Saturday, March 11, 2006
"A Johns Hopkins researcher, with colleagues in Sweden and at the Fred Hutchinson Cancer Research Center, suggests that the traditional view of cancer as a group of diseases with markedly different biological properties arising from a series of alterations within a cell's nuclear DNA may have to give way to a more complicated view. In the January issue of Nature Reviews Genetics he and his colleagues suggest that cancers instead begin with 'epigenetic' alterations to stem cells.
'We are not contradicting the view that genetic changes occur in the development of cancers, but there also are epigenetic changes and those come first,' says lead author Andrew Feinberg, M.D., M.P.H., King Fahd Professor of Medicine and director of the Center for Epigenetics in Common Human Disease at Johns Hopkins."
Hamilton Spectator: "To better understand Earth's climate in the time of huge tyrannosaurus-sized dinosaurs, McMaster University researchers will soon be growing "living fossils" and comparing them to fossilized plants buried for millions of years.
Gingko trees -- an ancient species that evolved 200 million years ago -- will be moved from a campus greenhouse to specialized chambers being installed in the basement of the General Sciences Building.
There, assistant professor Darren Grocke will be able to mimic conditions in the mid-Cretaceous period 95 million years ago to see how the trees respond." [Evolution]
"Islam does not have a story that has literal elements of Genesis. Though creatonist literature abounds in Mosque bookstores, it doesn't take into account the fact the the Qur'an has a very unique view on the origin of life which is different from the one professed in fundamental Christianity.
It is sad and disturbing that Muslim ulama, unschooled in science, have not grasped the very accurate Qur'anic concept of the origin of life on this planet earth billions of years ago and its gradual development into human beings spreading over a span of billions of years.
The Quran speaks of creation only in step by step progressive stages and categorically rejects the concept of spontaneous generation as is mentioned in Genesis." [Koran and Evolution]
Friday, March 10, 2006
The Guardian UK: "Hell hath no fury like a philosopher scorned - even one who doesn't believe in hell. Two of the leading philosophers of evolution have been caught in an email slanging match that has been printed on the blog of their mutual enemy William Dembski, a supporter of the rebranded creationism known as intelligent design.
There is a poetic justice to this, since the row started with an argument over how to combat creationism. In one camp is the British-born philosopher Michael Ruse, who testified against creationism in an important trial in Arkansas in 1989, but who has always argued that evolution, though true, does not compel atheism...
...On the other side is Darwinian Daniel Dennett, philosopher and friend of Richard Dawkins. Dennett's latest book, Breaking the Spell, is a vigorous attempt to preach atheism to the unconverted."
[The Dembski page referred to is here]
BBC News: "Creationist theories about how the world was made are to be debated in GCSE science lessons in mainstream secondary schools in England.
The subject has been included in a new syllabus for biology produced by the OCR exam board, due out in September.
Critics say the matter should only be discussed in R.E. because there is a danger of elevating religious theories to the status of scientific ones."
"Jacqueline Kim Dale, Ph.D., formerly a Senior Research Associate at the Stowers Institute for Medical Research, and Olivier Pourquie, Ph.D., Stowers Institute Investigator and an investigator with the Howard Hughes Medical Institute, have demonstrated that the long-studied family of transcription factors called Snail is expressed in a cyclic fashion during the formation of the vertebral precursors in the mouse and chick embryo.
The findings, which were published in the March 7 issue of Developmental Cell, indicate that the genes governing many cellular properties are downstream of the segmentation clock, the mechanism that controls the formation of the vertebral column."
'Jumping Genes': New Target For Body's Innate Immune Protection System Against Viruses
When HIV and other retroviruses invade a cell in the human body, a fierce battle ensues between the intruder and the cell's defense team: members of the APOBEC family, a handful of closely related antiviral proteins that try to disarm the invading virus by scrambling its genetic information.
But not every family member pitches in. One family member, APOBEC3A or A3A, is conspicuously absent when other APOBECs are battling HIV. Now, scientists at the Salk Institute for Biological Studies have discovered that A3A, the falsely accused deserter, specializes in defending against two different kinds of invaders: "jumping genes," pieces of DNA that can leap from one place in the human genome to another, and Adeno-associated virus (AAV), a tiny harmless virus very different from HIV.
The scientists report their findings in the current online edition of Current Biology .
"People thought that this particular family member didn't warrant a lot of attention because it didn't seem to do anything. But it turned out to have a very powerful effect when we looked in the right place," said Nathaniel Landau, Ph.D., professor in the Infectious Disease Laboratory at the Salk.
And the lab of his colleague Matthew Weitzman, Ph.D., at the Salk's Laboratory of Genetics turned out to be the perfect place.
"Together, we could not only assign a new function to a APOBEC family member that previously had none, but we also expanded the repertoire of different types of viruses against which this innate antiviral system is effective," said associate professor Weitzman, Ph.D., who studies virus-host interactions using Adeno-associated virus or AAV. "This implies that different members of the APOBEC family may have evolved to defend the cell against different types of parasites," he added.
To disarm the virus, members of the APOBEC family edit the genetic information carried by the virus, mutating it so badly that the virus can't function any longer. To do this, the APOBEC proteins remove an essential chemical group from cytosine, one of the four building blocks of DNA that spell out the genetic code, turning the DNA's message into gibberish.
Throughout evolution, cells had to defend themselves against the attack of viruses and "jumping genes," also called mobile genetic elements and either side could win these battles. Nowadays, mobile elements are mostly inactive, but since they successfully invaded the human genome millions of years ago, they are part of each person's genetic code, and their remnants account for more than 45 percent of our DNA. "In the case of HIV, the virus won the battle and it will spread through the human population until human ingenuity can outwit it," said Landau.
One group of "jumping genes" called retrotransposons is closely related to HIV but unlike their feared cousin have lost the ability to escape from their host cell. Marooned inside, they can only move via a "copy and paste" mechanism, taking up ever more space in their host's genome.
If allowed to multiply unchecked, these "jumping genes" can inactivate essential genes or activate cancer-causing genes. "In mice, you see the evolutionary hallmarks of the cells' struggle to keep these elements in check. Many existing copies of retrotransposons have been inactivated by APOBEC generated mutations," said Landau.
The tiny Adeno-associated virus depends on the help of the larger Adenovirus to multiply and does no harm in humans. "We think that a pathogenic virus that is like AAV could be the real target of 3A," said Weitzman. "One candidate might be parvovirus B19, which infects red blood cells and causes Erythema infectiosum (Fifth disease or 'slapped cheek syndrome') in children," he explained.
Unlike other members of the APOBEC family, A3A has no effect on HIV or other retroviruses. "One explanation could be that 3A appears to be active in the cell's nucleus where mobile elements and AAV multiply but the APOBEC-sensitive step during HIV replication happens outside the nucleus in the cytoplasm," speculates Landau.
Researchers who contributed to the work include co-first author Hui Chen and postdoctoral researchers Quin Yu and Jody Chou in the Infectious Disease Laboratory, co-first author Caroline E. Lilley as well as Darwin V. Lee and Iñigo Narvaiza in the Laboratory of Genetics.
The Salk Institute for Biological Studies in La Jolla, California, is an independent nonprofit organization dedicated to fundamental discoveries in the life sciences, the improvement of human health and the training of future generations of researchers. Jonas Salk, M.D., whose polio vaccine all but eradicated the crippling disease poliomyelitis in 1955, opened the Institute in 1965 with a gift of land from the City of San Diego and the financial support of the March of Dimes.
Source: Salk Institute PR March 07, 2006
 APOBEC3A Is a Potent Inhibitor of Adeno-Associated Virus and Retrotransposons
Hui Chen, Caroline E. Lilley, Qin Yu, Darwin V. Lee, Jody Chou, Inigo Narvaiza, Nathaniel R. Landau, and Matthew D. Weitzman
Current Biology, Vol 16, 480-485, 07 March 2006
APOBEC3 proteins constitute a family of cytidine deaminases that provide intracellular resistance to retrovirus replication and transposition of endogenous retroelements . One family member, APOBEC3A (hA3A), is an orphan, without any known antiviral activity. We show that hA3A is catalytically active and that it, but none of the other family members, potently inhibits replication of the parvovirus adeno-associated virus (AAV). hA3A was also a potent inhibitor of the endogenous LTR retroelements, MusD, IAP, and the non-LTR retroelement, LINE-1. Its function was dependent on the conserved amino acids of the hA3A active site, consistent with a role for cytidine deamination, although mutations in retroelement sequences were not found. These findings demonstrate the potent activity of hA3A, an APOBEC3 family member with no previously identified function. They also highlight the functional differences between APOBEC3 proteins. The APOBEC3 family members have distinct functions and may have evolved to resist various classes of genetic elements.
Thursday, March 09, 2006
St. Louis: "Eugenie Scott, Ph.D., will present 'Creationism and Evolution: It's Not Over Yet!' at 11 a.m. March 22 in Graham Chapel as the Arthur Holly Compton Lecture for the Assembly Series.
Scott is the executive director of the National Center for Science Education, a nonprofit organization that defends the teaching of evolution in the public schools. She has been both a researcher and an activist in the creationism vs. evolution controversy, including intelligent design, for more than 20 years."
It has the face of a rat and the tail of a skinny squirrel and scientists say this creature discovered living in central Laos is pretty special: It's a species believed to have been extinct for 11 million years.
The long-whiskered rodent made international headlines last spring when biologists declared they'd discovered a brand new species, nicknamed the Laotian rock rat.
It turns out the little guy isn't new after all, but a rare kind of survivor: a member of a family until now known only from fossils." [Living fossil]
"University scientists suggest extraterrestrial theories are flawed and that more down to earth factors could have accounted for past mass extinctions
Earth history has been punctuated by several mass extinctions rapidly wiping out nearly all life forms on our planet. What causes these catastrophic events? Are they really due to meteorite impacts? Current research suggests that the cause may come from within our own planet – the eruption of vast amounts of lava that brings a cocktail of gases from deep inside the Earth and vents them into the atmosphere.
University of Leicester geologists, Professor Andy Saunders and Dr Marc Reichow, are taking a fresh look at what may actually have wiped out the dinosaurs 65 million years ago and caused other similarly cataclysmic events, aware they may end up exploding a few popular myths."
BBC News: "Dr Francis Collins, the scientist leading the Human Genome Project, says he expects important new gene sequences governing aspects of personality, such as intelligence and behaviour, to be known very shortly.
While the project to crack our DNA code has been targeted at understanding and eradicating disease, Dr Collins believes the project will provide significant insights into a broad range of heritable aspects.
'We haven't discovered most of those yet, but frankly, we should be prepared for an avalanche of that kind of information coming in the next two or three years,' he told the BBC World Service's The Interview programme."
"AUSTIN, Texas--Studying neotropical poison dart frogs, biologists at the University of Texas at Austin uncovered a new way that the frog species can evolve to look similar, and it hinges on the way predators learn to avoid the toxic, brightly colored amphibians.
In the Mar. 8 issue of Nature, Catherine Darst and Molly Cummings show that a harmless, colorful frog living in the Amazonian rainforest gets protected from predators not by mimicking its most poisonous neighbor, but by looking like a frog who's poison packs less punch.
The Texas biologists studied three species of poison dart frogs--one highly toxic species, one less toxic species and one harmless species. All live in the same area and are brightly colored, which warns predators that they may be poisonous.
In a series of predator learning experiments, the researchers found that the frogs' predators--in this case birds--learned to avoid anything remotely resembling the most toxic species."
"Humans and chimpanzees have in common more than 98 percent of DNA and 99 percent of genes. Yet, in looks and behavior we are very different from them. For more than 30 years--well before either the human or chimpanzee genome had been sequenced--scientists have speculated that this might be due to the way that the common genes express themselves rather than differences in the genes themselves. A new comparison published in Nature seems to prove that theory."
Wednesday, March 08, 2006
"Newswise - ATHENS, Ohio - Salamanders and the tuatara, a lizard-like animal that has lived on Earth for 225 million years, were the first vertebrates to walk and run on land, according to a recent study by Ohio University researchers.
After studying the creatures at the Toledo Zoo, Stephen Reilly, associate professor of biological sciences, and doctoral student Eric McElroy determined that they use both forms of locomotion, which are energy-saving mechanisms generally believed to be important only in fast-running animals such as mammals and birds.
The research was published in the March 8 issue of the journal Proceedings of the Royal Society B: Biological Sciences. Andrew Odum, curator of herpetology at the Toledo Zoo, and Valerie Hornyak, head herpetology keeper, were co-authors of the study."
BBC News: "Marine biologists have discovered a crustacean in the South Pacific that resembles a lobster or crab covered in what looks like silky fur.
Kiwa hirsuta is so distinct from other species that scientists have created a new taxonomic family for it.
A US-led team found the animal last year in waters 2,300m (7,540ft) deep at a site 1,500km (900 miles) south of Easter Island, an expert has claimed.
Details appear in the journal of Paris' National Museum of Natural History."
"A poll by Zogby International reportedly shows most Americans support public school teachers presenting evolution and intelligent design theories.
The poll was conducted for the Center for Science and Culture, a Seattle-based organization that's part of the Discovery Institute, which promotes the belief that life is so complex, it must be the product of intelligent design and not the evolutionary process. "
A much-derided theory that five people who walk on all fours are products of "backward evolution" is plausible, and testable, said a U.S. biologist who weighed in on the controversy last week.
The debate erupted last month after a Turkish scientist proposed that the five siblings in Turkey, who also speak what he called a primitive language, had undergone backward evolution. The claim met with skepticism, even jeers, from some fellow scientists.
But Keith Crandall of Brigham Young University in Provo, Utah, said the idea is nothing extraordinary, calling it a "nice and testable hypothesis."
Tuesday, March 07, 2006
"The earliest recorded case of impacted wisdom teeth belongs to the renowned 'Magdalenian Girl,' a nearly complete 13,000- to 15,000-year-old skeleton excavated in France in 1911and acquired by The Field Museum in 1926.
For years this rare, early anatomically modern human skeleton was thought to be that of a girl because her wisdom teeth had not erupted, an event that typically occurs between 18 and 22 years of age. New analysis of Magdalenian Girl's bones, however, has lead Field Museum scientists to conclude that she was not a girl but actually a 25- to 35-year-old woman at the time of her death."
"A study by researchers at New York University and the University of London offers additional evidence that mammals and fruit flies share a common genetic makeup that determines the function of their internal biological clocks. The study appears in the latest issue of Current Biology. The research team consisted of post-doctoral researcher Ben Collins, Esteban Mazzoni, a graduate student, and Assistant Professor Justin Blau of NYU's Department of Biology and Professor Ralf Stanewsky of the University of London."
"Field Museum updates its take on Darwin and braces for challenges:
CHICAGO - A new exhibit at Chicago's Field Museum examines life in everything from the Precambrian to the Quaternary periods, but it's opening during a period when the theory of evolution is under attack by supporters of so-called "intelligent design."
Museum officials say that the timeliness is a coincidence - work began on "Evolving Planet" four years ago, and it replaces an exhibit that touched on many of the same themes.
But if there is any doubt about where the exhibit falls in the debate, it closes with a quote from Charles Darwin, who concluded that species evolve over time."
New York Times: "Providing the strongest evidence yet that humans are still evolving, researchers have detected some 700 regions of the human genome where genes appear to have been reshaped by natural selection, a principal force of evolution, within the last 5,000 to 15,000 years."
The genes that show this evolutionary change include some responsible for the senses of taste and smell, digestion, bone structure, skin color and brain function.
Many of these instances of selection may reflect the pressures that came to bear as people abandoned their hunting and gathering way of life for settlement and agriculture, a transition well under way in Europe and East Asia some 5,000 years ago.
Under natural selection, beneficial genes become more common in a population as their owners have more progeny.
A baby Triceratops skull suggests the impressive horns of the beast were for more than just attracting a mate.
The three-horned Triceratops dinosaur weighed up to 10 tons and had one of the largest skulls of any land animal on the planet.
Now the smallest skull of the species suggests what the horns were for.
"The baby Triceratops confirmed our argument that the horns and frill of the skull likely had another function other than sexual display or competition with rivals"
Monday, March 06, 2006
"Dodo birds are famous for two things: being dumb and being dead. So when Randy Olson calls fellow biologists 'dodos' in his new documentary 'Flock of Dodos: The Evolution-Intelligent Design Circus,' it's not meant as a compliment.
Dodos were flightless, odd-looking birds discovered by Portuguese sailors in the early 1500s on a tiny island in the Indian Ocean, just east of Madagascar. The birds were named after the Portuguese word for 'fool' because they were fearless of humans and would walk up to hungry hunters who simply clubbed them to death and ate them. The birds were extinct by the 17th century, less than 200 years after their discovery.
Olson, a Harvard-trained biologists-turned-filmmaker, thinks the dodo's fate is a good metaphor for biologists in today's changing media environment."
"PANSPERMIA, the idea that life on Earth was seeded by microbes from space, has had a boost from an unlikely source: the Columbia space shuttle, which broke apart on re-entry in February 2003.
Robert McLean at Texas State University in San Marcos had sent three strains of bacteria on the doomed Columbia sealed in a box to see how weightlessness would affect their growth. When the disaster happened, he assumed that the box had been destroyed. A few days later, however, a colleague spotted the charred container in a newspaper photograph of shuttle debris.
BBC NEWS (Science/Nature): Altruism 'in-built' in humans:
"Infants as young as 18 months show altruistic behaviour, suggesting humans have a natural tendency to be helpful, German researchers have discovered.
In experiments reported in the journal Science, toddlers helped strangers complete tasks such as stacking books.
Young chimps did the same, providing the first direct evidence of altruism in non-human primates.
Altruism may have evolved six million years ago in the common ancestor of chimps and humans, the study suggests."
Sunday, March 05, 2006
"SCIENTISTS examining the first dust samples collected from a comet have found complex carbon molecules, supporting the theory that ingredients for life on Earth originated in space.
The organic material was found in early studies of samples from the comet Wild 2, brought back to Earth by the Stardust space probe seven weeks ago.
Stardust collected hundreds of grains of dust as it flew through the tail of the comet two years ago.
Analysis suggests a high concentration of complex molecules of the kind thought necessary for the evolution of life."
"A study from the April issue of Current Anthropology explores the evolution of handedness, one of few firm behavioral boundaries separating humans from other animals. 'The predominant right-handedness of humans has been noted since at least the time of the Greek philosophers Plato and Aristotle,' write Amanda Blackburn (University of Manitoba) and Christopher Knusel (University of Bradford).
'Modern research has shown that hand preference occurs across human cultures and, through observations of ancient art, in ancient peoples.'
As researchers find new cultural behaviors among chimpanzees and other primates, language is the only other characteristic accepted to be unique to humans, and both language and handedness appear to relate to the separation of functions between the two halves of the human brain, also known as lateralization. "
"MADISON - The lights dimmed inside Parkway Pentecostal Church's sanctuary Sunday evening as Steve Grohman directed his laser pointer to an excerpt from a biology textbook projected onto a jumbo screen.
'The whole reason they came up with these ideas was to come up with an alternative to the Bible,' he said, speaking about evolution. 'They think there's a disagreement between the Bible and science.'
The leader of a traveling ministry called the Creation Seminar, Grohman is part of the growing creation evangelism industry, which seeks to undo secular teaching about the origin of the world.
As intelligent design debates have rippled recently through schools, courts and statehouses, these ministries have been toiling for years.
'We've been busy all along,' said Grohman, who for the past 13 years has been traveling the country in a mobile home with his wife and son leading creation seminars.
Grohman's 10-hour program mixes Biblical teaching with lessons about the atmospheric conditions during the time of Adam and Eve and how dinosaurs were just giant reptiles."