The Rise of the Zombie Empire: Resistance is Futile

They walk freely among us, unheeded. Infected by brain parasites, behaviours subtly altered. Two billion infected, and counting.
Zombies are popular fictional examples of brain alteration that is usually caused by a biological agent. But inside every fiction is the kernel of truth. Zombies are so popular in part because they are uncomfortably familiar.

LaughingSquid

At least two billion people worldwide are infected by the protozoan, many from eating infected meat. Initial symptoms are mild flu, after which the parasite forms cysts that lodge in the brain. There they remain for decades... _NYT

Two recent studies reveal how microbes can alter normal brain functioning. Researchers from California and Singapore detailed how the protozoan Toxoplasma Gondii is capable of blunting normal fear responses to threat in animals. Canadian and Irish researchers have discovered a mind-altering effect from probiotic bacteria -- specifically, a species of lactobacillus. The lactobacillus was found to lower stress, anxiety, and depression related behaviours in mice.

Microbes can change our brains, and make us somehow different. In extreme cases -- as in brain-eating amoeba or fatal encephalitis and meningitis -- they can kill our brains outright. But sometimes they kill or disable only a portion of our brains, and leave us alive, but altered. And sometimes they live inside of us, changing us chemically by their metabolic excreta.

These are not the "borg" of fiction. There are no brain implants or electrodes controlling us. But biology is much stranger than we understand. We can go to Robert Heinlein's "The Puppet Masters," for a vivid fictional account of extraterrestrial invaders able to attach to humans, growing tentacles into human brains and spinal cords. That would be an extreme example of biological control of humans by "the other."

Far more subtle, and easier to bring about, would be genetically controlled microbes able to insert themselves into particular parts of the brain, to bring about neurochemical alterations -- either temporary or permanent. By targeting the brain region of choice, behaviours could be manipulated according to an overall plan or scheme.

Even easier, would be normal body flora genetically altered to secrete brain-altering chemicals, such as benzodiazepine or amphetamine. Something a little extra in your yogurt or your moisturizing cream. Schools, prisons, and armies should take special note.

We are far beyond the skills needed for such simple manipulations. And given the apparent state control of modern popular media and scientific publishing, who would know -- or be able to say anything about it?

Here is how to make your own yogurt. Just in case. Some of us may not be infected yet. There may be safe retreats left, far from the teeming mobs. It may not be too late......Heh.

MIT Scientists Unleash DRACO: Viral Genocide Imminent

We have developed a new broad-spectrum antiviral approach, dubbed Double-stranded RNA (dsRNA) Activated Caspase Oligomerizer (DRACO) that selectively induces apoptosis in cells containing viral dsRNA, rapidly killing infected cells without harming uninfected cells. We have created DRACOs and shown that they are nontoxic in 11 mammalian cell types and effective against 15 different viruses, including dengue flavivirus, Amapari and Tacaribe arenaviruses, Guama bunyavirus, and H1N1 influenza. _PLoS

PLoS One: Broad Spectrum Anti-viral
The DRACO antiviral approach created by MIT researchers has the potential to develop into an all-purpose antiviral prophylactic and early-stage treatment. This development is a timely reminder that while microbes can be shifty and clever in avoiding antimicrobial medicines, humans have incredibly creative and resourceful brains -- if they would only use them.

Now, in a development that could transform how viral infections are treated, a team of researchers at MIT’s Lincoln Laboratory has designed a drug that can identify cells that have been infected by any type of virus, then kill those cells to terminate the infection.

In a paper published July 27 in the journal PLoS One, the researchers tested their drug against 15 viruses, and found it was effective against all of them — including rhinoviruses that cause the common cold, H1N1 influenza, a stomach virus, a polio virus, dengue fever and several other types of hemorrhagic fever.

The drug works by targeting a type of RNA produced only in cells that have been infected by viruses. “In theory, it should work against all viruses,” says Todd Rider, a senior staff scientist in Lincoln Laboratory’s Chemical, Biological, and Nanoscale Technologies Group who invented the new technology.

Because the technology is so broad-spectrum, it could potentially also be used to combat outbreaks of new viruses, such as the 2003 SARS (severe acute respiratory syndrome) outbreak, Rider says.

...When viruses infect a cell, they take over its cellular machinery for their own purpose — that is, creating more copies of the virus. During this process, the viruses create long strings of double-stranded RNA (dsRNA), which is not found in human or other animal cells.

As part of their natural defenses against viral infection, human cells have proteins that latch onto dsRNA, setting off a cascade of reactions that prevents the virus from replicating itself. However, many viruses can outsmart that system by blocking one of the steps further down the cascade.

Rider had the idea to combine a dsRNA-binding protein with another protein that induces cells to undergo apoptosis (programmed cell suicide) — launched, for example, when a cell determines it is en route to becoming cancerous. Therefore, when one end of the DRACO binds to dsRNA, it signals the other end of the DRACO to initiate cell suicide.

Combining those two elements is a “great idea” and a very novel approach, says Karla Kirkegaard, professor of microbiology and immunology at Stanford University. “Viruses are pretty good at developing resistance to things we try against them, but in this case, it’s hard to think of a simple pathway to drug resistance,” she says.

Each DRACO also includes a “delivery tag,” taken from naturally occurring proteins, that allows it to cross cell membranes and enter any human or animal cell. However, if no dsRNA is present, DRACO leaves the cell unharmed.

Most of the tests reported in this study were done in human and animal cells cultured in the lab, but the researchers also tested DRACO in mice infected with the H1N1 influenza virus. When mice were treated with DRACO, they were completely cured of the infection. The tests also showed that DRACO itself is not toxic to mice. _Physorg

So far, the treatment appears safe and non-toxic, and fairly effective when used pre-infection, and in the early stages of infection, for the viruses tested. Whether this general approach will lead to successful treatments for herpes viruses or HIV and other retroviruses, remains to be studied.

Since DRACO leads to the death of viral-infected cells, the potential exists that this approach might lead to eradication of "stealth viruses" which hide in particular cell types for a person's entire lifetime.

As for other stealth viruses living inside human cells which have not been discovered by human science, presumably some of these would also be killed by a DRACO-like approach. No one knows what the result of such a broad-spectrum clearance of body viruses might be, because no one knows what these undiscovered stealth viruses are doing in the first place. Assuming they are there, which is quite probable, according to Al Fin system biologists.

Algae are Optimistic about the Future

More: A study from the Pacific Northwest National Lab outlines how the US could replace 17% of its petroleum imports with homegrown algal fuels.
Abstract from study

NewScientist
While human academics and analysts are all too quick to write off algae as serious contenders in the energy race, the algae themselves are completely optimistic about their own futures. Perhaps the algae know something that we do not know? Well, for one thing, algae is already a big business. For another, algae has a lot of potential for productive yield -- and is just getting started.

ALGAE are being put to work performing a unique double duty: cleaning up sewage waste while simultaneously producing biofuel.

All algae feast on phosphates and nitrogen-containing compounds, converting them to lipids. Some of these oils can be converted to biofuel, but only a few algal species produce lipids of the right type and quantity to be easily converted to fuel. In theory, though, algae are a perfect renewable fuel source. The main obstacle is that brewing the right nutrient mix can be prohibitively expensive.

Now, in work for a master's thesis, Eric Lannan, a mechanical engineer at Rochester Institute of Technology (RIT) in New York and colleagues have identified three types of microalgae - Scenedesmus, Chlorella and Chlamydomonas - that efficiently convert nutrients to fuel on a diet of municipal waste water, while happily living in its harsh, salty environment. In a lab test, it took just three days for the algae to gobble up 99 per cent of the ammonia, 88 per cent of the nitrate and 99 per cent of the phosphates in a broth resembling that from a domestic sewage treatment plant, turning themselves into rich sources of fuel even as they purified the water.

"People had looked at algae to clean waste water, others to make biodiesel," Lannan says. "We're putting those ideas together." _NewScientist

The idea to use waste feedstocks for boosting algal production is not especially new, but it still needs to be demonstrated on a large scale. And the demonstration must show that the resulting algae can be used to produce valuable products to make the entire process self-sustaining and profitable.

Besides using wastewater, the use of high CO2 effluent from power plants and cement factories etc. would provide the carbon boost for rapid growth, which algae crave.

Algae do not need too much sunlight -- in fact too much sunlight can reduce yields for valuable algal products. Solazyme, for example, grows its algae in the dark by feeding them sugars from biomass for fuel. They claim an 80% lipid yield, which is quite high.

Artificially inflated prices for crude oil are driving a multitude of approaches to the production of alternative liquid fuels. Fuel from algae is but one of many alternative approaches to liquid fuels, and algal researchers are taking dozens of divergent approaches to create algal fuels. Other microbial fuels approaches appear equally promising at this time.

A lot of money is going into the effort to create microbial fuels and fuels from biomass. But the key discoveries will not necessarily come from the best-financed research labs. Time will tell.

Those who think "biofuel" means only maize ethanol, are going to be very surprised when they discover what is really happening.

Beware the Plastic Apocalypse!!!

Enviros See Armageddon In Every Plastic Bag
We are told the oceans are covered with floating plastic debris, clogging the ocean food chains and destroying free-swimming wildlife. But solid evidence of this eco-catastrophe is quite thin. And ever since a Canadian high-schooler (and another in Taiwan) in 2009 discovered species of microbes that thrive on eating plastic, most informed observers have been somewhat less concerned.

Since then, scientists in Ireland have begun to put microbes to work digesting waste plastics, and UK scientists have discovered plastic-eating microbes in ocean waters.

Sargasso SeaThe latest story in the long-running ocean apocalypse saga, involves scientists from the Woods Hole Oceanographic Institute in Massachusetts. Woods Hole scientists explored the Sargasso Sea, in search of plastic-eating bacteria.

Mincer and his colleagues examined bits of fishing line, a plastic bag and a plastic nurdle (a pre-production plastic pellet) fished out of the Sargasso Sea, an area of the North Atlantic where currents cause debris to accumulate. The region as a whole contains more than 1,100 tonnes of plastic1.

...Plastic-eating bacteria might help explain why the amount of debris in the ocean has levelled off, despite continued pollution. But researchers don't yet know whether the digestion produces harmless by-products, or whether it might introduce toxins into the food chain.

...Genetic analysis shows that the bacteria on the plastic differ from those in the surrounding seawater or on nearby seaweed, says microbiologist Linda Amaral-Zettler of the Marine Biological Laboratory, Woods Hole. So far, the DNA sequences obtained by her lab show that almost 25% of the bacteria on one polyethylene surface were vibrios, bacteria from the same group as the cholera bacterium.

...Amaral-Zettler and Mincer also found genetic and microscope evidence of eukaryotes — organisms with more complicated cells than bacteria — on the plastic. What she calls the "plastisphere" might contain complex living communities. "It may be a little world that we've created, for better or worse." _Nature_via_Impactlab

It is fascinating that particular ocean bacteria have adapted to using plastics as a food source. This is all quite reminiscent of the bacteria that have adapted to eating crude oil and methane gas around oil spills and and natural hydrocarbon seeps in the ocean floor.

To the bacteria, our discarded plastics are a feast and a windfall, allowing them to feed and reproduce to their microbial hearts' content. Of course the same phenomena occurs on land, except with a much wider range of microbes -- both prokaryotic and eukaryotic -- partaking of the cornucopian repast.

Environmentalists are concerned that the microbes may be releasing toxins into the seawater which will pollute larger sea creatures and perhaps get into the human food chain. A plastic apocalypse on the prowl, don't you see? And yet, in the middle of the ocean, nothing is wasted. If something can be seen as food, it will be used as food by something. That includes anything which humans may perceive as toxic.

Here is the amusing thing in all this: Waste plastics are increasingly being seen as valuable feedstocks in the production of synthetic fuels, chemicals, and other high-value substances. Gasification of solid wastes for production of power, process heat, and chemical/fuel feedstock is just getting started in the developed world. In the future, the only plastic wastes the oceans will see will be coming from places too primitive to know how to unlock their intrinsic value.

And no doubt there will be plenty of plastic-eating ocean microbes to take care of those remnants. Otherwise we will need to raise our seawalls quite high, to avoid the ocean plastic tsunamis that may come from Neptune, with a crashing vengeance.

Beware the plastic apocalypse.

More on plastic apocalypse 31March11: The death of the environment by plastic bags may have been exaggerated. (via Daily Bayonet)

That Feeling in Your Gut? Intestinal Flora

"As animals ourselves, we have more than 1000 different kinds of microorganisms living in our guts ...._abcnet

Intestinal microbes can determine the quality of your life, and your perception of it. Your guts are the repository of the majority of your microbial complement. Life without "normal flora" would be a different animal.

Professor Petterson and his colleagues bred a number of mice under normal and germ-free conditions. In stantardised tests of activity, the germ-free mice explored more of an "open-field activity box", rearing up on their hind legs more often, and showed less of the signs associated with anxiety.

In studies of the animals' brains, they showed higher levels of a number of hormones, and even differences in the expression of over 170 genes.

The result does not paint a clear picture of whether the development of the germ-free mice is specifically "better" or "worse" for the animals, Professor Pettersson explained, but is a "very, very interesting" first demonstration that the bugs can have such profound effects even within the brain.

It follows a long line of studies that suggest the bugs are far more involved in mammalian function than just in their digestion. _BBC

Very interesting. The germ-free animals lived longer and seemed more curious, but they were very fragile to stress and various types of injury, compared to animals with normal bacterial and skin flora.

If we are to swim in a sea of bacteria -- as it seems we are destined to do -- it is best that our bacterial partners be sympatico with us. If we wish to avoid chronic intestinal inflammation, fatty liver, obesity, and a wide range of other pathologies and malaise, we need to pay attention to our bacterial friends.

Gut inflammation allows the intrusion of large numbers of various protein intruders which are better kept out of the blood and lymph systems. Yes, we can eat more yoghurt, or take probiotic capsules or powders. Not a bad idea, actually. We may even want to begin to gene-engineer our probiotics for maximal benefit against these ailments. In situations of grave extremis, we may be forced into fecal transplants -- as a last resort.

Al Fin clinical and synth-bio microbiologists recommend genetically engineered probiotics out of all the choices mentioned above: from germ-free environments to fecal transplants. But different situations call for different remedies. Consider each case individually.

Researchers looked in detail at the molecular effects of the engineered bacteria and found that the production of regulatory immune cells, rather than of inflammatory immune cells, was enhanced. "When we treat mice with the new strain, we see more accumulation and generation of cells that produce regulatory proteins, which lure and generate regulatory T cells," says Mohamadzadeh. The regulatory T cells, a type of immune cell, counteract the effects of harmful immune cells that attack the cells lining the gut, he says.

...Mohamadzadeh's team is also exploring engineered probiotics as a treatment for colon cancer. In preliminary studies in mice designed to mimic colon cancer, treatment with the modified bacteria reduced the number of polyps the animals developed by 90 percent. "We observed an average of just three small polyps in treated mice, compared to about 35 to 50," he says.

He adds that the bacteria's ability to reduce inflammation isn't limited to the gut; the regulatory cells migrate throughout the body. That means the microbes may also be able to help treat other diseases linked to inflammation, such as rheumatoid arthritis and psoriasis. _TechnologyReview

Of course, once you start introducing targeted gene-engineered microbes into the gut, the possibilities for treatments and specific optimisations multiply rapidly.

You may be aware that peptic ulcers and gastric cancer are tied to a gastric microbe, helicobacter pylori. The development of counter-bacteria to H. Pylori would allow simple, food-assisted treatment for a number of illnesses specific to that microbe.

The same arguments could be applied to skin bacteria and other parts of the body where normal bacterial flora reside. There are plenty of diseases of multiple systems which are caused or made worse by absent or insufficient symbiotic bacteria.

But once we start applying, ingesting, and inserting engineered microbes for treatment and prophylaxis, we are likely to begin thinking about optimisation. Why take nutritional supplements, for example, when microbes can produce the needed substance just as well? The same applies to particular medications, enzymes, or hormones. And so on...

Now go eat your yoghurt.

Lipid Fermentation via Engineered Microbes for Bio-Jet Fuel

GCC
The US military's DARPA has awarded Logos technology with a $17.5 million phase 2 award to produce jet fuel from biomass, using microbial lipid fermentation.

This contract is to demonstrate an end-to-end Lipid Fermentation Process (LFP) at scale for the commercially viable production, from cellulosic biomass, of Hydrotreated Renewable Jet (HRJ) spec jet fuel—a near term surrogate for JP-8 that can be readily commercialized.

HRJ is produced from renewable oils (lipids) by methods common in petroleum refining. Fatty acids and triglycerides are hydrotreated to remove oxygen, and the resulting paraffinic hydrocarbons are processed to yield a mixture of straight-chain, branched-chain, and cyclic paraffinic hydrocarbons with collective properties that are similar to those of conventional jet fuel.

Oleaginous yeast can produce lipids from the sugars resulting from the pretreatment and hydrolysis of biomass; certain fungi can also produce lipids, either via solid-state fermentation of biomass or from the biomass hydrolyzate.

This primary program effort is to consist of optimized process development and engineering along with regionally specific economic modeling to produce fuel, demonstrate process energy efficiency and support commercialization.

...This phase of the BioJET program requires the delivery of larger quantities of jet fuel with a projected cost of production of JP-8 at commercial scale implementation (50Mgal/yr) at less than $3.00 per gallon. _GCC

Al Fin bio-synthesists believe that the greatest value of current advanced biofuels research is to put a rough ceiling on future prices of hydrocarbon fuels. Peak oil doomsayers claim that liquid fuels will have no price ceilings when "peak oil" truly hits the fan.

But that claim has already been falsified by the fact that shale gas cost per BTU is well less than half the cost of crude oil per BTU. As efficiencies of conversion from gas to liquids improve, we will see the "price ceiling" effect of shale gas begin to affect markets. Something similar will begin to happen in about ten years, as more efficient biomass to liquids processes begin to scale up.

Like everything associated with energy these days, oil futures markets are heavily politicised, and infiltrated by persons whose behaviour is -- shall we say -- somewhat less than ethical. The fluctuations of oil markets are highly profitable to those who know how to put their fingers on the scale in a reasonably surreptitious manner. But the conversion of alternative and unconventional fuels to liquid hydrocarbons: GTL, CTL, BTL, kerogensTL, BitumensTL, etc etc, provides a multiple bypass to the oil commodities markets. Such alternative routes to fuel makes the work of the energy mafias and faux environmentalists much harder -- unless they can use bribed politicians to stop the alternatives and unconventionals.

Cross-posted to Al Fin Energy

Craig Venter Aims to Replace the Entire Petrochemical Industry

“Designing and building synthetic cells will be the basis of a new industrial revolution,” Dr. Venter says. “The goal is to replace the entire petrochemical industry.” _NYT

NYT

Peak Oil will occur when humans no longer want to bother drilling into the ground to extract dark, gooey, messy liquids to turn into fuels. Instead, humans are slowly but surely developing other, more reliable and sustainable ways to fuel their industrial base and somewhat affluent lifestyles. Dieoff.orgiasts and other members of the Voluntary Human Extinction Movement hate to see any alternatives to Peak Oil Doom, or any skepticism to the orthodoxy of Catastrophic Anthropogenic Global Warming. But humans are innately a problem-solving and skeptical lot.

Craig Venter is one example of an unlikely problem solver. He was a poor student in his youth, and only after living through some harrowing experiences in Vietnam as a military medic was young Venter able to get his head on straight, and decide to do something with his life.

...Dr. Venter has a history of defying skeptics, and many people are betting that he will succeed this time as well. Dr. Walton, in fact, invested personally in Synthetic Genomics, and his venture firm, Oxford Bioscience Partners, recently wanted to sink a hefty sum into the company but was turned down when Dr. Venter found other investors offering better terms.

Exxon Mobil is giving Synthetic Genomics $300 million in research financing to design algae that could be used to produce gasoline and diesel fuel. (The new greenhouse will be used for that research.)

BP has invested in the company itself, turning to Synthetic Genomics to study microbes that might help turn coal deposits into cleaner-burning natural gas. Another investor, the Malaysian conglomerate Genting, wants to improve oil output from its palm tree plantations, working toward what its chief executive calls a “gasoline tree.”

...In the approach toward which Dr. Venter is driving, engineers would specify the entire genetic code of a cell — essentially the software that runs the cell — on computers, making design changes as if on a word processor. They would then press the “print” button, so to speak, and the DNA would be manufactured from its chemical components. The synthetic DNA would then be transplanted into an existing cell, where it would “boot up” and take control of the cell’s operations.

...Synthetic Genomics has about 130 employees. But much of its research, including the development of the synthetic cell, is done at the J. Craig Venter Institute. Synthetic Genomics pays for about 25 of the institute’s roughly 300 researchers, and has rights to their results. The rest of the institute’s funding comes mainly from federal grants and its endowment.... _NYT

Venter seems to love challenges and competitions. He lives to defy skeptics and to defeat rivals. And do you know the odd thing? The world is full of young Venters who have not yet -- and may never -- figured out what they want to do with their lives.

Pelted mercilessly with nightmarish predictions of doom and gloom, and instilled by governmenbt schools and indoctrinating universities with the futility of trying to fight their fate, hundreds of thousands of young Venters never amount to much -- when they might have done, given the right experiences in early life.

From an article published at Al Fin Energy