And now,

BIOLOGYIn The News!

Part III

Plus

Dillon Bustin!

Sunday, Dec. 07, 2008UK scientists explore pollution reducerBy Jim Warren - jwarren@herald-leader.comEliminating greenhouse gases and developing new, non-petroleum-based fuels are two of America's biggest environmental challenges. University of Kentucky researchers think algae might offer an answer.They propose to employ algae to scrub carbon dioxide from the flue-gases of coal-fire power plants — of which Kentucky has many — and use the algae to produce an oil that could then be refined into fuel.

"The reason algae is so interesting is that it can directly convert CO2 into biomass very quickly, more efficiently than anything else we know of," says Rodney Andrews, director of UK's Center for Applied Energy Research."Then, you basically squeeze the oil out of the algae and refine it as you would other natural oils."The energy center is working on the project along with the UK College of Agriculture's Department of Biosystems and Agricultural Engineering. The state of Kentucky has provided more than $500,000 for the effort.

As a first step in the research, Czarena Crofcheck, a biological engineer with the UK biosystems and agriculture engineering department, is searching for a strain of algae that would remove CO2 from power plant gases with the greatest efficiency. Finding the right strain could take a while. Crofcheck notes that there are at least 50,000 species of algae.

And, as in many alternative energy projects, there are some problems to be overcome. According to Andrews, capturing the carbon dioxide emitted from a 500-megawatt power plant would require 5,000 to 6,000 acres of ponds containing algae. To get around that, UK hopes to contain the algae in vessels that would operate more efficiently at much smaller size.Expense is another issue. As of now, it costs $18 to $30 a gallon to produce algae oil, which then has to be refined into fuel.

But Andrews says producing fuel really is a secondary goal of the UK effort."The main idea is to get rid of the CO2 and then figure out what you do with the algae," he said.

Visitors to ukTech10 will see a smaller scale version of the algae scrubber shown here that is used to grow algae for use in biofuels and bioproducts by using carbon dioxide and heat from coal-fired power plants. Researcher Mark Crocker of the Biofuels Research Group in the UK Center for Applied Energy Research will be on hand.

4 to 7 p.m. Thursday at The Penguin, on Main Street across from Lexington Center. Admission is free.

Monday, Apr. 05, 2010

Nets and New Drug Make Inroads Against MalariaBy DONALD G. McNEIL Jr.Published: February 1, 2008

Widespread distribution of mosquito nets and a new medicine sharply reduced malaria deaths in several African countries, World Health Organization researchers reported Thursday. The report was one of the most hopeful signs in the long battle against a disease that is estimated to kill a million children a year in poor tropical countries. “We saw a very drastic impact,” said Dr. Arata Kochi, chief of malaria for the W.H.O. “If this is done everywhere, we can reduce the disease burden 80 to 85 percent in most African countries within five years.”

There have been earlier reports of success with nets and the new medicine, artemisinin, a Chinese drug made from wormwood. But most have been based on relatively small samples; this is the first study to compare national programs. “This is extremely exciting,” said Dr. Michel Kazatchkine, executive director of the Global Fund to Fight AIDS, Tuberculosis and Malaria. “If we can scale up like this everywhere, we should be able to eliminate malaria as a major public health threat in many countries.”

In Ethiopia, deaths of children from malaria dropped more than 50 percent. In Rwanda, they dropped more than 60 percent in only two months.

Sweet Wormwood was used by Chinese herbalists in ancient times to treat fever, but had fallen out of common use, but was rediscovered in 1970 when the Chinese Handbook of Prescriptions for Emergency Treatments (340 AD) was found.In 1971, scientists demonstrated that the plant extracts had antimalarial activity in primate models, and in 1972 the active ingredient, artemisinin (formerly referred to as arteannuin), was isolated and its chemical structure described

From Wikipedia:

Restricting access to this technology to responsible manufacturers who will bundle artemisinin as part of an anti-malarial drug "cocktail" rather than selling it as a monotherapy should delay or even prevent malaria parasites from developing resistance. Recently, there have been reports of malaria parasites in West Africa showing some signs of resistance to artemisinin. "The problem has been that some manufacturers have sold artemisinin as a monotherapy rather than as a co-therapy as is recommended by the World Health Organization," said Jay Keasling

In addition to providing a simple and much less expensive means of making artemisinin, the most powerful anti-malaria drug in use today, synthetic biology can also help to extend the effectiveness of this drug. Fermenting artemisinin via engineered microbes, such as yeast, can be done at far lower costs than extracting the drug from Artemsisia annua, the sweet wormwood tree, making microbial-based artemisinin a much cheaper but equally effective treatment.

Synthetic biology can help extend anti-malaria drug effectivenessPublished: Friday, March 6, 2009 – e! Science News

In 2002, Keasling and members of his research group, using the tools of synthetic biology, set out to engineer a microbe that would perform most of the chemistry needed to make artemisinin in order to substantially reduce production costs. In 2003, they reported their first success. By transplanting genes from yeast and from the sweet wormwood tree into E. coli bacteria and then bypassing the E. coli's metabolic pathway and engineering a new one based on the mevalonate pathway in yeast, they were able to induce the bacteria to produce amorphadiene, a chemical precursor to artemisinin."Initially production was low, but we have used gene re-synthesis and other techniques to improve the yield of amorphadiene in E. coli by a million fold from where started," Keasling said.

"Any drug that is used as a monotherapy raises the possibility of microbes developing resistance to it. Right now artemisinin is grown by farmers all over the world and sold to anybody. Through the synthetic biology technique, access to the cheapest artemisinin can be restricted to manufacturers who agree to sell it as part of a co-therapy drug."

Keasling said that the same synthetic biology techniques used to make the microbial-based artemisinin should be equally effective in the drive to produce a next generation of biofuels – carbon-neutral transportation fuels derived from plant biomass."Artemisinin is hydrocarbon and we built a microbial platform to produce it. We can remove a few of the genes to take out artemisinin and put in a different hydrocarbon to make biofuels."As Keasling is fond of saying, "With the tools of synthetic biology, we don't have to just accept what Nature has given us."

In 2004, Keasling received a $42.6 million grant from the Bill and Melinda Gates Foundation, through the Institute for OneWorld Health, a San Francisco-based nonprofit pharmaceutical company, to further develop his microbial artemisinin technology

Back in the days the old books describeBack in the days of the Indian tribesThey prayed to the river to forever flowAnd the name that they give her was Ohio

They fished her clear waters they camped on her hillsbathed at the shallows they drank at the rillsSome Frenchmen they came scouting for gameGazed at that river and asked of her name

Chorus: La Belle Riviere the Great Shining WaterCasquinampogamou le Fleuve du Saint :LouisNo matter the name the meaning’s the sameShe’s the beautiful river the Ohio

The next to come in were the KentuckiansThe Buckeyes the Hoosiers the Suckers and thenThey bought off the Indians they cut down the treesFor their barns and their mills and their factories

Down by the cornfield she ran with the mudDown by the slaughterhouse she flowed with the bloodBelow the brewery she was covered with sudsIn the spring of the year she could not help but to flood

Chorus

The next to come in were the government menWith their bankers and lawyers their soldiers and thenThey told the shanty folk well you needn’t fearTo let the river be dammed by our engineers

With a lock over here a dock over thereBridges and trestles spanning the airWe’ll build a pump house above every townBring the fresh water in and let the sewage float down

The last to come in have been the industry menInvesting their billions around every bendReactors they spill refineries stink Yet it’s pleasant to swim in and healthful to drink

And I’m sitting here on the leveeWondering at this long historyI’m wondering at this river of fameAnd if she ever again will live up to her name

Chorus

La Belle Riviere - Dillon Bustin

Chorus

April 4, 2009Inquiry Is Opened Into Death of Last Known Jaguar in U.S.By JOHN DOUGHERTY NY Times

PHOENIX — The federal government has opened a criminal investigation into the capture and death of the last known jaguar in the United States, amid accusations that a biologist working for the state illegally baited a trap to attract the cat. The 118-pound male jaguar, known as Macho B, was captured on Feb. 18 in a leg-hold snare placed by the Arizona Game and Fish Department in a rugged mountainous area southwest of Tucson. The animal, which was described in field reports as healthy and robust, was tranquilized, equipped with a radio-tracking collar and released from the trap.

The jaguar, which was estimated to be 16 years old, was recaptured with tranquilizing darts on March 2 after wildlife personnel feared that it might be in poor health. It was flown by helicopter to the Phoenix Zoo, where a veterinarian said it had irreversible kidney failure. It was euthanized the same day.

The department and its oversight body, the Arizona Game and Fish Commission, “did not authorize or condone intentional initial capture of this jaguar,” it said in a statement on Thursday. Arizona fish and game officials have repeatedly maintained that the snare that first caught the jaguar had been intended for a mountain lion or a black bear.

But a staff member said that her boss — Emil McCain, the biologist working as a consultant for the department — in early February instructed her to place female jaguar scat within six feet of the leg-hold trap. The scat had been used several times to attract Macho B to come within camera range. She said that Mr. McCain had given her the scat, which he obtained from the Phoenix Zoo, and that a department employee had been present but said nothing when he told her to put it next to the trap.

A spokesman for the federal agency, Jose Viramontes, said Friday that the investigation would “look at all aspects leading up to the trapping of the animal all the way through to the decision to euthanize it.”

Jaguars were present in much of the Southwest until the early 20th century. By then, they had been nearly exterminated after 100 years of hunting, including a federal eradication program. Jaguars spotted occasionally in the United States are thought to be from a relatively large population living in Sonora, Mexico.

Thursday, January 21, 2010State's capture of jaguar Macho B was intentional, federal investigators conclude By Tony Davis and Tim Steller, Arizona Daily Star

The capture of Macho B, the last known wild jaguar in the United States, was intentional, according to a new investigative report by the Interior Department's Office of Inspector General. The report says Arizona Game and Fish Department employees meant to capture the jaguar Macho B on Feb. 18 last year, citing evidence gathered as part of an ongoing federal criminal investigation.

The Inspector General investigators reviewed the material gathered by criminal investigators of the Fish and Wildlife Service and concluded there is evidence of criminal wrongdoing by an Arizona Game and Fish employee and an Arizona Game and Fish subcontractor. The document doesn't name them. That conclusion is important because the game and fish department originally called the capture unintentional and because such "taking" of an endangered species may be a crime under the endangered species act.

Saturday, Apr. 17, 2010 Slimy salamander snared in Licking RiverBy KEVIN KELLY - The Kentucky Enquirer

VISALIA, Ky. -- Jimmy Blackaby was fishing with a buddy near the Visalia bridge in northern Kentucky when he pulled something out of the Licking River that he recalls seeing only one other time.

"It was a funny bite," the Morning View resident said. "It pecked and pecked and pecked and finally I just got tired of it pecking. When I set the hook, I thought, well, it's a catfish. As you could imagine, whenever we pulled that thing up, whoa, this ain't a catfish, man."

The nearly two-foot-long creature on the end of Blackaby's line was an eastern hellbender, a rare and most would say unsightly salamander whose populations are being studied in Kentucky. As Blackaby discovered, the eastern hellbender fancies crayfish and secretes mucus when handled.

Sometimes called a "snot otter" or "grampus," it has a flat head and body, elongated tail and stubby legs. Those features make the eastern hellbender well suited to live under rocks in the clean, flowing water that it prefers since it breathes through its skin.

"I look at them and see an animal that's superbly adapted for where it lives," said Greg Lipps, a herpetologist from Delta, Ohio.

Lipps is heading up an ongoing eastern hellbender survey in Kentucky with the Department of Fish and Wildlife Resources. There's never been a formal survey like it before in the state, he said.

"There's been a lot of interest recently looking at hellbender conservation because where surveys have been done we've noticed very large declines," Lipps said.

Kentucky does not have its own endangered species list, he said, but Ohio's Division of Wildlife lists the eastern hellbender as endangered.For the survey, Lipps scoured historical records on eastern hellbenders in Kentucky and found 52 documented occurrences through the years.

"The plan of attack has been to visit all of these places," Lipps said. "And the survey technique is just extremely labor intensive. I always like to tell people there's no rock too big for a hellbender, only rocks you can't lift."

The eastern hellbenders, which are harmless to humans and often confused with mud puppies, are measured and examined for abnormalities and disease. A small microchip also is placed under the skin of each in an effort to track them.

Of 27 sites surveyed in the Licking River and Kentucky River watersheds, two have turned up eastern hellbenders.The survey aims to help fill in gaps throughout the eastern hellbender's range where limited or no data exists about how they're doing. The data could lead the eastern hellbender closer to the federal endangered species list.

"The other purpose is can we identify where good hellbender populations are and what potential threat there may be and what actions can we take to conserve them," Lipps said.

Anglers who catch one are advised to remove the hook and put it back in the water. If the hook can't be removed, Lipps suggests contacting the fish and wildlife department.

Blackaby placed the eastern hellbender, which swallowed the hook, in a fish basket in the river and called the department about his catch.

John MacGregor, a herpetologist with the Kentucky Department of Fish and Wildlife Resources, collected the animal and took it to the Peter W. Pfeiffer Fish Hatchery north of Frankfort.

"It stayed alive," Blackaby said. "It was in good shape."

Around my barn - Dillon Bustin

When the hound begins to howlAnd I’ve not heard a hooting owlWhen the chickens begin to squawkThat’s the time I’ll take a walk

Refrain: around my barn, around my barnyard

Could be the wind in the treesCould be a rabbit or a groundhog sneezeEating the peppers in my garden spotHe’d better hope that I am not

Around my barn, around my barnyard

Could be a cloud across the moonCould be a fox or a sly raccoonComing down to make a mealHe don’t know the way I feel

About my barn, about my barnyard

You ask me what’s dirty trickSkinny old weasel in among the chicksAnd when he’s done gnawing their legsAn old skunk come and he’ll suck the eggs

That are left in my barn, left in my barnyard

Down in the cornfield see the deerEach one chewing on a yellow earAnd every squirrel that’s ever been bornWants to make a living off the little corn

That I get to my barn, get to my barnyard

All the milk that my milk cow makes Gets drunk up by a long milk snakeYou may not believe what I say is trueBut he ain’t eating mice I’m telling you

Out in my barn, out in my barnyard

Lindy tells me treat them like brothersI told her let them eat each otherIt’s what they done before I comeWhat they’ll do before I’m done

With my barn, done with my barnyard

Well I never expected life to beSimple or easy or completely freeBut I did not think that I’d have to fightTo get one drink or a single bite

Of food from my barn, food from my barnyard

February 26 2009Earliest modern gait found in ancient footprints WASHINGTON (AP)

More than a million years ago an ancient human ancestor walked across a sandy plain in eastern Africa, leaving footprints that scientists are now hailing as the earliest evidence of modern upright walking. The footprints, dated to between 1.51 million and 1.53 million years ago, were discovered at Ileret, Kenya, researchers report in Friday's edition of the journal Science.

With a large toe parallel to the other toes, the prints indicate a modern upright stride, the researchers said. They are likely to have been made by the early hominid Homo ergaster or early Homo erectus. Older footprints, dating to 3.6 million years ago found in Tanzania have been attributed to the less advanced Australopithecus afarensis. Those prints indicate an upright posture but with a shallower arch and a more ape-like, divergent big toe.

October 1, 2009Oldest Skeleton of Human Ancestor FoundJamie Shreeve, Science editor, National Geographic magazine

Move over, Lucy. And kiss the missing link goodbye. Scientists today announced the discovery of the oldest fossil skeleton of a human ancestor. The find reveals that our forebears underwent a previously unknown stage of evolution more than a million years before Lucy, the iconic early human ancestor specimen that walked the Earth 3.2 million years ago

The centerpiece of a treasure trove of new fossils, the skeleton—assigned to a species called Ardipithecus ramidus—belonged to a small-brained, 110-pound (50-kilogram) female nicknamed "Ardi." The fossil puts to rest the notion, popular since Darwin's time, that a chimpanzee-like missing link—resembling something between humans and today's apes—would eventually be found at the root of the human family tree. Indeed, the new evidence suggests that the study of chimpanzee anatomy and behavior—long used to infer the nature of the earliest human ancestors—is largely irrelevant to understanding our beginnings.

Ardi instead shows an unexpected mix of advanced characteristics and of primitive traits seen in much older apes that were unlike chimps or gorillas. As such, the skeleton offers a window on what the last common ancestor of humans and living apes might have been like.

"This find is far more important than Lucy," said Alan Walker, a paleontologist from Pennsylvania State University who was not part of the research. "It shows that the last common ancestor with chimps didn't look like a chimp, or a human, or some funny thing in between."

The Ardipithecus ramidus fossils were discovered in Ethiopia's harsh Afar desert at a site called Aramis in the Middle Awash region, just 46 miles (74 kilometers) from where Lucy's species, Australopithecus afarensis, was found in 1974. Radiometric dating of two layers of volcanic ash that tightly sandwiched the fossil deposits revealed that Ardi lived 4.4 million years ago.

The biggest surprise about Ardipithecus's biology is its bizarre means of moving about. All previously known hominids—members of our ancestral lineage—walked upright on two legs, like us. But Ardi's feet, pelvis, legs, and hands suggest she was a biped on the ground but a quadruped when moving about in the trees. Her big toe, for instance, splays out from her foot like an ape's, the better to grasp tree limbs. Unlike a chimpanzee foot, however, Ardipithecus's contains a special small bone inside a tendon, passed down from more primitive ancestors, that keeps the divergent toe more rigid. Combined with modifications to the other toes, the bone would have helped Ardi walk bipedally on the ground, though less efficiently than later hominids like Lucy. The bone was lost in the lineages of chimps and gorillas.

According to the researchers, the pelvis shows a similar mosaic of traits. The large flaring bones of the upper pelvis were positioned so that Ardi could walk on two legs without lurching from side to side like a chimp. But the lower pelvis was built like an ape's, to accommodate huge hind limb muscles used in climbing.

The team also found some 6,000 animal fossils and other specimens that offer a picture of the world Ardi inhabited: a moist woodland very different from the region's current, parched landscape. In addition to antelope and monkey species associated with forests, the deposits contained forest-dwelling birds and seeds from fig and palm trees. Wear patterns and isotopes in the hominid teeth suggest a diet that included fruits, nuts, and other forest foods.

If White and his team are right that Ardi walked upright as well as climbed trees, the environmental evidence would seem to strike the death knell for the "savanna hypothesis"—a long-standing notion that our ancestors first stood up in response to their move onto an open grassland environment.

Two hundred thousand years after Ardipithecus, another species called Australopithecus anamensis appeared in the region. By most accounts, that species soon evolved into Australopithecus afarensis, with a slightly larger brain and a full commitment to a bipedal way of life. Then came early Homo, with its even bigger brain and budding tool use.

Did primitive Ardipithecus undergo some accelerated change in the 200,000 years between it and Australopithecus—and emerge as the ancestor of all later hominids? Or was Ardipithecus a relict species, carrying its quaint mosaic of primitive and advanced traits with it into extinction? Study co-leader White sees nothing about the skeleton "that would exclude it from ancestral status." But he said more fossils would be needed to fully resolve the issue.

February 12, 2009Scientists in Germany Draft Neanderthal Genome By NICHOLAS WADE NY TImes

Scientists report that they have reconstructed the genome of Neanderthals, a human species that was driven to extinction some 30,000 years ago, probably by the first modern humans to enter Europe. The Neanderthal genome, when fully analyzed, is expected to shed light on many critical aspects of human evolution.

An early inference that can be drawn from the new findings, which were announced Thursday in Leipzig, Germany, is that there is no significant trace of Neanderthal genes in modern humans. This confounds the speculation that modern humans could have interbred with Neanderthals, thus benefiting from the genes that adapted the Neanderthals to the cold climate that prevailed in Europe in last ice age, which ended 10,000 years ago. Researchers have not ascertained if human genes entered the Neanderthal population.

Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig led a team that had to overcome daunting technical obstacles to produce the draft of the Neanderthal genome. Dr. Pääbo began his project more than 10 years ago, when he succeeded in extracting the first verifiable piece of Neanderthal DNA. Distinguishing human and Neanderthal DNA is hard because they are so similar.

He said at a news conference in Leipzig on Thursday that he now had retrieved usable DNA from six Neanderthals and analyzed 3.7 billion units of DNA. The Neanderthal genome, like that of modern humans, is 3.2 billion units in length. Because many units have been analyzed several times over, and many not at all, Dr. Pääbo can now see about 63 percent of the Neanderthal genome. He will continue to analyze it until he has accumulated the equivalent of 20 Neanderthal genomes, which will allow almost every unit to be accurately known.

Archaeologists have long debated whether Neanderthals could speak, and they have eagerly awaited Dr. Pääbo’s analysis of the Neanderthal FOXP2, a gene essential for language. Modern humans have two changes in FOXP2 that are not found in chimpanzees, and that presumably evolved to make speech possible. Dr. Pääbo said Neanderthals had the same two changes in their version of the FOXP2 gene. But many other genes are involved in language, so it is too early to say whether Neanderthals could speak.

Possessing the Neanderthal genome raises the possibility of bringing Neanderthals back to life. Ethical considerations aside, Dr. Pääbo said, Neanderthals could not be generated with existing technology. Dr. George Church, a leading genome researcher at the Harvard Medical School, disagreed. He said Thursday that a Neanderthal could be brought to life with present technology for about $30 million.