May 28, 2008, Forbes.com – Dr. Francis Collins, who became the public face for a watershed science project – unraveling the human genetic code – is resigning as the government’s gene guru.

Collins, arguably the nation’s most influential geneticist, announced Wednesday that he will leave the National Institutes of Health this summer to explore other opportunities.

The folksy geneticist helped translate the complexities of DNA into everyday vernacular, once famously calling the human genome or genetic code the “book of human life.” He became a leading advocate for the privacy of genetic information.

But Collins may be better known to laymen for his 2007 best-selling book about his belief in both God and science.

By Henry Fountain, May 27, 2008, The New York Times – Down below the ocean, there are some things that are very real — namely, bacteria and archaea. By some estimates, sub-seafloor prokaryotes may account for two-thirds of the biomass of these types of organisms on Earth.

The latest evidence for such a huge undersea biosphere, and a depth record of sorts, is reported in Science by R. John Parkes of Cardiff University and colleagues. They have found living prokaryotes 5,335 feet below the ocean floor off Newfoundland, about twice as deep as the previous record.

Intact cells were found in cores drilled through sediments up to 111 million years old, although the age of the prokaryotes themselves is an open question. The researchers were able to amplify genetic material, which strongly suggests that the cells are living, feeding on trapped methane, other hydrocarbons and organic carbon. Prokaryotes are simple organisms without a nucleus; they are an organism whose DNA is not contained within a nucleus, e.g. a bacterium.

Temperatures of the deepest core samples were estimated from 140 to 212 degrees Fahrenheit, so the cells qualify as extremophiles, able to withstand harsh conditions like those found around deep-sea hydrothermal vents. Some of the genetic sequences found match those from known heat-loving bacterial strains like Pyrococcus.

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Pyrococcus

Living cells have been found at greater depths under land, but the concentration of cells in the undersea cores (about a million per milliliter) is much higher. The finding is another that stretches the boundaries of where life can flourish — with all that implies about the situation on worlds other than Earth.

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Prokaryotes include the archaebacteria and bacteria. Shown here are two types of bacteria. On the left is a cyanobacteria, called an autotroph, or self-feeder, because it carries out photosynthesis and produces its own food. On the right is a species of Salmonella, which must ingest organic compounds and so is called a heterotroph, or other feeder. The numerous flagella seen here enable Salmonella to move through the intestinal tracts of animals, where they can cause the food-borne illness salmonellosis.

Prokaryote, is a relatively simple unicellular organism, such as a bacterium, characterized by the absence of a nucleus and other specialized cell structures. Scientists distinguish prokaryotes from eukaryotes, which are more complex organisms with cells that contain a nucleus, such as plants and animals.

Scientists classify prokaryotes in different ways, depending on the classification system used. In 1938 American biologist Herbert Copeland proposed that unicellular organisms lacking nuclei be classified in their own kingdom called Kingdom Monera, now called Kingdom Prokaryotae. All bacteria were categorized in this new kingdom. This scheme was the first to establish separate kingdoms for prokaryotes (organisms without nuclei) and eukaryotes (organisms with nuclei). In the 1970s scientists determined that cyanobacteria, formerly known as blue-green algae, have physical features that make them more closely related to bacteria than to algae. Although the exact classification of cyanobacteria is still under debate, some scientists now classify cyanobacteria in the Kingdom Prokaryotae, while algae remains classified in the Kingdom Protista.

In 1990 American microbiologist Carl Woese proposed that bacteria be divided into two groups, archaebacteria and bacteria, based on their structural and physiological differences. Archaebacteria consist of a small group of primitive anaerobes (organisms that do not require oxygen). They are found in a narrow range of habitats—often in extreme environments such as hydrothermal vents on the deep ocean floor. In contrast, bacteria live in a wide range of environments with or without oxygen, at various temperatures, and at various levels of acidity. In some classification systems, the archaebacteria are considered prokaryotes; in other systems they are classified in a category known as the Domain Archaea.

Prokaryotic cells are relatively small, ranging in size from 0.0001 to 0.003 mm (0.000004 to 0.0001 in) in diameter. With the exception of a few species, prokaryotic cells are surrounded by a protective cell wall. The cell walls of archaebacteria and bacteria contain forms of peptidoglycan, a protein-sugar molecule not present in the cell walls of fungi, plants, and certain other eukaryotes. The archaebacteria cell wall has a more diverse chemical composition than the cell wall of bacteria.

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Extremophiles

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Sea Vents

Life exists not just around vents, but inside them too. Unlike the life forms that crawl or swim around the vents, those inside are invisible. These microscopic bacteria (one-celled organisms) not only survive but even thrive in the dark and hot environment of the vent. In the absence of sunlight, specially adapted bacteria and similar organisms called Archaea convert the vent chemicals to usable bioenergy, in a process analogous to plants’ ability to use sunlight.

Yellowstone Hotsprings

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Researchers have discovered a bizarre group of microbes that live inside rocks in the inhospitable geothermal environment at Wyoming’s Yellowstone National Park. One scientist describes the life–form, found in the pores of rocks in a highly acidic environment, as “pretty weird,” and resembling a lichen. Scientists believe similar kinds of geothermal environments may have once existed on Mars. The Yellowstone discovery may help steer the hunt for evidence of life on Mars.

Antarctica – Subglacial Lakes

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In addition to the super-hot environment of sea vents and hot springs, bacterial life may also exist in the cold, dark environment beneath the Antarctic ice sheet. Scientists aren’t yet sure, but the suggestions are strong. Two separate research teams have drilled into Lake Vostok, a suspected body of water below the Antarctic ice sheet. (It is still “suspected,” and not proven, because scientists are reluctant to explore further until they know their actions will not contaminate a potentially unique environment.) Both teams found bacteria inside ice that is believed to be created from lake water. DNA analysis indicates that although the bacteria have been isolated for millions of years, they are biologically similar to known organisms.

Atacama Desert

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Scientists now know that life exists not only in very hot and very cold liquid environments, but in a very dry environment as well. Environmental microbiologists have discovered evidence of microbial life about a foot below the rough terrain of Chile’s Atacama desert, one of the driest places on Earth. Their finding contradicts previous beliefs that the desert is too dry to support life, and may influence how scientists look for life in the similarly dry environment of Mars.

Europa

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Europa ?

Some scientists speculate that if life does exist beyond Earth, it might be the form of vent bacteria. Because these microscopic life forms have already proven their ability to survive in the extreme environment of Earth’s hydrothermal vents, they might also survive in similar environments elsewhere – for example, on Europa. Europa is one of Jupiter’s moons, and is covered in ice. Scientists have recently uncovered strong evidence of liquid water beneath Europa’s ice, which may be due to hydrothermal vents, which may in turn host bacteria. Alternatively, scientists who have found evidence of bacteria living inside Antarctic ice speculate that they may also live inside Europa’s ice. The questions exceed the answers, but the clues are tantalizing.

Extremophiles act like alien organisms
By Bjorn Carey
LiveScience

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NASA / Univ. of Alabama
A fluorescent stain renders adds a green tinge to the corkscrew-shaped Spirochaeta americana from California’s Mono Lake. Green spots are spheroplasts. Reddish areas are dead cells.

Extremophilic microbes are a wild bunch. They can be found thriving in some of the most hostile environments imaginable — swimming in near-boiling water, eating rocks, lounging in subzero temperatures and hanging out where radiation levels rival nuclear reactors.

They’re tougher than duct tape, boldly going where humans dare not and cannot.

Extremophiles are also a multimillion-dollar-a-year business — some of them are employed to eat oil and help clean up spills. Others have important applications in medical research. But for many scientists, these hardy microbes are interesting because they suggest the potential for life on other planets.

Recent discoveries have greatly expanded the range of these wild things. Here’s a census of small creatures living in some of the worst conditions imaginable.

Microbial extremophiles have recently been discovered thriving in the extremely hostile environments in the depths of the Mediterranean Sea.

At nearly 2.5 miles (4 kilometers) below sea level, with salt concentrations 10 times higher than seawater, pressure 400 times greater than atmospheric pressure, and a lack of oxygen to boot, the conditions in which these microbes thrive are some of the most hostile environments on Earth.

In the Jan. 7 issue of the journal Science, researchers working on the European Biodeep project reported the discovery of new microbes in the anoxic basins, or “brine lakes,” located off the coast of Sicily.

It is these types of conditions, particularly the high concentrations of magnesium chloride, that have scientists imagining what the environments of other planets might consist of, and whether they contain life.

“Ascertaining the nature of the subsurface on other planets is tricky, but there is growing evidence for hypersaline environments on Mars and Jupiter’s moon, Europa. Indeed, Europa is believed to have a subsurface ocean rich in magnesium salts,” Terry McGenity, the lead scientist of the University of Essex group working on the Biodeep project, told LiveScience.

Since light cannot penetrate water of this depth, there are no photosynthetic bacteria in the basins. Most of the organisms the Biodeep workers have found reduce sulfates to run their metabolism.

Some of the microbes McGenity’s group found were completely unknown, including a new group of Archaea they have named MSBL-1. McGenity speculates that these microbes are methanogens because they are related to methane-producing Archaea, and no other methane-producing microbes were found in the basins, which are abundant with methane.

The European Mars Express mission detected hints of methane in Mars’ atmosphere last year, and some astrobiologists have speculated that the methane could be a by-product of extremophilic methanogens or some other form of microbial life.

Life fueled by hydrogen
Another recent extremophile study discovered microbes in the hot springs of Yellowstone National Park using hydrogen as their primary fuel source, refuting the popular conception that sulfur is the main source of energy for microbes living in thermal features.

The research was designed to find the main source of energy of microbes living in hot springs with temperatures over 158 degrees Fahrenheit (70 Celsius), a temperature too high for photosynthesis.

“It was a surprise to find hydrogen was the main energy source for microbes in hot springs,” said University of Colorado researcher Norman Pace, who led the team.

Pace’s colleague John Spear, lead author of the study published in January’s online edition of the Proceedings of the National Academy of Sciences, speculated about what the discovery of hydrogen-fueled microbes means for life on other planets.

“Hydrogen is the most abundant element in the universe,” Spear points out. “If there is life elsewhere, it could be that hydrogen is its fuel.”

Life in cold climates:

Hiding beneath sheets of ice in Siberia and Antarctica are microbes called psychrophiles or psychrotrophs. They consist mostly of bacteria, fungi and algae that thrive in freezing temperatures ranging from 23 to 59 degrees Fahrenheit (-5 to 20 Celsius).

In addition to being cold, the environments that these microbes are found in are sometimes at tremendous depths — more than 2 miles (3.2 kilometers) below the surface.

Psychrophiles help us clean up arctic oil spills. They also turn our milk sour. There is a good chance, scientists say, that extraterrestrial life could be similar to this class of microbes. In a solar system where many of the planets — including Mars — have large ice deposits and colder temperatures in general, psychrophiles might thrive.

Undersea hot spots
Rising as high as 15 stories off the ocean floor at depths of 7,000 feet (2,100 meters), hydrothermal vents that spew acidic, mineral-rich water are the places to be — if you can stand the heat. The water coming out of the vents can reach temperatures as high as 750 degrees Fahrenheit (400 degrees Celsius), but that’s just fine for undersea thermophiles.

The mineral-munching microbes living around these volcanic “chimneys,” which are so deep no sunlight can reach them, give yet another view of what life could be like on another planet, where lack of sunlight would hinder organisms relying on photosynthesis as their energy producing mechanism.

A number of the planets and moons in our solar system are covered in ice, but scientists speculate that below some of that ice are liquid oceans. If there is also volcanic activity on those ocean floors, it is possible that similar hydrothermal vents could be growing there as well. Although it is nearly impossible to know whether there is life in those oceans, such worlds would at least contain an environment in which we know organisms could live.

Life in the deep ocean, in rocks … and in space?
A sediment sample recently dredged up from Challenger Deep, the deepest part of the Pacific Ocean, was abundant in single-celled protists called foraminifera. Researchers were surprised to find these soft-shelled critters at depths of nearly 7 miles (11.2 kilometers), where the pressure is 1,100 times greater than at the surface.

“I am very surprised that so many very simple, soft-shelled foraminifera are dwelling at the deepest part of the ocean,” said Hiroshi Kitazato, of the Institute for Research on Earth Evolution at the Japan Agency for Marine-Earth Science and Technology.

Kitazato suggests that the deep trenches, where the creatures can feed on bits of sunken organic matter, may provide a refuge for the foraminifera.

The fossil record of foraminifera is more than 550 million years old. In last week’s issue of the journal Science, Kitazato suggested that these new creatures probably represent the remnants of a deep-dwelling group that was able to adapt to high pressures.

The rest of the wild bunch

· Endoliths and hypoliths are two types of extremophiles that live inside rocks or between the mineral grains. Endoliths have been found more than 2 miles below Earth’s surface, and if they can stand the heat, they could dwell much deeper. Early observations show that they feed on surrounding iron, potassium or sulfur. Water is scarce at these depths, and this slows down the procreation cycle of the organisms — some reproduce only once every 100 years! Hypoliths are photosynthetic organisms, so the rocks they live in must be translucent, like quartz. Hypoliths are commonly found in extreme deserts in cold climates, such as Antarctica on the Canadian Arctic’s Cornwallis Island. Their translucent homes provide them with many comforts, such as trapped moisture and protection from ultraviolet rays and harsh winds.

· Hyperthermophiles are organisms that prefer temperatures above 140 degrees F, some even as high as 250 degrees F (121 degrees C), although those have trouble reproducing. The hardiest of the 50 known species are those living near hydrothermal vents — these require temperatures of over 194 degrees F (90 degrees C) to live. In addition to being heat-resistant, many hyperthermophiles can withstand other environment stresses, such as high acidity and radiation. One thermophile, Thermus aquaticus, produces a DNA polymerase enzyme that is widely used in molecular biology research for use in high-temperature polymerase chain reactions used to replicate DNA.

· Toxitolerant organisms can withstand high levels of damaging agents. They can be found swimming around in benzene-saturated water or in the core of a nuclear reactor. One species of bacteria, Deinococcus radiodurans, can withstand a 15,000-gray dose of radiation – 10 grays would kill a human, and it takes over 1,000 grays to kill a cockroach. Extraterrestrial life forms would most likely need to possess similar tolerances to radiation, because the atmosphere on other planets, or lack thereof, filters out much less radiation than Earth’s.

· Oligotrophic bacteria survive in, and in some cases prefer, environments that are low in nutrients. They have evolved metabolic processes that allow them to produce their own sulfur and phosphorus, and they feed on their own organic waste.

While there is no evidence for life beyond Earth, information about extraterrestrial environments combined with the discoveries of life in places on our planet thought to be inhabitable keeps scientists optimistic.

“If it works this way on Earth, it’s likely to happen elsewhere,” says Spear, the University of Colorado scientist. “When you look up at the stars, there is a lot of hydrogen in the universe.”

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Eukaryotes have areas inside the cell separated off from the rest of the cell by membranes, like the cell membrane (see below). These areas include the nucleus, numerous mitochondria and other organelles such as the golgi body, and or chloroplasts within each of their cells. These areas are made distinct from the main mass of the cells cytoplasm by their own membrane in order to allow them to be more specialised. You can think of them as separate rooms within your house. The nucleus contains all the cell’s DNA, the Mitochondria are where energy is generated, chloroplasts are where plants trap the suns energy in photosynthesis. There are exceptions to every rule of course, and in this case the most obvious two are the red blood cells of animals and the sieve tube elements of plants, which, though living, have no nucleus and no DNA, normally these cells to do not live very long.

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Prokaryotes do not have a nucleus, mitochondria or any other membrane bound organelles. In other words neither their DNA nor any other of their metabolic functions are collected together in a discrete membrane enclosed area. Instead everything is openly accessible within the cell, though some bacteria have internal membranes as sites of metabolic activity these membranes do not enclose a separate area of the cytoplasm. See Cells: The Basis of Life