THE TWILIGHT ZONE

What's in your gut?
By David Biello

Modern science has revealed a startling fact that was first intimated by Anton von Leeuwenhoek scraping his teeth more than 400 years ago—you are more bacteria than you. Estimates put the number of microbial cells as constituting 10 times more of the cells in your body than actual human cells. What's worse, you better not get rid of them. Without them, you'll die.

This human microbiome, as scientists like to call it, has been the subject of much recent scrutiny, including a project to catalog the thousands or even millions of microbes within us and their function. After all, a better understanding of microbes and their role in our bodies could be the key to multiple health improvements and have led to new techniques, such as fecal transplants. Now a team of scientists led by microbiologist Jeffrey Gordon of Washington University in St. Louis has sequenced the "virome" or genetic code of "virus-like particles" from the poop of four pairs of female twins and their mothers, pulled from the Missouri Adolescent Female Twin Study that enlisted such women born between 1975 to 1986.

Perhaps unsurprisingly, female twins and their mothers tend to share the same set of such bacterial genetic material in their guts. After all, mothers inoculate infants with their gut bacteria during normal vaginal birth, and even C-section babies are almost instantly colonized by bacteria more commonly found on skin. But they don't share the same set of viruses—even though those viruses are living in roughly the same set of microbial cells. "Viromes are unique to individuals regardless of their degree of genetic relatedness," the researchers write in the July 15 issue of Nature. (Scientific American is part of the Nature Publishing Group.)

Such diversity could help explain the different health outcomes observed in even the most genetically related people, such as twins. And the virome is a treasure trove of new genetic material—more than 81 percent of the viruses or virus-like particles were new to science. This inner voyage of tiny discovery (with outsized potential) is just getting underway.

http://www.angelfire.com/hi/TheSeer/Lipton.html

The Science Of Innate Intelligence

In 1953 Watson and Crick discovered DNA. Studies of the protein machine reveal a complex polymerase, which is contained in every cell, so that every single human cell has enough information to reproduce an entire human. DNA is extremely stable and in fact studies of fossil material that is 50,000 years old show the DNA structure to be still intact and viable.

This gave rise to a belief in the primacy of DNA as being the causal agent in all life. Genetic determinism holds that all traits and characteristics are defined at the moment of conception. Crick’s hypothesis implies a fatalistic view which disempowers the individual and would have you believe that you are controlled by your genes. Acceptance of this hypothesis is so widespread that some women whose family has a history of breast cancer have undergone a mastectomy rather than risk getting the cancer. This belief was in the best interest of drug manufacturers who have become very powerful.

But the reductionist idea that a cell is a bag of protein parts has been challenged by recent findings about cellular awareness. DNA studies ignored the function of regulatory proteins which turn cells off and on, or activate them through chemicals generated by the environment. Cell membranes contain receptors or antenna-like parts which act like scanners, converting environmental signals into electro-magnetic stimuli which regulate proteins within the cell.

There are many kinds of these receptors whose specific shape enables detection of many kinds of stimuli such as glucose, histamines, insulin, and even light, etc. It was assumed to be the cell nucleus that directs the cell’s activities, but in fact, the cell can accomplish everything but reproduction with the nucleus removed, and will continue to function as usual for months until the individual parts need to be replaced or reproduced. A bacterium, which is the most primitive organism, doesn’t even have a nucleus, or internal parts (organelles). All its functions are contained in the cell membrane.

So it turns out that awareness (the brain) is in the membrane, or ectoderm. The skin of cells is composed of two parts that make up a bi-layer of protein and phospho-lipids. The outer layer has receptors which are antenna-like structures that receive signals from the environment.

The interior of the cell has a negative electrical charge. A receptor acts like a switch which permits a positive electrical charge from outside the cell to enter through the cell membrane. This causes an electrical spark, or signal, which causes a vibrational frequency like Morse code to be generated. These electrical signals affect the proteins of the cell and regulate its functions.

So there are receptors and processors and channels to allow environmental stimuli to evoke responses within the cell by changing the shape of the proteins in the membrane. And these receptors are so extremely sensitive that they can detect the presence of a single atom of glucose diluted with enough water to fill a whole harbor at the seacoast.

Cell membrane molecules are lined up like a kind of liquid crystal that change from conductor to non-conductor. The membrane is a semi-conductor with gates and channels. Electrical currents flow across the channels when the gates are open. This is exactly the same definition as a computer chip. The cell membrane is the same as a computer chip with individual receptors as the keys on the keyboard. The cell nucleus is like the hard drive that contains the software. If you remove the floppy disk that installed the program, the computer still works and you can select which software program you want to use at the moment.

There are 50 to 70 trillion cells in the human body, and each one contains in its DNA blueprint enough information to reconstruct an entire human body, but it does not determine or limit the potential of that human. Organisms can change to accommodate the environment.

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"A long, long time ago I can still remember how that music used to make me smile."

(Continued)

In 1988, a Harvard geneticist and biochemist named John Kearns published in Scientific American, perhaps the most important paper in the history of biology. He countered the idea of random cellular mutation as set forth by Darwin with the idea of specific mutation brought on by the conditions of the environment. The implications are enormous, establishing the primacy of the environment over genetic determinacy.

He found that bacteria placed in an inhospitable environment could adapt to that environment. Given only a food source that was incompatible, by sensing the protein structure of the food source that was available, the organisms adapted their digestive parts to accommodate the food source. He showed that a certain class of genes has the function of engineering the design of other genes. It means that the cell nucleus can create a biological pathway to accommodate the environment by sensing the conditions of the environment.

Up until this time science had mistakenly accepted as fact the hypothesis that control of cellular activity originated genetically from within the cell, according to random mutations of the genes. This body of work in fact proves that cells are regulated by responses to the environment. Genes are not causative, but only correlated, just blueprints that are altered as needed by environmental demands.

Everything in the universe has a characteristic resonance or frequency. Quantum physics addresses the issue of the resonances of everything being connected and the information transmitted by frequency resonances. For example, electromagnetic fields can change protein synthesis.

Magnetic fields are set up around the nerves, and thoughts emit the same variety of frequencies that activate biological processes within the cell. Individual humans have unique frequencies associated with all their cell membrane receptors. The immune system distinguishes friendly cells from invaders in this manner. In fact, people with major organ transplants may begin to emulate characters and traits of the donor because cell antenna identity or frequencies are transplanted with the tissue.

Survival requires protection as well as growth. Cells can be either in a growth mode or a protection mode, but not both at the same time. Physical injury to cell tissue results in the release of histamines by the mast cells, which open the blood vessels allowing the release of defense mechanisms like white blood cells to counter an infection. Trauma can cause a fight or flight response, where blood is shut off to the forebrain and diverted to the hindbrain, and the adrenals are activated for a burst of energy, and the immune system is compromised.

_________________
"A long, long time ago I can still remember how that music used to make me smile."

(continued)
Just as physical trauma causes triggering of histamine defense mechanisms, a perceived threat can cause a similar reaction from the brain resulting in the release of norepinephrine, which is similar to histamines in its effects on the body. These gluco-cortecoids are used to suppress the immune system in patients having organ transplants.

The levels of these stress-related hormones are very high in most people because of stressful lifestyles. Remaining in the protection mode will eventually destroy the body’s defenses because normal replacement of protein parts cannot be continued and can be especially harmful, resulting in various diseases.

We respond not just to stress, but to perceived stress. If an air raid siren sounds, the community stops normal functions and goes into a bomb shelter (protection mode). But when the "all clear" signal is sounded, normal activity resumes. However if the "all clear" is not sounded, the protection mode persists, the adrenal system shuts off the immune system.

Certain kinds of stress patterns attenuates the defense mechanisms and can result in psychological trauma so that the protection mode becomes chronic as in a subluxation, where the bodily posture is changed by bracing against trauma from either real or perceived danger. Besides physical bracing, prolonged stress can result in psychological bracing so that our belief systems include patterns of protective behavior.

Four billion bits of information come into the nervous system every second, but only about two thousand can be processed consciously, so more than ninety-nine percent is not processed consciously. Memory patterns automatically create belief filters in the brain, and most of our behavior comes from unconscious beliefs and expectations. Attitudes set up in early childhood or are passed on to us from our parents and early environment.

So, memory patterns are automatically created in the brain and once in place, these pre-programmed patterns and beliefs become automatic, and these pre-learned tapes and experiences usually run our lives. Only a considerable conscious effort can change these. This explains the difference between what we think and what we do, and why our emotional responses often over-ride the intellect.

Belief you don’t even know you have can affect what you do and who you are. You and your physical health are a summary of your beliefs and perceptions, the kind of data you are expecting. Your cells see what you see and the cell’s nucleus can create a pathway, so you can select what software you wish to use, so to speak.

"...a radically new understanding has emerged at the leading edge of cell science. It is now recognized that the environment, and more specifically, our perception (interpretation)of the environment, directly controls the activity of our genes. Environment controls gene activity through a process known as epigenetic control.

This new perspective of human biology does not view the body as just a mechanical device, but rather incorporates the role of a mind and spirit. This breakthrough in biology is fundamental in all healing for it recognizes that when we change our perception or beliefs we send totally different messages to our cells and reprogram their expression. The new-biology reveals why people can have spontaneous remissions or recover from injuries deemed to be permanent disabilities."

This new biology is called Epigenetics.

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"A long, long time ago I can still remember how that music used to make me smile."

I think we have a twin here, lol.

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Zoom! What was that? That was your life, Mate! That was quick, do I get another? Sorry, Mate. Back to the world of dreams. Yes, dear? ...

Yeah, long scientific lecture (...zzzz.zzzzz.zzz.), but an ending drawing close to (but not quite) a convergence with a spiritualist perspective. You have the IP codes Abe so that could be a clue. Do any zippy cartoons come with this? I challenged ZZZZZ once to draw his own zippy cartoons specific to the topics. Would still like to see one by his hand, even if it is a pencil sketch.

Here's some filler in the mean time, an awsome psytrance piece I came across to test those neurons. Mushroom season is upon us in central Mexico. I'll drop a line if I have any better topic related experiences to share.


BTW, I did read it all this morning, and it provided a few things to ponder, so thanks.
Not to mention the individual consciousness of each individual cells of the body, or of the bacteria in the gut, or of the person standing next to me, but it is not so much an issue of four billion bits of information and their locations, but rather the locus of the normally single bundle of unified attention which each one of us individually calls "self". It is a question of if the area of attention that I call "self" really is confined to a single physcal body which follows a rational progression in the waking state. Like as analogy the single awareness of the president of the US, taking the role of and representing a single point of awareness of a nation, but where the real attention of the individuals, is non existant, but is just represented by a hazy talk of rumors, ideas, etc. Never the less some of the individual might have even greater powers in terms of the size of a bundle of awareness. So to continue the analogy further, governments are often criticized as not bearing much apparent useful intelligence (not talking of data, but of decision making), in relation to individuals, and that very well could be true. Bundles of attention which are called self are naturally self limiting as a filter against the energy loss of dispersal into the infinite world of detail. It is this narrowing in range of awareness which maintains the balance, allowing life to be aware, and not dead through dispersal.

So is the one self that I know as "I", really cemented to an abstract area, often around my body? (See, that is not easy to define even under common circumstances) And if not, is it just my imagination or memory playing tricks? What are the bounds and what are the limits of perceptual change from the general normal limits? Is it only when experiences return to the 5 senses of the physical waking body, as opposed to say, dreaming, that events become rationally interconnected in almost, but not quite, exquisite perfection?

It just goes to show that the people that make up names don’t have much imagination. Epigenetics sounds like something you’d shave your legs with. They should have used a more interesting prefix like ‘acro’ or ‘meta’ or ‘tachy’. By the way the mechanism by which it works could be described as sugar coated DNA. So even if that’s wrong it sounds delicious. The normal genome for any two people is almost identical but the epigenome can adapt to the surroundings much faster. For instance someone whose last 100 generations lived in small, simple family-based or tribal societies would have a different epigenome than someone whose last 100 generations came from a large, complex society where many people didn’t know each other. The epigenome and biome may not be independent. After all a person’s microorganisms and sex organs and cells are in nearly the same place. History is full of examples of civilizations that have nearly wiped each other out with their contagious diseases. When they interbreed they would be exchanging biomes and epigenomes that may have diverged significantly with unpredictable results. It would be a similer effect on a person’s microecology as the introduction of an invasive species on an ecology. For example, a French-Canadian and a North American Indian.

Quote:
Yeah, long scientific lecture (...zzzz.zzzzz.zzz.), but an ending drawing close to (but not quite) a convergence with a spiritualist perspective.

That is funny! How can a long scientific lecture make you sleepy? (snorrrrrrrrrrrrrrrrr)

Of course that science has spiritual implication. How much of who and what we experience in a spiritual sense is influenced by information our cells pick up from external thoughts in the world around us, our ancestors, our environment? It poses some very interesting questions in my mind, at least.

_________________
"A long, long time ago I can still remember how that music used to make me smile."

A spiritual perspective is like a high-level summary but if you want any kind of precision on the details of how things work you generally have to refer to some kind of science. People like George W Bush or Sarah Palin probably do get sleepy with anything other than a summary since they don’t really understand the details (and only think they understand the summaries).

The idea of stalking stealing energy from dreaming does make sense, but also goes against itself. Like Henry pointed out. If one stalks to not lose energy (thus saving it), why does stalking take energy from dreaming? Is there overall less energy left, thus, even if we saved some, we lost some as well cause of our effort of saving, so generally we have less than we would have had if we hadn't stalked at all? The answer seems obvious, there's energy and there's Energy. One being the day to day energy, what we need to function with a good feeling and non-tiredness and the other, the one we need for the Other stuff. Might be that if in our day to day life we feel really shitty it impairs our Energy drawing/using capabilities.. [Although, I'm not so sure about that (or better I'd say it does not work like this in certain specific scenarios), considering how people in almost (or actually) traumatic situations often get a boost on D/dreaming and Other reality perceptions. This scenario might be argued away by the fact that their reality boundaries become shaky and more transparent, cause of losing strength or psychic stability (which is not the case in the other more normal cases). --- This is exactly what I don't like about my thinking/reasoning. I start of wanting to say one thing and then counter arguments drive me round in circles (sometimes I'm like 3 people leading a discussion in one) .]
I think stalking slowly leads to better manipulations with Energy. But considering how our lives are overflowed with bad energy management it's obvious that is where we have to start, thus spending our Energy. I think good stalkers eventually come round (get rid of bad energy habits and continue with getting rid of bad Energy habits, and also better Energy manipulation) and start Dreaming. If they go the right way that is. I see this around me: people (maybe coincidentally it is only men) who started of as pure stalkers (often with no dreams whatsoever), once they opened up to dreaming possibility ideas and over the years, started having Dreams. Maybe they will not be the intuitive Dreamers, but they will Dream.

I think the energy vs. Energy dependency might function like this: if you spend too much energy/or if you are too (emotionally or otherwise) drained you will not even think, or you might be blocked from, drawing from the Energy reservoir, so it more or less remains as it is and therefore its not that such activities drain it per se, it just makes it unreachable somehow. It seems logical that if we are drained, emotionally or otherwise having trouble coping with this world/reality/life we will not have a lot of interest in exploring the Other. If we put it in a funny way, we lack energy to reach for and make use of our Energy. People would need to be quite conscious to overcome this barrier and still it might not be done every time, but it's possible. Then what is the difference between e and E? If when missing e we get to missing E? I think that even when drained of energy one might learn to dig into the Energy reservoir, it just takes a lot to learn/do it. Its like overcoming some of our drives.. like going against ourselves in a certain fashion and also be able to control our emotions quite well. Also participate in creating our reality. Im not talking about instances when we are dead tired of course..
I find that stalking does take a lot of Energy (or maybe just energy, dunno, difficult to say for sure), from the beginning at least. Then it becomes like a reflex. It also leads to intuitive knowing, as does Dreaming. It is difficult to notice how much Energy a reflex takes, but it does take a bit at least. I think what is bad for me in my stalking is that I just can't control its effects sometimes (like my sticking to just one point of view, without considering or looking at others).
I would feel like an impaired person if I suddenly stopped doing it (though I do sometimes feel like an impaired person while (over)doing it):). Cause I also see it as Henry that it means/leads to "acting wisely prudently etc with onself and with others". I'm not saying that seeing different points of view IS stalking. It is just one effect that stalking might have.

I also took the path of stalking in my last years, due to having to get my life / emotions/ reactions in order. Before I've done both intuitively (but mostly Dreaming occupied my attention and stalking intuitively is only possible to limited aspects of stalking), then, first I concentrated on dreaming and Dreaming with some nice results but somehow I shifted to stalking. I've had made Dreaming advancements even during the period when I was actively working on my real life stalking. Now I can say my stalking does not occupy such a big part of my life, or maybe it is just easier and also combined with all the other things I've learned since then.. so it's a bit different. Lately my maneuverability in Dreaming has suffered. But it was my choice not to overmaneuver my Dreams before that, so I'm not sure if that is not some kind of adjustment because of this decision. Cause I noticed my D/dreams bring me important pieces into my development and if I am too conscious (and/ or experimental, which kind of goes hand in hand somehow) I might ruin the lessons. These do not have to occur in the same Dream, and more often don't, however, since I only have so much skill and Energy (or skill of making use of just so much Energy) I thus forgo chances of getting a lesson. Also when I'm active in my Dream I drain Energy faster and the Dream does not come to a conclusion / or to the important spot where it has been leading..
There are negative sides to my decision as well. Of course when I consciously explore the Dream I learn to be better in Dream manipulation, whereas if I leave the Dream to itself I learn from what it brought but I don't better my Dream skills from the lessons themselves (these tend to help in other areas of my life). However I've come to important realizations thanks to my decision of not interfering. Maybe I can switch to interfering again and see if something has changed.. I mean one can't have everything at once (seems like that's the case for someone of my abilities).. and getting lessons is just more important to me than more or less randomly trying out stuff. So I'm missing that now.. realizing that my Dreaming skills have worsened. Maybe by having the skills on some level I could tune into the lessons and now that they've worsened it is harder to do so. Which would mean I can't let myself just be taken on a ride, I have to keep doing the experimental hard work as well, even if it does not seem to give practical results, it helps with the overall Dream connecting. Seems like, or maybe I just have a down period in Dreaming and that's all there is to it .

Also concerning the lightheartedness that Ssil's talks about. I certainly second the notion that lighthearted does not mean full of Energy / or does not mean one was not drained of Energy. I've also noticed this of course. And you know what people generally say as a defense to having children in context of it draining Energy? It does not drain Energy, it can't, cause we get so much joy / inspiration etc from our children.. and they also tell us that they have learned a lot through their children, etc. Its pretty much the same thing.. They often refuse to acknowledge that even though what they say is right and actually those things that they learned or have thanx to their children might have "just" led to their being able to draw deeper into the Energy tank, or better manipulate the Energy they can reach (its well possible, or it just might be the case that they learned it with time and years of gaining knowledge and experience in general), it does not mean that the Energy tank overall has not shrunk. Still, what is the use of a large Energy tank if one can't make use of it?

_________________
don't stop
because you have not found your answer
and as you look into the eyes of the unknown
don't forget the intent you have come with

Totally agree with the aligning, like how you call it that they tug on each other like two magnets, it's what happens if you put them close enough . What I find the best that I've consciously reached so far on my own - i.e. without the help of other substances (and surely it does get better), is when one enters the "waking dream", into a dream like state while being awake, and as such is also doing the stalking as one is used to. Stalking helps with consciousness and stability. Then one is like a visitor in a magical world and I'm sure it leads to being a wizard in a magical world. Already as a visitor small bents of reality seem natural, creation is at the tips of your fingers. Stalking also helps you to see how you got into such a state. With dreamers it just happens and then just happens again, they don't see how (unless they employ some stalking). Stalkers track how it came about and find the key (dreamers use the key without realizing it). As such they are, in theory, more likely to recreate it when they want to, compared to dreamers. Though, in reality, dreamers just want and there it is (unless they have some kind of block - heh something like natural authors). Stalkers want, so they use the key (after they have found it with hard work), and there it is too . I love this .. .

Henry, it seems (though it might not be like that) that in your teen years, as it often happens in childhood and teen years (or early adulthood), you had a better connection to the Dreamer in yourself. I think most of us had it better when we were young. It might not be a thing of shutting the gates at all. I mean not that they were not shut then, but that they might not be shut now.. Cause as we know it so does happen quite a lot, but not every time, that after some mind blowing experience in Dreaming one is forced into some kind of dreaming pause. Your dreaming pause might have been just long enough to get over the teens / the better link with the Dreamer, making it obviously more difficult to start dreaming again.
It's interesting how you say that Death descended upon you.. Did it scare you? If yes, how badly? (I got my share of frights so I'm interested..)
But I thought you do Dream now and then, like most of us. I don't know why but the idea popped into my head just now of how DJ explained that once the Dreamer decides it is something s/he does not want to continue in (go through) then one can go further and leave that be (I think he was talking about the IBs). But it might be like that more generally. But in your case, I suppose that if you had let it be you would not want to go back to that kind of Dreaming, hm..
Cause, do you know what good it brings you that you pass the gates of Dreaming? I mean, one can pull a dream state into reality, align oneself with it and all that stuff without it. Hm, but then I don't know to what extent.. or how far one can go.. I also don't know what all the gates of Dreaming are or how many I've passed. I did not get over the one where you see yourself asleep.. (though some say you can also skip a gate, go right through the next one, but I dunno what follows). I did circle around it, but I never turned my head to look at myself, when I could.. Though I did get pulled there and back, so I knew Im there and there, I just did not turn to look at myself. It did not occur to me to do so . Cause I already knew.. In the last case (happened not more, or not much more, than a year ago), I was about to go out of my room, reaching for the door and while reaching I stopped in myself, thinking/knowing that is not all there is and so I felt into myself and whoops I started feeling (got the sensations of my body and knew) Im in my bed and so there I was in my bed, then I thought, but wait I was at the door just now, hope I didn't ruin that reality with coming back, and then I intended to be there again and whooo I was there about to open the door again, my hand reaching for the doorhandle.. and I did this shifting at least 2-3 times, cause it was kind of wonderful, until I was in my bed slowly having lost the other and the altered/Dream state, totally waking up (I mean I was awake before that just my body was in a sleep position and kept Dreaming) in this awareness and thus unable to go to the about to open the door position. So, I knew I'm 2 times, I felt both (one at a time), could switch here and there, however, it did not occur to me while in front of the door to turn my head and look at the bed..
Hm, I've just remembered a situation from CC where there was something similar but both "real", something like being taken by the stream of a river and running on the bank at the same time. But generally I've always connected these things to the stuff in CC where Genaro tells him about seeing himself lying in the grass dozing off. Except I did not look at myself.. guess I'm not ready yet, or just not investigative enough . But then maybe if Genaro could go there and back, he would have forgotten to look at himself as well . For him, if I remember correctly, he was walking/wondering around and happened to stumble upon himself. Remember, Henry, that Genaro then had a long pause of such endeavors.. how many years? I think it was a big number.
Like our shamanic teacher reminds us now and then, it is like collecting pieces of a puzzle. One day when we find the last piece (or maybe just a certain piece) it will fit together/ make sense / we will be able to make use of it. Might be that CC said something like that as well..

_________________
don't stop
because you have not found your answer
and as you look into the eyes of the unknown
don't forget the intent you have come with

Genes from Ebola Virus Family Found in Human Genome
A rush of new research has found evidence that some RNA viruses made their way into vertebrate genomes millions of years ago
By Katherine Harmon

Viruses do not make good fossils. But advances in genomic technology have allowed scientists to peer into the genetic material of viruses and their hosts to search for clues about their shared evolutionary history.

Genetic code from retroviruses has been found to compose some 8 percent of the human genome, having been copied in during replication and left to be inherited by us and our progeny. But non-retroviral RNA viruses do not use their host's DNA to replicate—and some do not even enter the host cell's nucleus. Nevertheless, new research has turned up surprising evidence that some of these viruses are enmeshed in the genomes of vertebrates—including humans and other mammals.

One of these new studies, published online July 29 in PLoS Pathogens, has uncovered some 80 examples of viral genetic data circulating in the genomes of vertebrate species for the past 40 million years.

To discover these connections, the group ran computer analyses of 5,666 genes from all known non-retroviral, single-stranded RNA virus families against the genomes of 48 vertebrate species. The strongest matches belonged to just two virus groups: Bornaviruses and filoviruses, the latter of which includes the deadly Ebola and Marburg hemorrhagic fever pathogens.

Another recent paper, published January 2010 in Nature, found bornavirus genes in the human genome. (Scientific American is part of Nature Publishing Group.)

Previous research had located evidence of viral fragments in the genomes of plants and insects, but in the past year new findings of these code segments in vertebrates surprised many biologists. "Retroviruses are an enormous fraction of the human genome, but that was a little understandable because the viruses have to inject their material into the DNA to survive," says Anna Marie Skalka, basic science director emeritus at Fox Chase Cancer Center in Philadelphia and co-author of the PLoS Pathogens paper. Otherwise, errant genetic material from viruses that are not retroviruses can find its way into the genome of germ line cells during the RNA copy process. That material can then get spliced into the genome by long interspersed repetitive elements (LINE) that are usually busy copying their own RNA.

When these infrequent flubs happen, they can be beneficial, harmful or neutral, Skalka explains. "There are LINE integrations that cause cancer or you could look at them as providing fodder for evolution—we have more sequences in there that can evolve and eventually make other genes."

Ancient code
Many viruses can undergo incredibly rapid adaptation, eluding immune systems that learn to recognize previous strains. But some researchers are pointing to emerging data on these viral "fossils" as indication that many viruses are in fact ancient—and have changed little since their material was integrated into host genomes.

"Previously there was no way to get an idea of how old they were," Skalka says of these viruses. But like tracing the evolutionary history of other organisms, genomic analysis can give scientists a new way to assess these estimates.

The new findings support a theory of Tufts University School of Medicine molecular biologist John Coffin that viruses in the bornavirus and filovirus groups "are really very old—despite the fact that card-carrying evolutionary biologists have concluded that they must be evolving very rapidly and probably [are] very recent," he says. "That is clearly very wrong." He cites this and other recent work to conclude that some of these hemorrhagic fever viruses have changed little in the course of primate evolution.

This time differential is both exciting to researchers who have been hunting for ancient evidence of the viruses' evolution and challenging to those who are trying to find these viral fossils in contemporary genetic codes.

"It is a big challenge" to match genes from modern viruses with those that might have entered animal genomes millions of years ago," Skalka says. "These RNA viruses evolve very, very rapidly and they change very, very rapidly—so the probability that you could find something that existed 40 million years ago could be very low."

Even though the recent assays have found several firm viral matches, many researchers assume there is likely much more virus material hiding out in our genomes. "All viruses make messenger RNAs, so it seems very possible that many others could have been picked up by LINEs and worked in," Skalka says. The others might be harder to find, however. It is possible that "they've evolved so rapidly that we don't recognize them any more."

Vetted viruses
Because these pieces have been present in vertebrate genomes for some 40 million years, "there might be some selective advantage to having them," Skalka says.For bornaviruses and filoviruses in particular, she notes, "there must be something special about these viruses," to have kept them around for so long.
Skalka speculates that these two virus groups might also be evolving more slowly. One reason for that might be because they have found a happy equilibrium with a reservoir species—such as bats—that has fostered the relative stasis.

Such a theory is "very tantalizing," Coffin says. "I think it makes perfectly good sense [but] it obviously requires some experimental verification."

Other possibilities for their more frequent appearance in vertebrate genomes are that they might have a special relationship with germ line cells or have RNA that is more recognized by LINE elements—and thus more prone to get copied and spliced into the host's genetic code.

Genetic immunity
Although strains of hemorrhagic fever can be fatal for many humans and animals, these viral genetics might also be conferring some protection on their hosts. Skalka explains that RNA from these integrated viral sequences could bind with RNA of the incoming virus and destroy it or that proteins from these code segments could be similar, albeit different enough to intruding viruses to "muck up the whole replication cycle," she says.

Some of the next steps will be to try to find more of these viral fossils in animal genomes. And as more genomes are sequenced and analysis tools become even more efficient, Coffin expects that "things that are older—and thus more diverged—will become easier to find."

But the real trick will be trying to figure out just what these genetic relics are doing in the genomes. "In the case of retroviruses" in the genome, "they have conferred benefits that have nothing to do with viruses," Coffin says, noting one retroviral gene that has been found to help with placental growth. "They are just genes that the host has found useful for one function or another."

Skalka and her team hope to uncover if the same is true for these non-retroviral genes, she says. "We would like to know what the significance is in human beings."
Vetted viruses
Because these pieces have been present in vertebrate genomes for some 40 million years, "there might be some selective advantage to having them," Skalka says.For bornaviruses and filoviruses in particular, she notes, "there must be something special about these viruses," to have kept them around for so long.
Skalka speculates that these two virus groups might also be evolving more slowly. One reason for that might be because they have found a happy equilibrium with a reservoir species—such as bats—that has fostered the relative stasis.

Such a theory is "very tantalizing," Coffin says. "I think it makes perfectly good sense [but] it obviously requires some experimental verification."

Other possibilities for their more frequent appearance in vertebrate genomes are that they might have a special relationship with germ line cells or have RNA that is more recognized by LINE elements—and thus more prone to get copied and spliced into the host's genetic code.

Genetic immunity
Although strains of hemorrhagic fever can be fatal for many humans and animals, these viral genetics might also be conferring some protection on their hosts. Skalka explains that RNA from these integrated viral sequences could bind with RNA of the incoming virus and destroy it or that proteins from these code segments could be similar, albeit different enough to intruding viruses to "muck up the whole replication cycle," she says.

Some of the next steps will be to try to find more of these viral fossils in animal genomes. And as more genomes are sequenced and analysis tools become even more efficient, Coffin expects that "things that are older—and thus more diverged—will become easier to find."

But the real trick will be trying to figure out just what these genetic relics are doing in the genomes. "In the case of retroviruses" in the genome, "they have conferred benefits that have nothing to do with viruses," Coffin says, noting one retroviral gene that has been found to help with placental growth. "They are just genes that the host has found useful for one function or another."

Skalka and her team hope to uncover if the same is true for these non-retroviral genes, she says. "We would like to know what the significance is in human beings."

How Can You Control Your Dreams?
The ability to manipulate our dream worlds goes beyond the science fiction plot of the movie Inception. A dream expert from Harvard University explains how it works
By Jordan Lite

Some dreams feel so revelatory—if only returning to sleep would take us back there. It turns out, however, that our ability to shape our dreams is better than mere chance. In the blockbuster movie Inception, Dom Cobb (Leonardo DiCaprio) and his compatriots use drugs and psychological profiles to trigger specific dreams in people. Although the heavy sedation and level of detail incited are far-fetched, dream control isn't entirely a Hollywood fantasy.

Techniques to control, or at least influence, our dreams have been shown to work in sleep experiments. We can strategize to dream about a particular subject, solve a problem or end a recurring nightmare. With practice we can also increase our chances of having a lucid dream, the sort of "dream within a dream" that Inception's characters regularly slip into.

The ability to influence other people's sleep worlds is still crude. But emerging technologies raise the prospect that, at the very least, we'll get an idea of what others are dreaming about in real time.

We asked Deirdre Barrett, author of the book The Committee of Sleep: How Artists, Scientists and Athletes Use Dreams for Creative Problem-Solving—and How You Can, Too (Crown, 2001) and assistant clinical professor of psychology at Harvard Medical School, about what dream-control strategies do and don't work—and why.

[An edited transcript of the interview follows.]


We're all familiar with dreams, but what's the scientific definition?
The literal definition is a narrative experience that occurs during sleep. A few people will define it as a REM (rapid eye movement) sleep experience but, actually, the research doesn't support that. Some things that seem to look like dreams occasionally occur in other stages of sleep.

Why do most dreams seem to occur in REM, and what's happening during that sleep phase that seems to produce dreams?REM is generally the only time during sleep that most of the cortex is pretty much as active as it is when we're awake. During this phase, there are rhythmic bursts of activity in the brain stem. There's one school of thought that this rhythmic firing is the sole cause of dreaming and all the upper cortical activity is a simple response to that. It just doesn't look that way. It looks like the lower brain stem activity wakes the cortex up and then the cortex does a lot of organized, meaningful thinking once it's activated.

The thing that is very frustratingly not neat and clean is that every once in awhile when you wake somebody out of a non-REM period, they report something that looks pretty much like the elaborate narrative of a dream. This is especially common in people who have big traumas and shift workers who have their sleep disrupted, so it may be that it happens mainly when something isn't operating completely properly with the regular sleep cycle.

During dreams, are certain regions more active than others or does that depend on what you're dreaming about?It's sort of halfway in between the extreme version of either of those.

On average, there are several areas that are more active than they would be during the waking state. Those are parts of the visual cortex, parts of the motor cortex and certain motion-sensing areas deeper in the brain. That's probably related to why dreams are so very visual compared to other sensory modes or types of content and also why they have a lot of motion and action in them relative to our waking experience. The parts of the brain stem that fire those bursts of activity are also active.

There are other areas that are less active on average during REM sleep. Those are the prefrontal areas, which have to do with the fine points of logical reasoning and also where you might say censorship resides. That's not only for censorship of things that are socially inappropriate, what Freud would have meant by censorship of sexual and aggressive impulses, but also the impulses that say, "that's not the logical way to do things." That seems to be why even though we continue to think about all kinds of problems and issues in our sleep, and sometimes come up with really creative, interesting solutions; their logic is less linear than our waking thought is.

Given that there's higher-level thinking going on in our dreams, to what extent can we control them?That we can control our own dreams is quite true and really much more so than people seem to know or realize. The details of how to do it are very different depending on whether you're trying to induce lucid dreams, whether you're trying to dream about particular content or whether you're trying to dream a solution to a particular personal or objective problem. Another really common application has been influencing nightmares, especially recurring post-traumatic nightmares—either to stop them or turn them into some sort of mastery dream.So how can you problem-solve in a dream?
Although any kind of problem can make a breakthrough in a dream, the two categories that really crop up a lot are things where the solution benefits from being represented visually, because the dreams are so vivid in their visual-spatial imagery, and when you're stuck because the conventional wisdom is just plain wrong.

You may have heard the example of August Kekulé and the benzene ring, which represents both these themes. He was thinking that in all nonchemical molecules, the atoms were lined up in some kind of straight line with 90-degree side chains coming off it. Once he knew the atoms in benzene, he was trying to come up with arrangements of them that were straight lines with side chains and it just wasn't working. Then he dreamt of the atoms forming as a snake, eventually reaching around with the snake's tail in its mouth. It seems exactly related to the fact that the prefrontal lobes that control censorship are, on average, much less active during dreams.

If you want to problem-solve in a dream, you should first of all think of the problem before bed, and if it lends itself to an image, hold it in your mind and let it be the last thing in your mind before falling asleep. For extra credit assemble something on your bedside table that makes an image of the problem. If it's a personal problem, it might be the person you have the conflict with. If you're an artist, it might be a blank canvas. If you're a scientist, the device you're working on that's half assembled or a mathematical proof you've been writing through versions of.

Equally important, don't jump out of bed when you wake up—almost half of dream content is lost if you get distracted. Lie there, don't do anything else. If you don't recall a dream immediately, see if you feel a particular emotion—the whole dream would come flooding back. [In a weeklong study I did with students that followed this protocol] 50 percent dreamed of the problem and a fourth solved them—so that's a pretty good guideline, that half of people would have some effect from doing this for a week.

What about if you want to, say, dream of a certain person or about a particular experience—how can you do that? If you're just trying to dream about an issue or you want to dream of a person who's deceased or you haven't seen in a long time, you'd use very similar bedtime incubation suggestions as you would for problem solving: a concise verbal statement of what you want to dream about or a visual image of it to look at. Very often it's a person someone wants to dream of, and just a simple photo is an ideal trigger. If you used to have flying dreams and you haven't had one in a long time and you miss them, find a photo of a human flying.

Image-rehearsal therapy has gotten attention as a strategy to overcome nightmares. How does this technique work, and is it effective?
Different people mean different things by that. The details are different but the techniques are very similar—they all grow out of the observation that when people are having bad, repetitive post-traumatic nightmares, a certain proportion seem to move on to having some kind of mastery dream spontaneously. The same way the nightmares had been re-traumatizing them, the mastery dream seemed to carry over into helping them feel much safer and more healed in their daytime state.

[Therapists or researchers] have the person work out an alternate scenario they want the dream to take, where they might ask them to close their eyes and imagine and generally talk them through a kind of vivid enactment of it. Usually the person incorporates some degree of the rehearsed scenario at bedtime or listens to a tape where the therapist or researcher is recounting the alternate scenario.

Barry Krakow does this in a group format and gets statistically significant, positive outcomes. He gets a remarkably high number of people who don't report the mastery nightmare and yet their nightmares stop and/or their daytime anxiety gets much better. We can't know whether they had a mastery dream and don't recall it or if something else about that positive, soothing imagery as you're falling asleep—even if it does not carry over into the dream—carries over into decreasing the number of the nightmares or the daytime anxiety, heightened startle response and flashbacks. In the one-on-one clinical studies there seems to be a much higher rate of actually having the rather dramatic mastery dream.

In the case of the successful techniques, what may be happening in the brain that allows these dream-control strategies to work?
Only if you're buying this idea that dreams should all be random or are being generated in the lower brain stem is there anything we need to explain about why you'd remember a suggestion you'd made to yourself for dream content or that intensely studying a problem before you fell asleep wouldn't be likely to turn up in your dream. Our ability to request that of ourselves at some point in the future is very analogous to what we might do awake. When it happens in a dream, it's happening in a state that by its nature is more vivid, much more intuitive and an emotional kind of thinking, and much less linear in its logic and much less verbal in orientation. That we're going to respond to this request from this very different biochemical state is what makes it such that sometimes we'll kind of respond but it will be in this vaguely nonsensical kind of way; other times it will be that we have this amazing breakthrough because we're thinking about this problem we've had this false bias about how to solve when we're awake.

Can we dream that we're dreaming?
Yes. That is the most common definition of a lucid dream—a dream where you know you're dreaming as the dream is occurring. A few writers on lucidity have chosen to make some degree of dream control part of the definition, but most choose to see that as a separate, additional element. Lucid dreams are infrequent—less than 1 percent of dreams in most studies—but they certainly do crop up in any large collection of lots of people's dreams.

How can you up your chances of having a lucid dream?
By reminding yourself you want to just as you're falling asleep, either as a verbal statement or idea: "Tonight when I dream, I want to realize I'm dreaming." That's the single most important thing, other than simply getting enough sleep. For any sort of dream recall or influencing of dreams, or for lucidity, simply getting enough sleep is one of the most boring pieces of advice, but one of the most important. When you deprive yourself of sleep, you are getting a lower proportion of REM. We go into REM every 90 minutes through the night, but each REM period gets much longer and occupies a larger chunk of that 90-minute cycle each time. So if you're only sleeping the first part of a normal eight hours of sleep, you're getting very little of the REM sleep you could.

Beyond that, if you check on whether you're actually awake in a systematic way during the day, you'll eventually find yourself doing this in a dream, and that can make it likelier that you will have lucid dreams.

You can do this by identifying something that is consistently or usually different from your sleeping and waking experience. Lots of people find they can't read text in a dream, that if they see text it's almost always garbled or hieroglyphics or doesn't make sense or it's fuzzy. People who can read in a dream will still report that the text is not stable; if they look away and then back, it says something different or there's no longer any writing there. So trying to read something in a dream is a good test for lots of people. Others find that things like light switches and other knobs that are supposed to turn things on and off work normally in their real world and don't do what they expect them to in a dream.

If you work out one specific check and then ask yourself, does everything look logical, you'll find yourself doing that in a dream. Some of these techniques are successful in as many as 10 percent of people in the course of a week for a few studies.

What are less effective ways of controlling a dream?
People who decide that they want to alter their nightmares or solve a problem through lucid dreaming have carved out an infinitely more difficult path—not that it's impossible but there's a lot more hard work and a lot less chance of success that way.

When lucidity was getting press in the 1970s, people were thinking it's a great way to end nightmares and have problem-solving dreams. But it turns out that lucidity takes a lot more effort and happens more unreliably than other forms of dream control. The study where I had students select real-life problems within their ability to solve—with strong motivation, in one week half dreamed about the problem and one fourth dreamed an answer to their problem, and that's much higher than you'd get for lucidity techniques. In transforming-nightmare studies, that rate is higher and happens quicker than it does for lucidity. So approaching these goals by almost demanding that the dream do what really you can do much better awake is not the smartest approach.

What about controlling someone else's dream—is this possible?
Occasionally there are some ways that one might influence someone else's dream content ahead of time via waking suggestions or during sleep via sensory stimuli that are impinging on the dreams.

The auditory seem to things work best, such as water or a voice saying something. Very strong stimuli wake us up. You want it to get in some narrow threshold where it gets detected by the brain and processed but it doesn't wake you up, and then there's a shot at it getting incorporated into the dream.

In his research on lucid dreams, psychophysiologist Steve LaBerge tested a dream light that sleep subjects wore on their faces that detected REM and flashed a low-level, red light during that phase. He found that it often got incorporated into people's dreams—they saw a pulsing red glow. If you combine that with the suggestion that when you see the flashing red light you know you're dreaming, you can promote lucidity.

Magnetic input is being done in the waking state to improve depression and to halt psychomotor seizures. If you can influence mood awake, it would seem you could influence the mood of a dream. We will get more precise about what we know about different brain areas and targeting magnetic signals toward them.

Lastly, we can image the brain well enough awake or asleep to know things like: there's an unusual amount of motor activity; or this person is probably doing mathematical calculations right now; or this person is processing incoming language or speaking or writing or is very likely sad or very likely happy. And we will probably get better at that. We can already do more things with animals: If you've trained rats in a maze, during REM sleep they look like they're dreaming the maze—they show the same pattern of firing left-right turns. That's done by sinking needle electrodes into their brains, which we obviously don't do to humans. But we may get good enough at imaging nonintrusively from the outside to see a lot more about the content. That's not directly controlling a dream, but it's one of the things that you might want to know if you were trying to control dream content.

The techniques discussed in the article really work as advertised. I’ve used many of them every day for many years. In school and then work it went on for quite a while that I’d dream the solutions to the previous day’s problems and plan what I was going to do about them with all the major contingencies. When I woke up the day was spent carrying out the plans and collecting information for the next night’s dreams. I once remarked that I did my best work while sleeping. It was no joke. Most of my analytical and creative work was done in dreams.

One technique that was new to me (at least in that context) was to induce a lucid dream by questioning whether you’re awake or dreaming you’re awake while awake. It makes sense. You often dream of what you think of while awake so eventually you’ll question whether you’re awake while dreaming. If you have a good way of determining you’re dreaming this will set up a sort mobius strip of consciousness. The rest of the post is in hieroglyphics.

Most of the things called technology are clumsy and inefficient copies of what nature has been doing for hundreds of millions of years. One example of this is nanotechnology. If anyone ever figures out how to make it work pundits say it will do what viruses already do much better. They are about the size that nanomachines would be and already live inside of all other living things (if they could be considered alive). They seem to control the major directions of biological evolution (by creating species) and also fine-tune it (through epigenetics) as well as most of the things in between.

One might think of the biosphere as a device that is able to adapt and extract energy from its surroundings very efficiently. Focusing on anything from honeybees to humans as individuals is a mistake. They are all part of one thing and are best thought of collectively.

The best achievement yet of biological evolution is placental mammals. They reproduce quickly and are able to adapt to a wide range of conditions. Social mammals tend to cluster together and, since they also reproduce quickly they need to have a way to sense and slow their reproduction when they become overcrowded. This can be done in the womb by the placenta as it builds a new individual by ‘programming’ behaviors that make it difficult or impossible to reproduce. Behaviors such as schizophrenia, autism, homosexuality or attention deficit can do that. Antisocial behaviors such as worship of the individual and distrust and dislike of any kind of organization work on an even higher level – sort of a collective form of cancer. Communication devices like telephones, televisions, radios, PCs and so on may make it appear to the placenta (which senses the environment through the expectant mother) that there are more individuals around than there actually are. Incidentally, external eggs that were one of the earliest mechanisms for sexual reproduction contain a structure that was the forerunner of the placenta. It would not be surprising to find that it too is controlled by endogenous viruses (actually slightly different ones for each species)