription) and construction materials that a system or technology is built from and fueled by, then the structure and functionality of that system will inevitably change as a result. This logic is obvious when applied to any of our technologies but paradoxically we haven’t applied it to the thing involved in generating our perception, which just happens to be the most complex piece of kit we know. Our perception is directly correlated with and ‘effectively’ a product of the extremely sensitive structure and bio-chemistry of our brain and this has changed out of all recognition in a very short time. (more on this symbiosis)

competing visions of a computer-controlled future

Spiegel | Federico Faggin has lived in the United States for more than 40 years, but he's still living la dolce vita in classic Italian style in his magnificent house on the edge of Silicon Valley. The elderly Faggin answers the phone with a loud "pronto" and serves wine and antipasti to guests. Everything about him is authentic. The only artificial thing in Faggin's world is what he calls his "baby." It has 16 feet -- eight on each side -- and sits wrapped in cotton in a cigarette case.

About four decades ago, Faggin was one of the first employees at Intel when he and his team developed the world's first mass-produced microprocessor, the component that would become the heart of the modern era. Computer systems are ubiquitous today. They control everything, from mobile phones to Airbus aircraft to nuclear power plants. Faggin's tiny creation made new industries possible, and he has played a key role in the progress of the last few decades. But even the man who triggered this massive revolution is slowly beginning to question its consequences.

"We are experiencing the dawn of a new age," Faggin says. "Companies like Google and Facebook are nothing but a series of microprocessors, while man is becoming a marginal figure."

The Worrying Speed of Progress
This week, when German Chancellor Angela Merkel and Google chairman Eric Schmidt opened CeBIT -- the digital industry's most important annual trade fair -- in the northern German city of Hanover, there was a lot of talk of the mobile Internet once again, of "cloud computing," of "consumer electronics" and of "connected products." The overarching motto of this convention is "Trust" -- in the safety of technology, in progress and in the pace at which progress unfolds.

This effort to build trust seems more necessary than ever, now that those who place their confidence in progress are being joined by skeptics who also see something dangerous about the rapid pace of development.

In his book "The Lights in the Tunnel: Automation, Accelerating Technology and the Economy of the Future," American computer scientist Martin Ford paints a grim picture. He argues that the power of computers is growing so quickly that they will be capable of operating with absolutely no human involvement at some point in the future. Ford believes that 75-percent unemployment is a possibility before the end of the century.

"Economic progress ultimately signifies the ability to produce things at a lower financial cost and with less labor than in the past," says Polish sociologist Zygmunt Bauman. As a result, he says, increasing effectiveness goes hand in hand with rising unemployment, and the unemployed merely become "human waste."

Likewise, in their book "Race Against the Machine," Erik Brynjolfsson and Andrew McAfee, both scholars at the Massachusetts Institute of Technology (MIT), argue that, for the first time in its history, technological progress is creating more jobs for computers than for people.

how your cat is making you crazy..,

TheAtlantic | No one would accuse Jaroslav Flegr of being a conformist. A self-described “sloppy dresser,” the 53-year-old Czech scientist has the contemplative air of someone habitually lost in thought, and his still-youthful, square-jawed face is framed by frizzy red hair that encircles his head like a ring of fire.

Certainly Flegr’s thinking is jarringly unconventional. Starting in the early 1990s, he began to suspect that a single-celled parasite in the protozoan family was subtly manipulating his personality, causing him to behave in strange, often self-destructive ways. And if it was messing with his mind, he reasoned, it was probably doing the same to others.

The parasite, which is excreted by cats in their feces, is called Toxoplasma gondii (T. gondii or Toxo for short) and is the microbe that causes toxoplasmosis—the reason pregnant women are told to avoid cats’ litter boxes. Since the 1920s, doctors have recognized that a woman who becomes infected during pregnancy can transmit the disease to the fetus, in some cases resulting in severe brain damage or death. T. gondii is also a major threat to people with weakened immunity: in the early days of the AIDS epidemic, before good antiretroviral drugs were developed, it was to blame for the dementia that afflicted many patients at the disease’s end stage. Healthy children and adults, however, usually experience nothing worse than brief flu-like symptoms before quickly fighting off the protozoan, which thereafter lies dormant inside brain cells—or at least that’s the standard medical wisdom.

But if Flegr is right, the “latent” parasite may be quietly tweaking the connections between our neurons, changing our response to frightening situations, our trust in others, how outgoing we are, and even our preference for certain scents. And that’s not all. He also believes that the organism contributes to car crashes, suicides, and mental disorders such as schizophrenia. When you add up all the different ways it can harm us, says Flegr, “Toxoplasma might even kill as many people as malaria, or at least a million people a year.”

An evolutionary biologist at Charles University in Prague, Flegr has pursued this theory for decades in relative obscurity. Because he struggles with English and is not much of a conversationalist even in his native tongue, he rarely travels to scientific conferences. That “may be one of the reasons my theory is not better known,” he says. And, he believes, his views may invite deep-seated opposition. “There is strong psychological resistance to the possibility that human behavior can be influenced by some stupid parasite,” he says. “Nobody likes to feel like a puppet. Reviewers [of my scientific papers] may have been offended.” Another more obvious reason for resistance, of course, is that Flegr’s notions sound an awful lot like fringe science, right up there with UFO sightings and claims of dolphins telepathically communicating with humans.

But after years of being ignored or discounted, Flegr is starting to gain respectability. Psychedelic as his claims may sound, many researchers, including such big names in neuroscience as Stanford’s Robert Sapolsky, think he could well be onto something. Flegr’s “studies are well conducted, and I can see no reason to doubt them,” Sapolsky tells me. Indeed, recent findings from Sapolsky’s lab and British groups suggest that the parasite is capable of extraordinary shenanigans. T. gondii, reports Sapolsky, can turn a rat’s strong innate aversion to cats into an attraction, luring it into the jaws of its No. 1 predator. Even more amazing is how it does this: the organism rewires circuits in parts of the brain that deal with such primal emotions as fear, anxiety, and sexual arousal. “Overall,” says Sapolsky, “this is wild, bizarre neurobiology.” Another academic heavyweight who takes Flegr seriously is the schizophrenia expert E. Fuller Torrey, director of the Stanley Medical Research Institute, in Maryland. “I admire Jaroslav for doing [this research],” he says. “It’s obviously not politically correct, in the sense that not many labs are doing it. He’s done it mostly on his own, with very little support. I think it bears looking at. I find it completely credible.”

What’s more, many experts think T. gondii may be far from the only microscopic puppeteer capable of pulling our strings. “My guess is that there are scads more examples of this going on in mammals, with parasites we’ve never even heard of,” says Sapolsky.

life as art: the legacy of lynn margulis

RealitySandwich | Richard Dawkins, formidable commander of both the Queen's English and a veritable worldwide army of devoted reductionists, once referred to the late Lynn Margulis as the "high priestess of symbiosis". Was this a warm colourful accolade or a shrewd slight? Given that Dawkins has spent decades steadfastly clinging to his beloved selfish gene paradigm and has even spoken of selfish cooperation when dealing with the symbiotic side of life that Margulis championed, I suspect his sentiment was not entirely benign. Although Dawkins openly admired Margulis for persevering with the theory that various cell organelles evolved through a process of endosymbiosis, and while aware, like any biologist, that the web of life evinces all manner of symbiotic relationships, he always seemed distinctly rattled by the social connotations that symbiosis invariably evokes. After all, unlike the notion of selfish genes, mutually beneficial cooperation sounds nice. Two or more organisms working together in an integrated and coherent way? Why, symbiosis has an almost ‘lovey-dovey' and ‘new-agey' air to it! Goddess forbid that we should draw any social lessons from such intimate biological arrangements! Best, then, to employ a cunning linguistic trick and make this embarrassingly alluring aspect of life disappear. Or at least shove it out of the way. Hence Dawkins use of the clumsy term ‘selfish cooperation' (as opposed to speaking of, say, emergent higher order selves, or even unconscious cooperation).

According to Dawkins, we might be impressed by two living systems working in some sort of mutually beneficial accord but in reality it is nothing more than a convoluted extension of selfishness. Don't be too moved by the astonishing sight of a pollen dusted humming bird feeding on a symbiotic nectar rich bloom! Don't let exotic symbiotic corals (that are a union of an animal and an alga) blow your mind! Don't gloat too long over a picture of a bobtail squid packed full of symbiotic bioluminescent bacteria! Move on people, this symbiosis business is all smoke and mirrors. Life is, at heart, no more than inert bits of digital DNA code that know nothing of cooperation and harmonious coexistence but only the competitive drive to replicate. If their phenotypic expression is involved in some exquisite symbiotic arrangement or another, then this is really beside the point.

Such was the kind of paradigmatic resistance that Margulis was up against. It is probably no coincidence that it was a woman who came to the fore promoting the significance of symbiosis in the evolution of life -- and not just the symbiotic origins of mitochondria and chloroplasts or the symbiosis evinced by corals or flowering plants and their pollinators, but even the emergence of new species through the process of symbiogenesis (this is still a contentious issue -- but examples continue to emerge). Is there something deeply feminine about cooperation? Is the drive for co-existence somehow more active in the female psyche than in the male psyche? In any case, legend tells us that Margulis had a really hard time convincing her academic male superiors that certain organelles within mammalian cells were once free living bacteria. It's one thing to note the symbiotic alliance of, say, cleaner fish with their bigger fish customers (who could easily gobble up the diminutive cleaners if they wanted), but when you realise that mitochondria (the energy engines of animals) and chloroplasts (the energy engines of plants) were once separate living micro-organisms that are now symbiotically woven inside animals and plants, symbiosis emerges as a kind of advanced technique learned by life, so sophisticated and subtle in deployment that we may be blind to it. If, however, we acknowledge the important role symbiosis has played in life's evolution, the way we perceive life begins to change. Life is no longer seen to be wholly red in tooth and claw -- but rather symbiotic in embrace and interchange (at least where possible).

as above, so below: the worldview of Lynn Margulis

realitysandwich | "In the arithmetic of life, One is always Many."

Lynn Margulis, biologist and Distinguished Professor of Geosciences, composed a grand and powerful view of the living and the non-living. Integrating the work of obscure Russian scientists, DNA pulled from cell organelles, computer-generated daisies, and the hindguts of termites, her vision was wider in scope and more profound in depth than any other coherent scientific world view. At the time of her death on November 22nd, 2011, it is a vision that remains misunderstood and misconstrued by many scientists.

Much of this view came from her uncanny ability to first lean forward and see the smallest inhabitants of the Earth; to hover there, and then to leap back at the speed of thought to conceptualize the entire planet. Lean forward, then stand back. This inner movement, this seeing from soil to space, marked a unique scientific endeavor.

This perspective was earned only through walking through diverse areas of study -- geology, genetics, biology, chemistry, literature, embryology, paleontology. Those fields, are sometimes separated by an untraversed distance at universities: they are housed in separate buildings which may as well be different worlds. In Margulis, they found agreement and discussion with each other; they were reconnected, just as they are intrinsically connected in nature.

This journey led her to emphasize in all her scientific work two phenomena -- the fusing of distinct beings into a single being: symbiosis; and the interaction of organisms and their environments to create relational "loops" that led to regulation of many Earth systems: Gaia Theory.

Taken separately these concepts have the ability to redefine, respectively, how we understand organisms and the environment.

Taken together, they can redefine our consciousness.

infection link to mental illness...,

LATimes | Brody Kennedy was a typical sixth-grader who loved to hang out with friends in Castaic and play video games. A strep-throat infection in October caused him to miss a couple of days of school, but he was eager to rejoin his classmates, recalls his mother, Tracy.

Then, a week after Brody became ill, he awoke one morning to find his world was no longer safe. Paranoid about germs and obsessed with cleanliness, he refused to touch things and showered several times a day. His fear prevented him from attending school, and he insisted on wearing nothing but a sheet or demanding that his mother microwave his clothes or heat them in the dryer before dressing.

So began a horrific battle with a sudden-onset mental illness that was diagnosed as pediatric autoimmune neuropsychiatric disorder associated with streptococcus, or PANDAS. The puzzling name describes children who have obsessive-compulsive disorder that occurs suddenly — and often dramatically — within days or weeks of a simple infection, such as strep throat.

"He washed his hands over and over and was using hand-sanitizer nonstop," said Tracy Kennedy, who has home-schooled her 11-year-old son since early November. "He had never been like this before. Ever. He just woke up with it."

The bizarre illness, first recognized in the mid-1990s, has been cloaked in controversy. Now, however, studies are reinforcing the belief that some psychiatric illnesses can be triggered by ordinary infections and the body's immune response. While the theory remains unproved, the research raises the possibility that some cases of mental illness might be cured by treating the immune system dysfunction.

"Some people get sick with whatever infection, and they recover and they're fine," says M. Karen Newell Rogers, an immunologist at Texas A&M Health Science Center College of Medicine in Temple, Texas, who studies such illnesses. "Other people get sick and recover, but they are not the same."

PANDAS is thought to be caused by antibodies generated as a result of an infection, usually strep. Normally, an infection causes the body to generate antibodies that fight the infection and promote healing. But in PANDAS, the antibody response is thought to go awry, attacking brain cells and resulting in OCD symptoms.

A greater understanding of the link between strep and OCD has opened the door to the study of other psychiatric or neurological illnesses that may be linked to improper immune response, including cases of autism, schizophrenia and anorexia.

levels of symbiotic cooperation previously unknown...,

Hotspots in the top right triangle, which compares all gene transfer events, shows microbes that live in the same niche more readily exchange genetic material. Looking at antibiotic resistance genes (bottom left triangle), however, paints a more complex and nuanced portrait of genetic transfer. (Nature)

Wired | Researchers have discovered an underworld of genetic exchange among bacteria, one more vast than previously imagined.

A comparison of thousands of bacterial genomes from around the world found genes flowing easily between species separated by hundreds, even thousands of miles. Whether the bacteria were related or not didn’t matter — a fascinating phenomenon on its own, but disturbing when the genes involved could turn pathogens into drug-resistant superbugs.

“We should have done this study and asked these questions five years ago,” said microbiologist Eric Alm of MIT, leader of a study published online Oct. 30 in Nature. “The significance was off the charts.”

Bacteria readily exchange DNA between closely related species, and much less frequently across unrelated lineages. This so-called horizontal gene transfer fuels adaptation, allowing for rapid adjustments to local pressures. Its full extent, however — especially in bacteria associated with humans, including those in our bodies, where bugs outnumber cells by 10 to 1 — are unknown.

To get a global picture of horizontal gene transfer, Alm, two graduate students and other collaborators compared 2,235 different bacterial genomes. “I was hoping to find five to 10 examples of recent gene transfers,” he said. “My students came back in a week with 10,000 different genes that had been transferred.”

The researchers compared transfers in several ways: first by the microbes’ genetic similarities, and then by geographic distance separating the locations of their collection. Neither followed a predictable pattern, but patterns did emerge when the researchers analyzed ecological niches.

Instead of swapping genes with microbes genetically related to them, or near them, bacteria seem to be swapping with microbes fulfilling similar roles. Alm’s team also found that genes especially important to humans — those found in our stomach flora, for example, or genes conveying antibiotic resistance — are particularly good at long-distance swaps.

In the future, Alm hopes to look more closely at gene transfer in virulent microbes, such as those that cause meningitis. Tracking genes that are especially likely to flow could help identify new disease-battle targets. Alm also wants to find out exactly how business is conducted in what he called a genetic “black market.” DNA can travel on dead cell fragments, viruses, and other sub-cellular vehicles, and the exact routes remain unknown.

“It could be almost anything,” he said. “We have no idea. I would love to know.” Fist tap Dale.

told you so...,

The Scientist | Like many great political alliances, symbiotic relationships in biology may have started with antagonism, before the two parties reached mutual understanding—at least according to some evolutionary biologists. The often cited example is the mitochondrion, the eukaryotic cell’s energy-supplying organelle, which may have first existed as a prokaryote. As the story goes, this prokaryote was engulfed by a second cell, and the two eventually formed such a close symbiotic alliance that one could not live without the other. This mutual dependence, however, formed over many millennia.

Our own symbionts, the microbes that reside throughout our bodies, primarily in our guts, have a more independent—some might say downright rocky—relationship with us, their hosts.

Although gut bacteria have long been called commensal (in which only one party derives benefit, but neither is harmed), it is now clear that we draw many benefits from their colonization of our body, some of them essential to our health. Our relationship with gut bacteria is complicated, however. While involved in metabolizing food into energy, producing micronutrients, and shaping our immune systems, gut microbes are also increasingly being linked to medical conditions including obesity, inflammatory bowel disease, and diabetes. And our understanding of their influence continues to widen: these bacteria may play a critical role in cancer, either protecting us from it, or in some cases, promoting its initiation and progression.