Saturday, October 07, 2006


A smart battle against intelligent design (Paradigm Magazine)

Whithead Institute for Biomedical Research: Paradigm Magazine - Despite a victory in the Dover school board trial, the battle against creationism needs a steady stream of recruits:

For the last 100 years, scientists, teachers and parents have been relying mostly on lawyers to keep religion out of public school science classes in this country. So far, the lawyers have been doing a pretty good job.

But the burden is shifting to the scientists themselves, say experts involved in recent cases defending public school science curricula from anti-evolution revisions. "The buck stops with university professors," says Eugenie Scott (author of "Evolution vs. Creationism: An Introduction": Amazon UK | US), executive director of the National Center for Science Education in Oakland, California.

It is tempting for scientists to insist that creationist perspectives should not be dignified with a response, says Richard Katskee, assistant legal director of Americans United for Separation of Church and State and one of the four principal lawyers in last year's rout of the Dover, Pennsylvania, school board mandate to teach intelligent design as an alternative to evolution. But the stakes are too big.

Continued at "A smart battle against intelligent design"

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A Review of The Language of God: 'ID The Future' Webcast

The latest 'Intelligent Design The Future' Webcast:

"On this episode the Center for Science and Culture's Logan Gage provides an insightful review into Dr. Francis Collins' recent book, The Language of God. According to Gage, Collins gives an excellent overview of design in physics and cosmology. Yet, when it comes to biology, Collins gets hung up on a common misperception about ID in biology, namely that it is an argument from ignorance. Gage shows how Collins view of design in cosmology is at odds with his dismissal of the possibility of design in biology." [CSC, Evolution, Podcast]

The Language of God: A Scientist Presents Evidence for Belief by Francis S. Collins (Amazon UK | US)

Listen to "A Review of The Language of God" here (and view the archives).

Alternatively, down load the podcast as a mp3 file and/or visit the webpage.

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Genetic evidence for punctuated equilibrium

From The Scientist: Evidence for punctuated equilibrium lies in the genetic sequences of many organisms, according to a study in this week's Science. Researchers report that about a third of reconstructed phylogenetic trees of animals, plants, and fungi reveal periods of rapid molecular evolution.

'We've never really known to what extent punctuated equilibrium is a general phenomenon in speciation,' said Douglas Erwin of the National Museum of Natural History in Washington, D.C., who was not involved in the study. Since its introduction by Stephen Jay Gould and Niles Eldredge in the 1970s, the theory of punctuated equilibrium - that evolution usually proceeds slowly but is punctuated by short bursts of rapid evolution associated with speciation - has been extremely contentious among paleontologists and evolutionary biologists.

While most studies of punctuated equilibrium have come from analyses of the fossil record, Mark Pagel and his colleagues at the University of Reading, UK, instead examined phylogenetic trees generated from genetic sequences of closely related organisms. [Paleontology, Evolution, Palaeontology, Biology, Tree, Phylogeny, Sequence]

Continued at "Genetic evidence for punctuated equilibrium"

Based on the jounal Science paper "Large Punctuational Contribution of Speciation to Evolutionary Divergence at the Molecular Level" (Abstract)

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

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UCR-led research team receives grant to study interaction of ecology and evolution

Research could provide insight into how environmental changes cause organisms to evolve and how evolving organisms change the ecosystem:

Riverside, California - An interdisciplinary team of researchers led by David Reznick (homepage), an evolutionary biologist at University of California, Riverside, has been awarded $5 million over five years by the National Science Foundation (NSF) to conduct an experimental study on how ecology - a branch of science concerned with the interrelationship of an organism and its environment - and evolution interact. The findings of the study are expected to help explain how environmental changes influence an organism's evolution as well as how the evolving organism, in turn, changes the ecosystem in which it is embedded.

Reznick, a professor of biology and the principal investigator of the grant from NSF's Frontiers in Integrative Biological Research (FIBR) program, in collaboration with colleagues specializing in molecular biology, population ecology, ecosystems science, biogeochemistry and applied mathematics, will perform the study of evolution/ecology interactions in natural stream communities on the island of Trinidad.

Specifically, the team will focus on guppies - small fresh-water fish biologists have studied for long - that coexist in the stream with Hart's killifish, a predator. The team will examine not only what causes the guppies to evolve as they might but also the co-evolution of the killifish.

Continued at "UCR-led research team receives grant to study interaction of ecology and evolution"

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Remains of giant 100,000-year-old camel discovered in Syria

Damascus, Syria, October 6 2006 (Reuters) - Swiss researchers have discovered the 100,000-year-old remains of a previously unknown giant camel species in central Syria.

'This is a big discovery, a revolution in science,'. Professor Jean-Marie Le Tensorer of the University of Basel told Reuters. 'It was not known that the dromedary was present in the Middle East more than 10,000 years ago.'

'Can you imagine? The camel's shoulders stood three metres (yards) high and it was around four metres tall, as big as a giraffe or an elephant. Nobody knew that such a species had existed.'

A group of humans apparently killed the camel while it was drinking from a spring, said Tensorer, adding that 100,000-year-old human remains were discovered nearby...

...The human bones were transported to Switzerland, where they underwent anthropological analysis...

..."The bone is that of a homo sapiens, or modern man, but the tooth is extremely archaic, similar to that of a Neanderthal. We don't know yet what it is exactly." said Tensorer. [Neandertal]

Continued at: Remains of giant camel discovered in Syria

Also reported by SANA (Syrian Arab News Agency): "Huge Camel Lived 100,000 Years Before in the Syrian Desert"

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Why Do Cold Animals Make Bigger Babies? (American Naturalist)

Reproduction involves a critical decision: Should an organism invest energy in a few large offspring or many small ones?

In a new study from the journal The American Naturalist, Michael Angilletta (Indiana State University), Chris Oufiero (University of California, Riverside), and Adam Leache (University of California, Berkeley) used a new statistical approach that can test multiple theories at the same time, an approach they hope will shed light on many evolutionary problems.

...So why do animals in colder climates produce larger offspring? One theory suggests the larger size of offspring counteracts their slow growth in the cold. Yet another theory suggests large offspring are not directly linked to temperature at all. Instead, large offspring just happen to be produced by large mothers, who grow large because they require more energy to reproduce in the cold.

When they tested the theories simultaneously with their new approach, the team concluded that temperature's effect on reproduction is a byproduct of its effect on adult size. "This result could have widespread significance," says Angilletta.

Continued at "Why Do Cold Animals Make Bigger Babies?" [Statistics, Strategy]

Based on "Direct and Indirect Effects of Environmental Temperature on the Evolution of Reproductive Strategies: An Information-Theoretic Approach" (Abstract - Full Text is also currently available via a link on the Abstract page).

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Friday, October 06, 2006


Fossils pinpoint tropics as Earth's most fruitful biodiversity spawning ground

A team of scientists has completed a study that explains why the tropics are so much richer in biodiversity than higher latitudes. And they say that their work highlights the importance of preserving those species against extinction.

'If you came from outer space and you started randomly observing life on Earth, at least before people were here, the first thing you'd see was this incredible profusion of life in the tropics,' said the report's lead author, David Jablonski, the William Kenan Jr. Professor in Geophysical Sciences at the University of Chicago. 'This is the single most dramatic biodiversity pattern on this planet.'

Jablonski and his co-authors, Kaustuv Roy, of the University of California, San Diego, and James Valentine, of the University of California, Berkeley, present their new findings on the origins of this global diversity trend in the October 6 2005 issue of the journal Science.

Why the tropics are so much richer in species and evolutionary lineages than elsewhere on Earth has loomed as one of the largest questions facing biologists for more than a century. Biologists have proposed virtually every possible combination of origination, extinction and immigration to explain the pattern at one time or another.

...The fossil data of the past 11 million years has broken this logjam. [Evolution, Paleobiology, Palaeobiology, Lineage]

Continued at Fossils pinpoint tropics as Earth's most fruitful biodiversity spawning ground

Related news report "Tropics source of much of world's biodiversity"

Based on "Out of the Tropics: Evolutionary Dynamics of the Latitudinal Diversity Gradient" (Abstract)

David Jablonski is editor of the book "Evolutionary Paleobiology: In Honor of James W.Valentine" (Amazon UK | US)

Also reported in the Washington Post's 'Science Notebook' entry "Tropics Nurture Marine Species".

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Richard Dawkins and Nobel Prize Winners on 'Science Friday' (Webcast)

Online audio webcast of NPR's 'Science Friday' for the 6th October 2006:

This link takes you to the Science Friday homepage should you be in time to catch the broadcast!

The title link, however, takes you to a page where you can choose which segment to listen to once the program has been archived.

October 6, 2006: Hour One: 2006 Nobel Prizes

This week, the winners of the 2006 Nobel Prizes in physics, chemistry, and physiology or medicine were announced. Physicists George Smoot (homepage) and John Mather (homepage) won the prize in physics for their work in analyzing the cosmic microwave background radiation, work that helped to support theories about the Big Bang. Andrew Fire (homepage) and Craig Mello (homepage) won the prize in Medicine or Physiology for for their discovery of RNA interference - gene silencing by double-stranded RNA. And Roger Kornberg (homepage) won the prize in Chemistry for his work in DNA transcription, the process by which information stored in the genes is copied, and then transferred to the parts of cells that produce proteins. (more info)

October 6, 2006: Hour Two: Richard Dawkins / Salmon Farming

In his new book "The God Delusion" (Amazon UK | US) evolutionary biologist Richard Dawkins says fundamentalist religion "subverts science and saps the intellect." Join guest host Joe Palca in this hour of Science Friday for a chat with Dawkins on religion, the teaching of evolution and creationism in science class, and his call for atheists to "out" themselves.

Plus, does fish farming harm wild salmon populations? A new study suggests it might, tying parasitic sea lice infestations from farmed salmon to declines of wild salmon populations in Europe and Canada."We counted sea lice on more than 14 thousand juvenile salmon migrating past fish farms, and conducted mortality experiments with more than 3 thousand fish," explained Martin Krkosek, one of the authors of the report, describing how the study was performed. (more info)

[Podcast, Evolution, Prize, Intelligent Design, ID]

Featured books: "RNA Interference Technology: From Basic Science to Drug Development" by Andrew Fire et al. (Amazon UK | US)

and "Rnai: A Guide to Gene Silencing" edited by Gregory J. Hannon (Amazon UK | US)

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Thursday, October 05, 2006


The Gene 'Hothead' Now Looking Less Hot (Scientific American)

From Scientific American Blog Sciam Observations: One of the most exciting results in biology last year (1) was a possible violation of the most basic rules of genetic inheritance, reported to occur in the lab plant Arabidopsis. If true, it would be an enormous discovery. But in a brief communication published in last week's Nature (2), a second group (Peng et al. of the University of California, Los Angeles) reports they were unable to replicate the result, which is generally not a good sign.

To recap the earlier report, researchers said that the offspring of plants possessing two mutated copies of a gene called hothead unexpectedly received one or two regular versions of the gene instead, apparently violating Mendel's rule that an organism's genes are a grab-bag from its parents. The plants showed the same oddity in other genes across the genome...

...In the Nature communication, Peng et al. of UCLA report that when they grew hothead mutants in isolation, the offspring did not revert back, even in thousands of plants... Tellingly, they say they did find reversions when they grew hothead mutants around other plants, suggesting that the mutants are highly susceptible to cross-pollination, rather than being exclusively self-fertilized as is normal for Arabidopsis...

...In a published reply (3), Lolle, Pruitt and their original co-authors agree that Peng et al.'s findings do indeed smack of cross-pollination, but they contend that some of their results, such as double reversions of both mutant genes to the regular form, are inconsistent with cross-pollination being the whole story in their case.

(1) "RNA to the Rescue: Novel inheritance patterns violate Mendel's laws" (Sciam)
(2) "Plant genetics: Increased outcrossing in hothead mutants" (Abstract)
(3) "Increased outcrossing in hothead mutants (Reply)" (Abstract)

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We Are All Microbes: Symbiogenesis and Lynn Margulis (Part 2)

An interview with NASA's Astrobiology Magazine, Part 2:

"Microcosmos: Four Billion Years of Microbial Evolution (Amazon UK | US), co-authored by Lynn Margulis and her son Dorion Sagan, was first published twenty years ago. Astrobiology Magazine recently interviewed Margulis, to find out how her and Sagan's ideas have stood the test of time. In this, the second part of a four-part interview, she talks about four specific microbial organisms that, through fusion, yielded modern plant and animal cells.

Part 1 of the interview via: "Microbial Planet: Symbiogenesis and Lynn Margulis"
Part 3 of the interview via "Bacteria Don't Have Species: Symbiogenesis and Lynn Margulis"
Part 4 of the interview via: "Bacterial Intelligence: Symbiogenesis and Lynn Margulis"

From Lynn Margulis' homepage:

She argues that inherited variation, significant in evolution, does not come mainly from random mutations. Rather new tissues, organs, and even new species evolve primarily through the long-lasting intimacy of strangers. The fusion of genomes in symbioses followed by natural selection, she suggests, leads to increasingly complex levels of individuality. Dr. Margulis is also acknowledged for her contribution to James E. Lovelock's Gaia concept. Gaia theory posits that the Earth's surface interactions among living beings sediment, air, and water have created a vast self-regulating system.

James Lovelock has recently written "The Revenge of Gaia: Earth's Climate Crisis and the Fate of Humanity" (Currently appearing on the 'Featured Books' page of the Evolution Book Store: UK | US - or go directly to the Amazon book webpage: UK | US - see "The End of Eden: Gaia and James Lovelock"

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'Monster' fossil find in Arctic: Pliosaur - Tyrannosaurus Rex of the Sea

Hurum Ichthyosaur Plesiosaur Fins Fish (Evolution Research: John Latter / Jorolat)From BBC News UK: Norwegian scientists have discovered a 'treasure trove' of fossils belonging to giant sea reptiles that roamed the seas at the time of the dinosaurs.

The 150 million-year-old fossils were uncovered on the Arctic island chain of Svalbard - about halfway between the Norwegian mainland and the North Pole.

The finds belong to two groups of extinct marine reptiles - the plesiosaurs and the ichthyosaurs.

One skeleton of a gigantic pliosaur has been nicknamed 'The Monster' because of its enormous size.

These animals were the top predators living in what was then a relatively cool, deep sea.

Palaeontologists from the University of Oslo's Natural History Museum discovered the fossils during fieldwork in a remote part of Spitsbergen, the largest island in the Svalbard archipelago.

Continued at "'Monster' fossil find in Arctic: Pliosaur - Tyrannosaurus Rex of the Sea" [Evolution, Predator, Norway, Dinosaur, Paleontology, Palaeontology]

Similar news reports include the Washington Post's "Remains of Ancient Reptile Are Found" and "'Monster' Reptile Fossil Found on Arctic Island" plus the International Herald Tribune's "Researchers find prehistoric remains of giant, sea reptile on Arctic island"

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

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

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Does Evolution Have Practical Benefits for Science?: 'ID The Future' Webcast

The latest 'Intelligent Design The Future' Webcast:

"On this episode of the ID The Future podcast Casey Luskin looks at what evolution has given us. Recently some mainstream scientists have been discussing what practical benefits Darwinian evolution holds for society? Surprisingly, they see little practical applications for Darwinian evolution, going so far as to admit that "evolution hasn't yielded many practical or commercial benefits." Last year, National Academy of Sciences (PNAS) member Phillip Skell made the observation last year that Darwinism is not the foundation of all biological research, and indeed exerts little influence in much of the research being done today."

Phillip Skell's article "Why Do We Invoke Darwin? Evolutionary theory contributes little to experimental biology" can be found here.

Listen to "Does Evolution Have Practical Benefits for Science?" here (and view the archives).

Alternatively, down load the podcast as a mp3 file and/or visit the webpage.

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Genetics Of Multi-chambered Heart Evolution: Hearts Or Tails?

A new paper in the October 1 2006 issue of Genetics and Development elucidates the genetics of heart formation in the sea squirt, and lends surprising new insight into the genetic changes that may have driven the evolution of the multi-chambered vertebrate heart.

Brad Davidson and colleagues in Michael Levine's lab at UC Berkeley have discovered that the transcription factor Ets1/2, along with the signaling molecule FGF, controls early heart formation in the sea squirt, Ciona intestinalis.

Sea squirts are most commonly found in shallow ocean waters attached to algae, rocks or seaweed. They have been used for over 100 years as a highly useful experimental model organism for the study of animal development. A simple chordate, Ciona is being used in the lab to study the heart development of higher organisms because it shares several characteristics with vertebrates - although ultimately, Ciona, develops a heart with just one chamber (as opposed to vertebrates' multi-chambered heart). [University of California]

Based on "FGF signaling delineates the cardiac progenitor field in the simple chordate, Ciona intestinalis" (Abstract)

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Wednesday, October 04, 2006


Cracking the egg: Unraveling our first transitions (Genes and Development)

Sexual reproduction is not necessarily sexy (especially when scientists start analyzing it), but it is fascinating. As we all know, the basics entail bringing together an egg and a sperm, a whole lot of cell division and growth, and sooner or later a young organism that carries a mix of genes from both parents. There are many startling events along the way, but one of the most fundamental and important is the transition from unfertilized egg to fertilized embryo.

Think about it: The former is and will remain an egg if left alone, while the latter has within it the means to unleash the dazzling cascade of events needed to create a viable organism. What's already in the egg that enables it to make the transition? How is it the same and how is it different across species? And what changes occur when the egg is fertilized? Scientists led by Drs Barbara Knowles (homepage) and Alexei Evsikov (homepage) at The Jackson Laboratory have certainly been thinking about this topic for years. A new paper in the journal Genes and Development presents significant new information about what is happening within a fully grown (pre-ovulatory) egg and some of the changes that occur during transition to the two-cell stage embryo.

Continued at "Cracking the egg"

Based on the paper "Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo" (Abstract) [Evolution]

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A Meaningful World: How the Arts and Sciences Reveal the Genius of Nature (Book)

Synopsis of "A meaningful World: How the Arts and Sciences Reveal the Genius of Nature" (Amazon UK | US):

In this groundbreaking book, Wiker and Witt show that nature offers all of the challenges and surprises, all of the mystery and elegance, we associate with design and, further, with artistic genius. They begin in Shakespeare and range through the fine-tuning of the laws of physics, the Periodic Table of Elements, the artistry of ordinary substances like carbon and water, the intricacy of biological organisms, and the drama of scientific exploration itself. In contrast to contemporary claims that the world is ultimately meaningless, Wiker and Witt reveal a cosmos charged with both meaning and purpose.

From "Reviews and Endorsements": "A Meaningful World is simply the best book I've seen on the purposeful design of nature. In sparkling prose Benjamin Wiker and Jonathan Witt teach us how to recognize genius, first in Shakespeare's plays and then in nature. From principles of geometry to details of the periodic table, the authors portray the depth, elegance, clarity and pure cleverness of a universe designed to nurture the intelligent life that one day would discover that design. A Meaningful World recovers lost purpose not only for science, but for all scholarly disciplines." - Michael J. Behe, author of Darwin's Black Box (Amazon UK | US)

Read the Prologue and Chapter One (pdf files)

"An (audio) interview with Jonathan Witt" is in the playlist of "'Intelligent Design The Future' - Weekly Web/Podcasts from the Discovery Institute" (21nd entry from the end of the list: scroll down and subtract 22 from the number of the final entry - this is the easiest way to do it because the number of entries increases weekly*). [Evolution, Review, ID, Podcast]

* Update: I've sent an email asking if the numbering system can be reversed: At the moment all the podcast numbers change when a new show is added. Reversing the system would mean the numbers stay the same with a new number being permanently assigned to each new show as it appears.

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University of Pennsylvania Researchers Discover 'Killer' B Cells - New Link in the Evolution of Immunity

Philadelphia: Researchers from the University of Pennsylvania School of Veterinary Medicine have discovered a unique evolutionary link between the immune systems of fish and mammals in the form of a primitive version of B cells, white blood cells of the immune system. Their studies link the evolution of the adaptive immune system in mammals, where B cells produce antibodies to fight infection, to the more primitive innate immunity in fish, where they found that B cells take part in phagocytosis (literally: cell eating), the process by which cells of the immune system ingest foreign particles and microbes.

The finding, which appears in the online version of the journal Nature Immunology and will be featured on the cover of the October issue, represents a sizeable evolutionary step for the mammalian immune system and offers a potential new strategy for developing much-needed fish vaccines.

'When examining fish B cells we see them actively attacking and eating foreign bodies, which is a behavior that, according to the current dogma, just shouldn't happen in B cells,' said J. Oriol Sunyer (homepage), a professor in Penn Vet's Department of Pathobiology. 'I believe it is evidence for a very real connection between the most primitive forms of immunological defense, which has survived in fish, and the more advanced, adaptive immune response seen in humans and other mammals.'

Continued at "University of Pennsylvania Researchers Discover 'Killer' B Cells - New Link in the Evolution of Immunity"

Based on "B lymphocytes from early vertebrates have potent phagocytic and microbicidal abilities" (Abstract) [Behaviour]

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

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Mastodons Driven to Extinction by Tuberculosis, Fossils Suggest

Oligocene  Miocene Plio-Pleistocene HoloceneFrom National Geographic News: Tuberculosis was rampant in North American mastodons during the late Ice Age and may have led to their extinction, researchers say.

Mastodons lived in North America starting about 2 million years ago and thrived until 11,000 years ago - around the time humans arrived on the continent - when the last of the 7-ton (6.35-metric-ton) elephant-like creatures died off.

Scientists Bruce Rothschild and Richard Laub pieced together clues to the animals' widespread die-off by studying unearthed mastodon foot bones.

...Based on the finding, it's likely that virtually every late Ice Age mastodon in North America had tuberculosis, Laub says.

Continued at Mastodons Driven to Extinction by Tuberculosis, Fossils Suggest

Rothschild and Laub's work appears in the the journal Naturwissenschaften paper "Did ice-age bovids spread tuberculosis?" (Abstract: here or here) [Science, Evolution, Extinct]

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Tuesday, October 03, 2006


Genome archaeology illuminates the genetic engineering debate

The journal Genome Research's cover story for October 2nd, 2006 tells a tale of 'genome archaeology' by genetic researchers who dug deeply into the long history of maize and rice. Their resulting insights into plant genomic evolution may well fuel the fires of the genetically modified organism (GMO) controversy.

"Our findings elucidate an active evolutionary process in which nature inserts genes much like modern biotechnologists do. Now we must reassess the allegations that biotechnologists perform 'unnatural acts,' thereby creating 'Frankenfoods,'" said Professor Joachim Messing (homepage), project leader and director of the Waksman Institute of Microbiology at Rutgers, The State University of New Jersey.

By comparing corresponding segments of two maize (corn) chromosomes with each other, and then to a corresponding segment of rice, project scientists reconstructed a genetic history replete with "reconfiguration and reshuffling, reminiscent of working with Lego blocks," Messing said.

Continued at "Genome archaeology illuminates the genetic engineering debate"

Based on "Uneven chromosome contraction and expansion in the maize genome" (Abstract)

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'Intelligent Design The Future' - Weekly Web/Podcasts from the Discovery Institute

Intelligent Design and Evolution Podcasts From the Discovery Institute:

Use the small scrollbar to browse the archives and then click on the one you want. Allow time for the program to begin loading. If your browser does not show the embedded Player, or if you would like to read descriptions of the podcast entries, click here.

"The ID The Future (IDTF) podcast carries on Discovery Institute's mission of exploring the issues central to evolution and intelligent design. IDTF is a short, weekly podcast providing you with the most current news and views on evolution and ID. IDTF delivers brief interviews with key scientists and scholars developing the theory of ID, as well as insightful commentary from Discovery Institute senior fellows and staff on the scientific, educational and legal aspects of the debate."

Future broadcasts will automatically appear in the player list (if you want to bookmark this page) plus they will have their own individual entry in this blog.


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How did bilaterally symmetric flowers evolve from radially symmetric ones?

How did bilaterally symmetric flowers evolve from radially symmetric ones? To address this important question, geneticists Francisco Perfectti and Juan Pedro M. Camacho, and ecologist Jose M. Gomez (Universidad de Granada, Spain) explored how different flower shapes affected plant fitness in natural populations of Erysimum mediohispanicum, a Mediterranean herb. Their findings will be published in the October issue of The American Naturalist.

The researchers found that plants bearing bilaterally symmetrical flowers were more visited by pollinators and had higher fitness, measured by both the number of seeds produced per plant and the number of seeds surviving to the juvenile stage, than plants with radially symmetric flowers. [Bilateral, Radial, Symmetry, Ecology, Evolution, Genetics]

Based on "Natural Selection on Erysimum mediohispanicum Flower Shape: Insights into the Evolution of Zygomorphy" (Abstract)

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

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Nobel Prize for Medicine: RNA Interference - Open Access to Papers and Animation

The journal Nature is providing open access to a 'web focus' on RNA Interference:

Cells utilize RNA interference (RNAi) to regulate protein expression in many contexts. The discovery of RNAi has transformed our understanding of gene regulation as well as our ability to manipulate it. Gathered here is a selection of research and comment on RNAi published in the pages of Nature, including groundbreaking research from today's issue. This focus also brings together news and reviews from across the Nature Publishing Group, and a fantastic animation offers the chance to view the RNAi process in action.

See "RNA Interference: Open Access to Nobel Prize Winners Original Paper" for links to the homepages of Andrew Fire and Craig Mello and their original paper "Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans (C. Elegans)".

Featured books: "RNA Interference Technology: From Basic Science to Drug Development" by Andrew Fire et al. (Amazon UK | US)

and "Rnai: A Guide to Gene Silencing" edited by Gregory J. Hannon (Amazon UK | US)

[Science, Medicine]

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RNA Interference: Open Access to Nobel Prize Winners Original Paper

RNA Inteference: The journal Nature is allowing open access to Nobel Prize Winners Andrew Fire's and Craig Mello's original paper:

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans (C. Elegans)


(1) Carnegie Institution of Washington, Department of Embryology, 115 West University Parkway, Baltimore, Maryland 21210, USA
(2) Biology Graduate Program, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
(3) Program in Molecular Medicine, Department of Cell Biology, University of Massachusetts Cancer Center, Two Biotech Suite 213, 373 Plantation Street, Worcester, Massachusetts 01605, USA

Experimental introduction of RNA into cells can be used in certain biological systems to interfere with the function of an endogenous gene 1,2. Such effects have been proposed to result from a simple anti-sense mechanism that depends on hybridization between the injected RNA and endogenous messenger RNA transcripts. RNA interference has been used in the nematode Caenorhabditis elegans to manipulate gene expression 3,4. Here we investigate the requirements for structure and delivery of the interfering RNA. To our surprise, we found that double-stranded RNA was substantially more effective at producing interference than was either strand individually. After injection into adult animals, purified single strands had at most a modest effect, whereas double-stranded mixtures caused potent and specific interference. The effects of this interference were evident in both the injected animals and their progeny. Only a few molecules of injected double-stranded RNA were required per affected cell, arguing against stochiometric interference with endogenous mRNA and suggesting that there could be a catalytic or amplification component in the interference process.


Updated 21 February 2007: The above link is currently not working but has been left in place because it still shows up in the Nature search engine - perhaps it'll come back!. An alternative source (pdf) for the paper can be found here

In addition, here is the original press release (dated 2 October 2006) from the Nobel Foundation announcing 'The Nobel Prize in Physiology or Medicine 2006' award:


This year's Nobel Laureates have discovered a fundamental mechanism for controlling the flow of genetic information. Our genome (Human Genome Project) operates by sending instructions for the manufacture of proteins from DNA in the nucleus of the cell to the protein synthesizing machinery in the cytoplasm. These instructions are conveyed by messenger RNA (mRNA). In 1998, the American scientists Andrew Fire and Craig Mello published their discovery of a mechanism that can degrade mRNA from a specific gene. This mechanism, RNA interference, is activated when RNA molecules occur as double-stranded pairs in the cell. Double-stranded RNA activates biochemical machinery which degrades those mRNA molecules that carry a genetic code identical to that of the double-stranded RNA. When such mRNA molecules disappear, the corresponding gene is silenced and no protein of the encoded type is made.

RNA interference occurs in plants, animals, and humans. It is of great importance for the regulation of gene expression, participates in defense against viral infections, and keeps jumping genes under control. RNA interference is already being widely used in basic science as a method to study the function of genes and it may lead to novel therapies in the future.

The flow of information in the cell: from DNA via mRNA to protein

The genetic code in DNA determines how proteins are built. The instructions contained in the DNA are copied to mRNA and subsequently used to synthesize proteins (Fig 1). This flow of genetic information from DNA via mRNA to protein has been termed the central dogma of molecular biology by the British Nobel Laureate Francis Crick. Proteins are involved in all processes of life, for instance as enzymes digesting our food, receptors receiving signals in the brain, and as antibodies defending us against bacteria.

Our genome consists of approximately 30,000 genes. However, only a fraction of them are used in each cell. Which genes are expressed (i.e. govern the synthesis of new proteins) is controlled by the machinery that copies DNA to mRNA in a process called transcription. It, in turn, can be modulated by various factors. The fundamental principles for the regulation of gene expression were identified more than 40 years ago by the French Nobel Laureates Fran├žois Jacob and Jacques Monod. Today, we know that similar principles operate throughout evolution, from bacteria to humans. They also form the basis for gene technology, in which a DNA sequence is introduced into a cell to produce new protein.

Around 1990, molecular biologists obtained a number of unexpected results that were difficult to explain. The most striking effects were observed by plant biologists who were trying to increase the colour intensity of the petals in petunias by introducing a gene inducing the formation of red pigment in the flowers. But instead of intensifying the colour, this treatment led to a complete loss of colour and the petals turned white! The mechanism causing these effects remained enigmatic until Fire and Mello made the discovery for which they receive this year's Nobel Prize.

The discovery of RNA interference

Andrew Fire and Craig Mello were investigating how gene expression is regulated in the nematode worm Caenorhabditis elegans (Fig. 2). Injecting mRNA molecules encoding a muscle protein led to no changes in the behaviour of the worms. The genetic code in mRNA is described as being the 'sense' sequence, and injecting 'antisense' RNA, which can pair with the mRNA, also had no effect. But when Fire and Mello injected sense and antisense RNA together, they observed that the worms displayed peculiar, twitching movements. Similar movements were seen in worms that completely lacked a functioning gene for the muscle protein. What had happened?

When sense and antisense RNA molecules meet, they bind to each other and form double-stranded RNA. Could it be that such a double-stranded RNA molecule silences the gene carrying the same code as this particular RNA? Fire and Mello tested this hypothesis by injecting double-stranded RNA molecules containing the genetic codes for several other worm proteins. In every experiment, injection of double-stranded RNA carrying a genetic code led to silencing of the gene containing that particular code. The protein encoded by that gene was no longer formed.

After a series of simple but elegant experiments, Fire and Mello deduced that double-stranded RNA can silence genes, that this RNA interference is specific for the gene whose code matches that of the injected RNA molecule, and that RNA interference can spread between cells and even be inherited. It was enough to inject tiny amounts of double-stranded RNA to achieve an effect, and Fire and Mello therefore proposed that RNA interference (now commonly abbreviated to RNAi) is a catalytic process.

Fire and Mello published their findings in the journal Nature on February 19, 1998. Their discovery clarified many confusing and contradictory experimental observations and revealed a natural mechanism for controlling the flow of genetic information. This heralded the start of a new research field.

The RNA interference machinery is unraveled

The components of the RNAi machinery were identified during the following years (Fig 3). Double-stranded RNA binds to a protein complex, Dicer, which cleaves it into fragments. Another protein complex, RISC, binds these fragments. One of the RNA strands is eliminated but the other remains bound to the RISC complex and serves as a probe to detect mRNA molecules. When an mRNA molecule can pair with the RNA fragment on RISC, it is bound to the RISC complex, cleaved and degraded. The gene served by this particular mRNA has been silenced.

RNA interference - a defense against viruses and jumping genes

RNA interference is important in the defense against viruses, particularly in lower organisms. Many viruses have a genetic code that contains double-stranded RNA. When such a virus infects a cell, it injects its RNA molecule, which immediately binds to Dicer (Fig 4A). The RISC complex is activated, viral RNA is degraded, and the cell survives the infection. In addition to this defense, higher organisms such as man have developed an efficient immune defense involving antibodies, killer cells, and interferons.

Jumping genes, also known as transposons, are DNA sequences that can move around in the genome. They are present in all organisms and can cause damage if they end up in the wrong place. Many transposons operate by copying their DNA to RNA, which is then reverse-transcribed back to DNA and inserted at another site in the genome. Part of this RNA molecule is often double-stranded and can be targeted by RNA interference. In this way, RNA interference protects the genome against transposons.

RNA interference regulates gene expression

RNA interference is used to regulate gene expression in the cells of humans as well as worms (Fig 4B). Hundreds of genes in our genome encode small RNA molecules called microRNAs. They contain pieces of the code of other genes. Such a microRNA molecule can form a double-stranded structure and activate the RNA interference machinery to block protein synthesis. The expression of that particular gene is silenced. We now understand that genetic regulation by microRNAs plays an important role in the development of the organism and the control of cellular functions.

New opportunities in biomedical research, gene technology and health care

RNA interference opens up exciting possibilities for use in gene technology. Double-stranded RNA molecules have been designed to activate the silencing of specific genes in humans, animals or plants (Fig 4C). Such silencing RNA molecules are introduced into the cell and activate the RNA interference machinery to break down mRNA with an identical code.

This method has already become an important research tool in biology and biomedicine. In the future, it is hoped that it will be used in many disciplines including clinical medicine and agriculture. Several recent publications show successful gene silencing in human cells and experimental animals. For instance, a gene causing high blood cholesterol levels was recently shown to be silenced by treating animals with silencing RNA. Plans are underway to develop silencing RNA as a treatment for virus infections, cardiovascular diseases, cancer, endocrine disorders and several other conditions.

Fire A., Xu S.Q., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998; 391:806-811.


Featured books: "RNA Interference Technology: From Basic Science to Drug Development" by Andrew Fire et al. (Amazon UK | US)

and "Rnai: A Guide to Gene Silencing" edited by Gregory J. Hannon (Amazon UK | US)

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