Saturday, August 12, 2006


The Hidden Code of Stem Cells

The DNA of embryonic stem cells is labeled in a unique and characteristic way, according to new research from scientists in California. The pattern could shed light on how embryonic stem cells maintain their ability to become any type of cell and might also help efforts to clone these cells, allowing scientists to develop better stem cell therapies...

...Epigenetic changes to DNA are those that alter expression of certain genes, for instance by reversibly tagging those genes, without changing the sequence of the DNA itself. In a paper published last week in Genome Research, researchers studied one such process, called DNA methylation, in which certain molecules within the gene are chemically modified, altering the activity of that particular gene...

The above is based on "Human embryonic stem cells have a unique epigenetic signature" (open access).

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AAAS book explores evolution and Christianity's response

Darwin Origin Species Intelligent Design Creationism (Evolution Research: John Latter / Jorolat)

In an unusual undertaking for a science society, the American Association for the Advancement of Science has produced a new book that discusses evolution and the rich diversity of Christian responses to the theory along with the quest for common ground on what has become a contentious issue in many school districts across the nation.

The book, The Evolution Dialogues (Amazon US), was written with the input of both scientists and theologians. Meant specifically for use in Christian adult education programs, it offers a concise description of the natural world, as explained by evolution, and the Christian response, both in Charles Darwin's time and in contemporary America. It has a glossary of terms from both science and religion, with 'bacteria' and 'Biblical infallibility' defined on the same page.

As an introduction to each chapter, the book features a narrative about the personal dilemma of a fictional college student, Angela Rawlett, as she struggles to reconcile her traditionalist Christian upbringing with her keen interest in biology.

Her story is rooted in reality, according to Connie Bertka, director of the AAAS's Dialogue on Science, Ethics and Religion program, which produced the book. [Bible, Intelligent Design]

Original AAAS news release here

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Dig This: Trilobites Made Tunnels

trilobite evolution research

Trilobites, the extinct marine creatures famous to fossil-hunters everywhere, may have once done digging of their own, say British and Swedish researchers.

Rocks found in a Swedish limestone quarry contain the remains of trilobites inside networks of tunnels, which appear to have been sub-surface thoroughfares for the little bug-like critters.

'It's very rare to find a trilobite in a burrow,' said Amherst College paleontologist Whitey Hagadorn, an expert on tracks, burrows and other "trace" fossils that can give important clues to a long-lost species' behavior and environment.

The above is based on the Geology paper "Tunneling trilobites: Habitual infaunalism in an Ordovician carbonate seafloor": Abstract

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Key Event in Cell Death Occurs as Single, Quick Event

Scientists at St. Jude Children's Research Hospital have demonstrated that a key event during apoptosis (cell suicide) occurs as a single, quick event, rather than as a step-by-step process. Apoptosis eliminates extraneous cells from the developing body; and disposes of cells that sustain irreparable harm to their DNA or are infected with microorganisms.

The researchers photographed individual cells undergoing that process, allowing investigators to observe the release of certain proteins from pores in the membranes of mitochondria. These cellular structures contain enzymes that extract energy from food molecules, and the space within the membrane surrounding them holds a variety of proteins that are released during apoptosis.

Results of the study indicate the formation of pores in the mitochondrial membranes is a rapid process that allows a nearly simultaneous rather than a sequential release of many apoptosis proteins, according to Douglas Green, Ph.D., chair of the St. Jude Department of Immunology. Green is senior author of a report on this work that appears in the August 1 issue of Proceedings of the National Academy of Sciences (PNAS).

The above is based on "Different mitochondrial intermembrane space proteins are released during apoptosis in a manner that is coordinately initiated but can vary in duration" which is open access: Abstract | Full Text

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Jurassic Park (Washington Post)

The Washington Post: 'Jurassic Park - The richest undisturbed cache of dinosaur fossils in North America may change the way we see the distant past. It's already transformed rancher Allen Cook's present'.

IT WAS THE PROSPECTOR WHO FOUND IT FIRST. Maybe 30 years ago, back when uranium was worth a lot, when people thought nuclear power was your friend. He was working a ridge up at Spring Creek, Wyo., looking for ore with a scintillometer, a modern-day Geiger counter. He was getting a lot of hits.

But there was something else. Big, off-color rocks in strange shapes were lying loose on the ground where the wind had blown the dirt off them. The prospector was a geologist. He knew what those were. Dinosaur bones. From big dinosaurs - like the ones that fill up museum exhibits... [Five page article]

And, if you live in the Washington D.C. area, tomorrow's Washington Post contains "Hunt for Dinosaurs":

Find any dinosaur fossils lately? Maybe you're not looking hard enough. After all, they're all around us. Prehistoric teeth, tracks, and to a lesser extent, bones are surprisingly common in parts of the District, Virginia and Maryland. The corridor between Washington and Baltimore, known among paleontologists as "Dinosaur Alley," produced the second dino fossil ever discovered on the East Coast.

If you can't hunt for these relics yourself, you can visit dinosaur exhibits in the area or tap the expertise of local paleontologists to learn about the legendary creatures that literally romped through our back yards and today enthrall parents and kids alike.

Another recent Washington Post article which may be of interest is: "And the Evolutionary Beat Goes On . . ."

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Digging Deep for Life on the Red Planet

Mars Phoenix Lander Evolution Research

The launch of the Mars Phoenix Lander is just a year away. The spacecraft will be aiming for the martian north pole, and if it lands successfully it will dig in snow and ice in one of the few places on Mars where scientists think life could be preserved.

Chris McKay, a planetary scientist with NASA's Ames Research Center, is a co-investigator for the Phoenix Lander, as well as for the Mars Science Laboratory, which is scheduled for launch in 2009. In this interview with Astrobiology Magazine editor Leslie Mullen, McKay explains why future Mars missions must dig deeper to learn about the martian potential for life. [Interview follows]

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Friday, August 11, 2006


Study Evolution losing favor in US

The United States ranks near the bottom, just ahead of Turkey, in a new survey measuring public acceptance of evolution in 34 countries.

The study ("Public Acceptance of Evolution": Summary), led by University of Michigan researcher Jon Miller, found that 40 percent of Americans accept evolution, down from 45 percent over the past 20 years. Among the nations examined, only Turkey had a lower rate of acceptance of evolution, with 25 percent accepting it and 75 percent rejecting it.

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Light Guides Flight Of Migratory Birds

Songbirds use multiple sources of directional cues to guide their seasonal migrations, including the Sun, star patterns, the earth's magnetic field, and sky polarized light patterns. To avoid navigational errors as cue availability changes with time of day and weather conditions, these "compass" systems must be calibrated to a common reference. Experiments over the last 30 years have failed to resolve the fundamental question of how migratory birds integrate multiple sources of directional information into a coherent navigational system.

Last autumn, Rachel Muheim, a postdoctoral associate in biology professor John Phillips' lab at Virginia Tech, captured Savannah sparrows in the Yukon before they headed south. She was able to demonstrate that the birds calibrate their magnetic compass based on polarized light patterns at sunset and sunrise.

The research appears in the Aug. 11, 2006, issue of Science, in the article, "Polarized Light Cues Underlie Compass Calibration in Migratory Songbirds," (Abstract) by Muheim, Phillips, and Suzanne Akesson.

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Pope to Dissect Evolution With Former Students

Vatican City, August 10 - Pope Benedict XVI will conduct a weekend seminar in early September examining Charles Darwin's theory of evolution and its impact on Roman Catholicism's teaching of Creation.

The seminar, titled "Creation and Evolution," is sure to attract the attention of supporters of "intelligent design" - the idea that the world is too complex to have been created by natural events alone - and Vatican scientists who do not consider it valid science.

The seminar is the latest edition of the annual "Shulerkreis," or "student circle," a meeting Benedict has held with his former Ph.D. students since his days as a theology professor at the University of Regensburg in Germany in the 1970s.

The seminar is to take place Sept. 2-3 at Castel Gandolfo, the pope's summer residence south of Rome.

[This news report also appears here]

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Mussels evolve quickly to defend against invasive crabs

Invasive Crab Species And Blue Mussels Evolution Research

Durham, N.H. - Scientists at the University of New Hampshire (UNH) have found that invasive crab species may precipitate evolutionary change in blue mussels in as little as 15 years. The study, by UNH graduate student Aaren Freeman with associate professor of zoology James Byers and published in the Aug. 11 issue of the journal Science, indicates that such a response can evolve in an evolutionary nanosecond compared to the thousands of years previously assumed. The paper is called "Divergent induced responses to an invasive predator in marine mussel populations." (Abstract)

"It's the blending of ecological and evolutionary time," says Freeman, a Ph.D. candidate in the department of zoology. "It's an important development in the arms race between these crabs and these mollusks." Crabs prey on blue mussels by crushing their shells. [Evolution]

Original UNH Report here (contains a link to larger image than above)

Also carried by this week's Washington Post 'Science Notebook' under the title "Mussels Quickly Evolved To Foil a New Predator Crab".

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A cross between a Dog and a Hare: New mammal discovery made by Case paleontologist

Fossils of a new hoofed mammal that resembles a cross between a dog and a hare which once roamed the Andes Mountains in southern Bolivia around 13 million years ago was discovered by Darin A. Croft, assistant professor of anatomy at the Case Western Reserve University School of Medicine and a research associate at the Cleveland Museum of Natural History.

With Federico Anaya from Universidad Autonoma Tomas Frias, Croft reported on the new mammal find named Hemihegetotherium trilobus in the Journal of Vertebrate Paleontology article, 'A New Middle Miocene Hegetotherid (Notoungulata: Typotheria) and a Phylogeny of the Hegetotheriidae.' (Abstract) It is named for the distinctive three lobes on its back lower molar teeth.

The animal belonged to a group of animals called notoungulates—hoofed mammals native only to South America. The group originated in South America soon after the dinosaurs went extinct and evolved to include hundreds of species over a span of more than 50 million years; all of them are now extinct.

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Thursday, August 10, 2006


Love and Sex Influence Disease Evolution

Love and Sex Influence Disease Evolution: "Dating, going steady, hooking up, settling down. There are many ways to be a couple and avoid the lovesick blues. Now it appears that in addition to lovesickness, there is a link between the types of relationships people have and how illness affect us all.

In a study of sexually transmitted diseases, scientists have concluded that the length of time people stay together can determine which infectious diseases circulate in a community and therefore how diseases evolve multiple strains.

Up to now, studies looking at how disease travels in groups worked with models that assumed people bump into each other at random, on a crowded street or some other public place. One disease strain could then hop easily from host to host until maximum infection was achieved.

In reality, of course, our interactions are more complicated. Some people have one long-term partner, while others come in contact with many people, each only for a short time. [Evolution]

The above is based on Coexistence and Specialization of Pathogen Strains on Contact Networks (Abstract)

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Genetic snooze button governs timing of spring flowers

In the long, dark days of winter, gardeners are known to count the days until spring. Now, scientists have learned, some plants do exactly the same thing.

Addressing scientists today (Aug. 9) at a meeting of the American Society of Plant Biologists, University of Wisconsin-Madison researcher Richard Amasino described studies that have begun to peel back some of the mystery of how plants pace the seasons to bloom at the optimal time of year.

...In a series of studies of Arabidopsis, a small mustard plant commonly used to study plant genetics, Amasino and his colleagues have found there are certain critical genes that repress flowering...

Recent publications by Richard Amasino:

Epigenetic maintenance of the vernalized state in Arabidopsis requires like heterochromatin protein 1

The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis.

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Scientist Exposes Evolution's Weaknesses in Politically Incorrect Book About Darwinism and Intelligent Design (Book Review)

Book Review: Seattle, Washington - 'This book is going to upset defenders of Darwin's theory, because it exposes just how weak the evidence for it is and how irrational their criticisms of intelligent design really are,' says biologist Jonathan Wells author of the controversial new book "The Politically Incorrect Guide to Darwinism and Intelligent Design". The book will be published on August 21st by Regnery as part of their popular series of "Politically Incorrect Guides."

In clear, non-technical language, Wells explains who is fighting whom, the root of the conflict, and the evidence for and against Darwinism and Intelligent Design. He also explains what is ultimately at stake for liberals and conservatives, Christians and non-Christians, educators, policymakers, and scientists.
"The Politically Incorrect Guide to Darwinism and Intelligent Design" is currently appearing on the 'Featured Books' page of the Evolution Book Store: UK | US)

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Wednesday, August 09, 2006


Evolution of a penis worm (Synchrotron X-ray tomographic microscopy of fossil embryos)

Evolution Research Penis Worm SRXTM Tomography

The detailed images of embryos more than 500 million years old have been revealed by an international team of scientists, led by the University of Bristol. Writing in the journal Nature, Dr Phil Donoghue and colleagues reveal the various developmental stages of fossilised embryos, from the first splitting of cells to pre-hatching, using synchrotron-radiation X-ray tomographic microscopy (SRXTM).

In one instance this has exposed the internal anatomy of the mouth and anus of a close relative of the living penis worm. Another case has revealed a unique pattern for making embryonic worm segments, not seen in any animals living today.

Phil Donoghue, from the University of Bristol, said: "Because of their tiny size and precarious preservation, embryos are the rarest of all fossils. They are just gelatinous balls of cells that rot away within hours. But these fossils are the most precious of all because they contain information about the evolutionary changes that have occurred in embryos over the past 500 million years." [Tomography]

The above news release (another, the Washington Post's "Paleontologists X-Ray Fossil Embryos", is available here) is based on "Synchrotron X-ray tomographic microscopy of fossil embryos" (Nature). At the time of writing both Abstract and Full Text are available without subscription.

There is also an Editor's Summary.

Original Bristol University News Release.

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Ethiopia: Researchers Find New Human, Animal Fossils

Addis Ababa, Ethiopia: The Authority for Research and Conservation of Cultural Heritage (ARCCH) announced that new fossils including human ancestors have been recovered in the Lower Omo Valley by researchers.

The Omo Group Research Project (OGRP) Team Leader Dr. Jean-Renaud Boisserie, from the Paris National Museum, told a press conference yesterday that the fossils discovered by his team date from 2 to 3 million years.

Dr. Jean-Renaud indicated that the paleontology team discovered abundant fossil assemblages, collecting identifiable specimens in 15 different places.

'The sampled fossil fauna is dominated by different species of monkeys related to modern baboons and other monkeys, but also includes remains of fossil pigs, antelopes, hippopotamuses, giraffes, horses and large cats,' he said.

According to the researcher, three hominid specimens were also found in association with the fauna.

Books on Fossils from the Science and Evolution Bookshop: UK | US

Books on Paleontology from the Science and Evolution Bookshop: UK | US

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Mammoth remains found in southern Hungary

The remains of a mammoth have been found near the town of Zok in southern Hungary, an expert from the institute of geography at the University of Pecs said Wednesday.

"The skull, a 150-centimetre (60-inch) piece of tusk and several of the animal's teeth were found on a hill covered with vineyards," national news agency MTI quoted Gyula Konrad as saying.

The original MTI (Hungarian News Agency Corporation) report is here (the news is only an hour old so I guess there'll be more later).

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Kansas Board of Education to Tackle Evolution

Another Washington Post report on the recent intelligent design v. evolution election result:

Topeka, Kansas - Moderates who will control the state Board of Education next year say it's only a matter of time before they unravel the work of conservatives who had pushed anti-evolution standards back into Kansas schools.

'I imagine everybody is anxious to get the science standards changed back to the mainstream,' Democratic member Bill Wagnon said Tuesday.

Evolution skeptics lost their 6-4 majority earlier this month with the outcome of primary races.

Related recent Washington Post reports include:

Nothing Wrong With Kansas

Anti-Evolution Incumbent in Kansas Wins

Anti-evolution forces lose power in state primary

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How Life takes Shape: Microtubules and Pattern Formation

Microtubules Pattern Formation Evolution Research

Providence, Rhode Island - How life takes shape is a mystery. Butterfly or baby, cells organize themselves into tissues, tissues form organs, organs become organisms. Over and over, patterns emerge in all living creatures. Spiders get eight legs. Leopards get spots. Every nautilus is encased in an elegant spiral shell.

This phenomenon of pattern formation is critical in developmental biology. But the forces that govern it are far from clear. Alan Turing, father of modern computer science, suggested that the basis for pattern formation was chemical. New research .. supplies another surprising answer: Physical, as well as chemical, forces can dictate pattern formation.

In a two-year study (Abstract of Microtubule bundling and nested buckling drive stripe formation in polymerizing tubulin solutions), Brown physicists James Valles and Jay Tang puzzled over the patterns created by proteins called microtubules. Shaped like long, skinny straws, these proteins are puny - they measure only about 250 atoms wide - but play critical roles in the body. Microtubules help cells divide. They also act as scaffolds, giving cells their shape, and serve as train tracks of sorts, moving important bits like chromosomes and mitochondria around inside of cells.

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Tuesday, August 08, 2006


Why Does Sex Exist?

Why does sex exist? A long-popular view holds that sexual reproduction creates new gene combinations that help the next generation resist rapidly co-evolving parasites. Each species constantly changes to achieve the same result - evolutionary advantage - prompting evolutionary biologists to dub this hypothesis the Red Queen (who tells Alice in Through the Looking Glass "it takes all the running you can do, to keep in the same place").

Recent theoretical studies have challenged the generality of the Red Queen hypothesis, suggesting that even though parasites can exert selection pressures that favor sex under some conditions, more often they select against it. They do this, the studies found, by selecting against genes that increase the degree of genetic mixing. And now, Aneil Agrawal has come to the Red Queen's rescue with his own theoretical analysis. While the recent models assumed that host-parasite encounters are random, Agrawal shows that when nonrandom interactions are assumed - so that a host is more likely to acquire parasites from its mother - selective pressures from parasites are much more likely to favor sex.


The above news report is based on:

Similarity Selection and the Evolution of Sex: Revisiting the Red Queen

John Latter / Jorolat
Evolution Research

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Structural Biologists Get First Picture of Complete Bacterial Flagellar Motor

When it comes to tiny motors, the flagella used by bacteria to get around their microscopic worlds are hard to beat. Composed of several tens of different types of protein, a flagellum (that's the singular) rotates about in much the same way that a rope would spin if mounted in the chuck of an electric drill, but at much higher speeds-about 300 revolutions per second.

Biologists at the California Institute of Technology have now succeeded for the first time in obtaining a three-dimensional image of the complete flagellum assembly using a new technology called electron cryotomography. Reporting in Nature, the scientists show in unprecedented detail both the rotor of the flagellum and the stator, or protein assembly that not only attaches the rotor to the cell wall, but also generates the torque that serves to rotate it.

The accomplishment is a tour de force within the field of structural biology, through which scientists seek to understand how cells work by determining the shapes and configurations of the proteins that make them up. The results could lead to better-designed nanomachines.


The above news report is based on "In situ structure of the complete Treponema primitia flagellar motor": Abstract | Full Text

No subscription is necessary at the moment because its an "advance publication". (NB The PhysOrg report does give a link to the full text but it has a typo in it - one of my usual tricks!)

John Latter / Jorolat
Evolution Research

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Scientists Reverse Evolution, Reconstruct Ancient Gene

University of Utah scientists have shown how evolution works by reversing the process, reconstructing a 530-million-year-old gene by combining key portions of two modern mouse genes that descended from the archaic gene.

"It provides further evidence at the molecular level of how evolution has occurred and is occurring, and thus makes the process less mysterious," says Mario Capecchi, distinguished professor and co-chairman of human genetics at the University of Utah School of Medicine and an investigator with the Howard Hughes Medical Institute.

Mouse Reverse Evolution Research

"We've shown some of the elements involved in the process of evolution by reversing this process and reconstructing a gene that later became two genes," he adds.

The study by Capecchi and postdoctoral fellow Petr Tvrdik was set for publication Monday, Aug. 7 in the August 2006 issue of the journal Developmental Cell.

The process of one gene splitting into multiple genes, which then mutate, "has occurred many times in evolution, but no one has put it back together again," Tvrdik says. "We are first to reconstruct an ancient gene. … We have proven that from two specialized modern genes, we can reconstruct the ancient gene they split off from. It illuminates the mechanisms and processes that evolution uses, and tells us more about how Mother Nature engineers life."

The ability to reconstruct an ancient gene from descendant genes also raises the possibility of a new type of gene therapy, in which a portion of a related gene could be inserted into a disease-causing mutant gene to restore its normal function and cure the disease, Capecchi and Tvrdik say.

Genes that Divided are Now Reunited

The study involved what are known as Hox genes, which are like orchestra conductors directing the actions of other genes during development of an animal embryo.

Until sometime between 530 million and 480 million years ago, early animals had 13 Hox genes. Then, in jawed fish - the last common ancestors of modern vertebrate animals - each Hox gene had split into four, so 13 became 52. Later, duplicate Hox genes either mutated in a way that proved useful, or vanished because they were redundant, so today in humans and other mammals there are 39 instead of 52 Hox genes.

The study focused on two modern Hox genes:

- The Hoxa1 gene, which helps control how an embryo's brain stem develops and is compartmentalized into seven sections called rhombomeres. When Hoxa1 is disabled or "knocked out" in an embryonic mouse, the embryo dies shortly after birth because the brain stem is malformed, including the part necessary for breathing. (About 20 people with the same defect have been found among Apache and Navajo Indians in Arizona and in families in Turkey and Saudi Arabia. Their brain stem defects result in problems with breathing, hearing, balance and control of the eyeballs.)

- The Hoxb1 gene, which orders the formation of particular nerve cells in rhombomere 4 - nerves that ultimately control facial expressions in animals. When a mouse is born with a disabled Hoxb1 gene, it suffers facial paralysis, and is unable to blink its eyes, wiggle its whiskers or pull back its ears.

Tvrdik and Capecchi say that by combining critical portions of Hoxa1 and Hoxb1, they effectively recreated a gene with the function that the original Hox1 performed more than 530 million years ago.

The result: A mouse with a disabled Hoxb1 gene still was able to move eyelids, whiskers and ears because the reconstructed gene made up for the loss of Hoxb1.

How the Study was Conducted

Evolution proceeds as cells divide and each gene within them duplicates. Having two identical genes allows one to keep doing its normal job and the other can change, or mutate. Most mutations are for the worse and disappear. Others persist because they perform a new job that holds some advantage for allowing an organism to adapt. The quadrupling of Hox (and also other genes) a half-billion years ago provided animals with an advantage "because they had more genes to use for specialized jobs," including adapting to environmental changes, Tvrdik says.

Each gene is made of DNA. Some of the gene's DNA carries a code or blueprint that makes a protein to carry out some specific function in an organism. Some genetic mutations change this "coding region" and thus change the protein a gene makes.

Other mutations change other parts of the gene, known as "regulatory sequences," which decide when and where the gene and its protein act in an organism's body.

Because the gene's regulatory sequences can be 10 to 100 times larger than the gene's coding region, mutations are more likely there.

A key question was whether the Hoxa1 and Hoxb1 genes are different because their protein-coding regions have changed or their regulatory sequences have changed. So the scientists switched the two genes' coding regions. Each gene then produced the other gene's protein. Mice born with the switched genes were essentially normal.

That means the coding regions were interchangeable, and that evolution has changed each gene's regulatory sequence, not the protein-making coding region.

Next, Tvrdik and Capecchi took a small portion of the regulatory sequence from gene Hoxb1 (which controls facial expressions) and put it into Hoxa1, (which allows mice to breathe and survive after birth). And they disabled the remainder of Hoxb1.

Mice suffered facial paralysis when they were born with disabled Hoxb1 and without a portion of that gene inserted into the Hoxa1 gene. In response to a puff of air in the face, they couldn't blink their eyes, wiggle their whiskers and fold back their ears.

But when a portion of the Hoxb1 regulatory sequence was inserted into Hoxa1, the new gene performed the jobs of both genes. Mice born with the combined gene still were able to breathe and survive thanks to the Hoxa1 gene, and they could move their facial muscles, thanks to the small bit of the Hoxb1's regulatory sequence.

Capecchi says that by combining parts of both Hoxa1 and Hoxb1, he and Tvrdik reversed evolution.

"What we have done is essentially go back in time to when Hox1 did what Hoxa1 and Hoxb1 do today," he says. "It gives a real example of how evolution works because we can reverse it."

The hybrid Hoxa1-Hoxb1 gene is not fully identical to the half-billion-year-old Hox1 because it lacks Hoxc1 and Hoxd1. But Hoxc1 vanished during evolution because it was redundant, and Hoxd1 plays a minor role. So the combined Hoxa1-Hoxb1 gene performs essentially all the functions of the ancient gene, Capecchi says.

A New Approach to Gene Therapy?

Capecchi says scientists hypothesized that when a gene duplicates into identical genes, mutations can occur so the once-identical duplicates evolve to split the original job - a process is called subfunctionalization.

"We are giving an example of how it actually happened - what elements are involved and how you initially separate the functions, and how can you reconstruct the [ancient] gene to put the functions back again," Capecchi says.

The study raises the prospect of a new approach to gene therapy, Tvrdik says.

If a gene duplicated into two and they evolved separate functions in the body - for example, one gene works in the liver and the other in the brain - then "if the brain version of the gene becomes mutated or deleted [to cause a disease] and its gene replacement is difficult or impractical, then our work shows that the ‘liver copy' potentially could be recruited to do the brain functions," Tvrdik says.

In other words, regulatory elements from the brain gene might be inserted into the liver gene to reconstruct a gene similar to the normal brain gene.

Capecchi speculated on a possible example: a form of inherited anemia named beta-thalassemia, which occurs when a mutant beta hemoglobin gene results in faulty production of hemoglobin. The new study suggests it might be possible to use regulatory sequences from the faulty gene to activate a similar gene, essentially creating an embryonic or juvenile beta hemoglobin gene that could make hemoglobin normally during adult life.

Source: University of Utah August 7, 2006


Based on:

Reversal of Hox1 Gene Subfunctionalization in the Mouse

Petr Tvrdik and Mario R. Capecchi

Developmental Cell, Vol 11, 239-250, August 2006

In vertebrates, paralogous Hox genes play diverse biological roles. We examined the interchangeability of Hoxa1 and Hoxb1 in mouse development by swapping their protein-coding regions. Remarkably, the mice expressing the Hox-B1 protein from the Hoxa1 locus, and vice versa, are essentially normal. We noted, nonetheless, a specific facial nerve hypomorphism in hemizygous Hoxb1A1/- mice and decreased viability in homozygous Hoxa1B1/B1 embryos. Further, we established a mouse line in which we have inserted the 107 bp Hoxb1 autoregulatory enhancer into the Hoxa1 promoter. Strikingly, the newly generated autoregulatory Hoxa1 gene can deliver the functionality of both paralogs in these mice, providing normal viability as well as proper facial nerve formation even in the Hoxb1 mutant background. This study affirms that subfunctionalization of the transcriptional regulatory elements has a principal role in the diversification of paralogous Hox genes. Moreover, we show that the ancestral vertebrate Hox1 gene can still be experimentally reconstructed.

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Washington Post Editorial Contains Inaccurate Information about Kansas and Intelligent Design

Discovery Institute: An editorial in yesterday's Washington Post, 'Nothing Wrong With Kansas' (there are links to related news entries here), contains many inaccurate statements about the Kansas Science Standards and intelligent design.

First, it wrongly frames the Kansas issue as being about intelligent design:

The conservatives regained the majority in 2004 and moved to promote intelligent design -- a challenge to Darwinian theory based not on biblical inerrancy or overt creationism but on purportedly scientific flaws in the theory.

('Nothing Wrong With Kansas,' Washington Post, Sunday, August 6, 2006)

But the standards are not about intelligent design. Not only do they clearly state, 'the Science Curriculum Standards do not include Intelligent Design' (Kansas Science Standards, pg. ii), but the standards only require teaching about scientific criticisms of Neo-Darwinism in a way that does not get into intelligent design (see here for an explanation).

Because the editorial board at The Washington Post mistakenly thinks Kansas is dealing with intelligent design, it then goes on to promote a mistaken and straw version of intelligent design, asserting that ID is all about the supernatural.

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Monday, August 07, 2006


Deep Oceans Called Home Of Diverse Microbial Life

The Washington Post 'Science Notebook' (scroll down the page for this item): Scientists fishing for genes in the deep oceans have netted a huge catch of surprisingly diverse genetic snippets, providing the best evidence yet that the seas are home to far more microbial diversity than researchers had thought.

The work indicates that the world's oceans, once thought to be virtually sterile on the microbial scale, are teeming with bacteria and related organisms that have been evolving and swapping genes for billions of years.

Mitchell Sogin of the Marine Biological Laboratory in Woods Hole, Mass., led the new work - part of an ongoing census of marine microbial life. [microbes]

The paper the above refers to is:

Microbial diversity in the deep sea and the underexplored "rare biosphere" [Abstract] [Full Text (pdf)]

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Stressed-out plants warn their offspring?

Plants under stress not only activate their own defences, but also manage to pass on a possible protective strategy to their descendants. That's the surprising conclusion of a study published online today by Nature: "Transgeneration memory of stress in plants" (Abstract).

Stresses such as pathogen infection or ultraviolet radiation can trigger increased rates of genetic mutation in some plant cells, occasionally even scrambling regions of their DNA. Some scientists hypothesize that by augmenting their genomic flexibility, plants boost their ability to produce genetic changes that could allow them to adapt to stressful environments. Now it seems that plants can also pass this genetic pliability on to their offspring.

Researchers in Barbara Hohn's lab at the Friedrich Miescher Institute for Biomedical Research in Basel, Switzerland, study a process in which one piece of DNA within the genome replaces another fragment of similar sequence. This process, called 'homologous recombination', occurs more frequently in stressed plants. Plants grown near the site of the Chernobyl nuclear-reactor accident, for example, were found to have rates of homologous recombination that increased with the dose of radiation they received.

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Sunday, August 06, 2006


Nothing Wrong With Kansas

Washington Post: For the second time in less than a year, voters have turned out of office policymakers who insisted on teaching kids bad science. Last year, the people of Dover, Pennsylvania, got rid of a group of school board members who injected the theory of 'intelligent design' into high school biology.

Last week, Republican primary voters in Kansas ousted the conservative majority on the state Board of Education, which had adopted science standards embracing intelligent design and casting doubt on Darwinian evolution. Moderate Republicans replaced two conservatives -- giving those supporting science at least a 6-to-4 majority, even if the other conservatives hold on in the general election.

The vote, which should lead to changes to those embarrassing standards, is an encouraging sign that even in conservative jurisdictions, most people want kids to be taught biology, not religion.

The Kansas board has been fighting over evolution since 1999, when it moved to eliminate references to Darwinian theory from statewide standards.

See "Anti-Evolution Incumbent in Kansas Wins" or Anti-evolution forces lose power in state primary

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