Saturday, December 16, 2006
A new report (see below) from the U.S. House of Representatives has condemned officials at the Smithsonian Institution for imposing a religious test on scientists who work there. And it suggests their attacks on a scientist who just edited an article on intelligent design are just the tip of the iceberg of an industry-wide fear of anything that suggests man might not have come from a puddle of sludge.
The report, which cited a 'strong religious and political component' in the dispute (info), was prompted by a complaint from Dr. Richard Sternberg (homepage), who holds biology doctorates from Binghamton and Florida International universities and has served as a research associate at the Smithsonian's National Museum of Natural History.
It was prepared for U.S. Representative Mark Souder, R-Ind., chairman of the subcommittee of criminal justice, drug policy and human resources, and easily confirmed Sternberg's harassment and discrimination allegations that his managers criticized him, created a hostile work environment for him, and now have demoted him because of the article*, which he didn't even write.
Continued at "Congress slams Smithsonian's anti-religious attacks"
*PROCEEDINGS OF THE BIOLOGICAL SOCIETY OF WASHINGTON 117(2):213-239. 2004
The origin of biological information and the higher taxonomic categories by Stephen C. Meyer: Full Text
Executive Summary of the Report:
In January 2005, an opinion piece published in the Wall Street Journal first raised public awareness about disturbing allegations that officials at the Smithsonian Institution's National Museum of Natural History (NMNH) had retaliated against museum Research Associate (RA) Richard Sternberg because he allowed publication of an article favoring the theory of intelligent design in a biology journal.1 A well-published evolutionary biologist with two doctorates in biology, Dr. Sternberg claimed that after publication of the article, his colleagues and supervisors at the NMNH subjected him to harassment and discrimination in an effort to force him out as a Research Associate.
In November of 2004, Dr. Sternberg filed a complaint with the U.S. Office of Special Counsel (OSC), the agency charged with "protecting federal employees and applicants from prohibited personnel practices, especially reprisal for whistleblowing." The OSC eventually found evidence to corroborate Dr. Sternberg's complaint, concluding that "[i]t is... clear that a hostile work environment was created with the ultimate goal of forcing" Dr. Sternberg out of the Smithsonian. Despite this finding, the OSC was unable to pursue its investigation due to a question of jurisdiction. In August of 2005, subcommittee staff initiated their own investigation into the possible mistreatment of Dr. Sternberg by the Smithsonian. During their investigation, staff met with Dr. Sternberg and senior Smithsonian officials, and reviewed internal emails provided by the Smithsonian in response to requests from the subcommittee.
The staff investigation has uncovered compelling evidence that Dr. Sternberg's civil and constitutional rights were violated by Smithsonian officials. Moreover, the agency's top officials - Secretary Lawrence Small and Deputy Secretary Sheila Burke - have shown themselves completely unwilling to rectify the wrongs that were done or even to genuinely investigate the wrongdoing. Most recently, Burke and Small have allowed NMNH officials to demote Dr. Sternberg to the position of Research Collaborator, despite past assurances from Burke that Dr. Sternberg was a "Research Associate in good standing" and would be given "full and fair consideration" for his request to renew his Research Associateship. 2 The failure of Small and Burke to take any action against such discrimination raises serious questions about the Smithsonian's willingness to protect the free speech and civil rights of scientists who may hold dissenting views on topics such as biological evolution.
Major findings of this staff investigation include:
* Officials at the Smithsonian's National Museum of Natural History created a hostile work environment intended to force Dr. Sternberg to resign his position as a Research Associate in violation of his free speech and civil rights. There is substantial, credible evidence of efforts to abuse and harass Dr. Sternberg, including punitively targeting him for investigation in order to supply a pretext for dismissing him, and applying to him regulations and restrictions not imposed on other researchers. Given the factual record, the Smithsonian's pro-forma denials of discrimination are unbelievable. Indeed, NMNH officials explicitly acknowledged in emails their intent to pressure Sternberg to resign because of his role in the publication of the Meyer paper and his views on evolution. On September 13, 2004, Dr. Jonathan Coddington, chair of the zoology department, wrote to crustacean curator Dr. Rafael Lemaitre that he could not find a legal basis for terminating Sternberg, but added: "I suppose we could call him on the phone and verbally ask him to do the right thing and resign?" 3 A few hours later, Dr. Lemaitre responded that "a face to face meeting or at least a 'you are welcome to leave or resign' call with this individual, is in order." 4 Finally, in an email on October 6, 2004, Dr. Coddington (in his capacity as Dr. Sternberg's "supervisor") stated that he was planning to meet with Dr. Sternberg to convey the message "that if he had any class he would either entirely desist or resign his appointment." 5 Clearly, the NMNH management was trying to make Dr. Sternberg's life at the Museum as difficult as possible and encourage him to leave, since they knew they had no legal grounds to dismiss him.
* In emails exchanged during August and September 2004, NMNH officials revealed their intent to use their government jobs to discriminate against scientists based on their outside activities regarding evolution. For example, Dr. Hans Sues, Associate Director for Research and Collections, suggested in emails on August 30, 2004, and again on September 9, 2004, that Dr. Sternberg would never have been appointed as an RA if Smithsonian officials had known about his non-governmental activities regarding evolution. Sues even blamed the scientist who nominated Sternberg as a Research Associate for not adequately investigating his background: "Sternberg is a well-established figure in anti-evolution circles, and a simple Google search would have exposed these connections." 6 The clear implication was that had a background check been conducted on Sternberg's non-governmental activities, he would have been barred from being a Research Associate. Given the attitudes expressed in these emails, scientists who are known to be skeptical of Darwinian theory, whatever their qualifications or research record, cannot expect to receive equal treatment or consideration by NMNH officials. As a taxpayer-funded institution, such blatant discrimination against otherwise qualified individuals based on their outside views and activities raises serious free speech and civil rights concerns. With regard to Dr. Sternberg, this discriminatory attitude makes it all-but-impossible for him to be fairly considered for reappointment when his current term as Research Associate ends in 2007. Indeed, NMNH officials expressed in their emails a clear expectation that Dr. Sternberg would not be reappointed as a Research Associate after expiration of his current appointment. True to their statements at the time, NMNH officials have recently notified Dr. Sternberg that they will not renew his position as a Research Associate. Rather, they will only permit him to continue his research at the Smithsonian as a Research Collaborator - a demotion from his previous position. 7
* The hostility toward Dr. Sternberg at the NMNH was reinforced by anti-religious and political motivations. Dr. Sternberg's OSC complaint describes efforts to discover or disparage his supposed religious and political beliefs, and the OSC investigation concluded that there was "a strong religious and political component to the actions taken after the publication of the Meyer article." The emails reviewed by subcommittee staff corroborate this finding. In a memo prepared on February 8, 2005, NMNH scientist Marilyn Schotte admitted that after publication of the Meyer paper, Dr. Coddington wanted to know "if Dr. Sternberg was religious." Dr. Schotte further admitted telling Coddington that Sternberg "was a Republican." Schotte even conceded that Coddington may have asked her whether Sternberg "was a fundamentalist" and whether "he was a conservative." Dr. Schotte insisted that by asking such questions "Dr. C. was not being judgmental, only curious." 8 But given the demonstrably hostile atmosphere toward Sternberg at the NMNH during the period in question, there is nothing innocuous about an official with supervisory authority inquiring into Sternberg's religious and political beliefs. The email traffic also substantiates Sternberg's concern about a viscerally anti-religious culture existing at the Museum. For example, on February 22, 2005, NMNH Research Associate Sue Richardson sent an email of solidarity to Dr. Coddington regarding the Sternberg situation. She complained about the time she spent living in the "Bible Belt," mockingly reporting that "the most fun we had by far was when my son refused to say the Pledge of Allegiance because of the 'under dog' part..." 9 Would similar expressions of disparagement have been tolerated by Smithsonian officials if directed at a racial minority?
* NMNH officials conspired with a special interest group on government time and using government emails to publicly smear Dr. Sternberg; the group was also enlisted to monitor Sternberg's outside activities in order to find a way to dismiss him. In cooperation with the pro-evolution National Center for Science Education (NCSE), Museum officials attempted to publicly smear and discredit Dr. Sternberg with false and defamatory information. While NMNH officials have the right to criticize scientific views with which they disagree, using government time and resources to publicly smear with false information someone whom they supervise is an abuse of their authority as government employees. In addition, Dr. Sues promised the director of the NCSE on August 26, 2004, that "[f]rom now on, I will keep an eye on Dr. (von) Sternberg, and I'd greatly appreciate it if you or other NCSE specialists could let me [know] about further activities by this gentleman in areas poutside [sic] crustacean systematics." 10 The clear purpose of having the NCSE monitor Sternberg's outside activities was to find a way to dismiss Sternberg. Dr. Sues hoped that the NCSE could unearth evidence that Sternberg had misrepresented himself as a Smithsonian employee, which would have been grounds for dismissal as a Research Associate.
* Secretary Small and Deputy Secretary Burke have exhibited a head-in-the-sand attitude toward wrongdoing at their agency; they have engaged in stonewalling and spin rather than dealing forthrightly with the discrimination that has occurred. In Deputy Secretary Burke's most recent response dated May 3, 2006, she acknowledged that Dr. Sternberg’s viewpoint on evolution sparked "strong disagreement" among other scientists at the NMNH, but insisted that "[w]hile the tone of the disagreement between scholars may seem harsh, disagreement does not equal discrimination." 11 However, the issue is not the disagreement of Smithsonian scientists with Dr. Sternberg's views on evolution, but rather their effort to use their official powers to punish Dr. Sternberg by seeking to remove him as a Research Associate, and their effort to publicly smear him with false information on government time using government emails. More broadly, NMNH officials have made clear their intent to prevent any scientist publicly skeptical of Darwinian theory from ever being appointed as a Research Associate, no matter how sterling his or her professional credentials or research. This is discrimination, plain and simple. The abject failure of the Secretary and Deputy Secretary to protect the basic rights of Dr. Sternberg to a civil work environment is indefensible.
Because of the Smithsonian's continued inaction in the Sternberg case, Congress should consider statutory language that would protect the free speech rights regarding evolution of scientists in the Smithsonian and other federally-funded institutions. Since the treatment of Dr. Sternberg came to light in early 2005, evidence has accumulated of widespread discrimination against other qualified scientists who dissent from Darwinian theory, making further violations by federal agencies likely. While the majority of scientists embrace Darwinian theory, it is important that neither federal funds nor federal power be used to punish or retaliate against otherwise qualified scientists merely because they dissent from the majority view.
A heat-loving archaeon capable of fixing nitrogen at a surprisingly hot 92 degrees Celsius, or 198 Fahrenheit, may represent Earth's earliest lineages of organisms capable of nitrogen fixation, perhaps even preceding the kinds of bacteria today's plants and animals rely on to fix nitrogen.
The genetic analysis reported in the December 15 issue of the journal Science supports the notion that the gene needed to produce nitrogenase - an enzyme capable of converting nitrogen gas, that's unusable by life, to a form like ammonia that is useable - arose before the three main branches of life - bacteria, archaea* and eukaryotes - diverged some 3.5 billion years ago, according to oceanographer Mausmi Mehta (info), who recently received her doctorate from the UW, and John Baross, UW professor of oceanography. This is opposed to the theory that the nitrogenase system arose within archaea and was later transferred laterally to bacteria.
'There's been lots of evidence that point to high-temperature archaea as the first life on Earth but the question has been, 'So why can't we find archaea that fix nitrogen at high temperatures?' says Baross, who's been on a 20-year quest to find just such a microbe. Archaea are single-celled organisms that live under extreme environmental conditions, such as the high temperatures and crushing pressures below the seafloor. If heat-loving archaea were the first life on the planet, they would have needed a usable source of nitrogen, Baross says.
Known as FS406-22 because of the fluid and culture samples it came from, the archaeon discovered by the UW researchers is the first from a deep-sea hydrothermal vent that can fix nitrogen, says Mehta, first author on the Science paper.
It was collected at Axial Volcano** on the Juan de Fuca Ridge off the coast of Washington and Oregon. Fixing nitrogen at 92 C smashes the previous record by 28 C, a record held by Methanothermococcus thermolithotrophicus, an archaeon that was isolated from geothermally heated sand near an Italian beach and fixes nitrogen at temperatures up to 64 C.
Continued at "Microbe fixes nitrogen at a blistering 92 C" [Evolution, Extremophiles, Ocean Deeps]
Based on the Science paper:
"Nitrogen Fixation at 92 degrees C by a Hydrothermal Vent Archaeon"
A methanogenic archaeon isolated from deep-sea hydrothermal vent fluid was found to reduce N2 to NH3 at up to 92 C, which is 28 C higher than the current upper temperature limit of biological nitrogen fixation. The 16S ribosomal RNA gene of the hyperthermophilic nitrogen fixer, designated FS406-22, was 99% similar to that of non-nitrogen fixing Methanocaldococcus jannaschii DSM 2661. At its optimal growth temperature of 90 C, FS406-22 incorporated 15N2 and expressed nifH messenger RNA. This increase in the temperature limit of nitrogen fixation could reveal a broader range of conditions for life in the subseafloor biosphere and other nitrogen-limited ecosystems than previously estimated.
*Info on Archaea:
The Domain Archaea wasn't recognized as a major domain of life until quite recently. Until the 20th century, most biologists considered all living things to be classifiable as either a plant or an animal. But in the 1950s and 1960s, most biologists came to the realization that this system failed to accomodate the fungi, protists, and bacteria. By the 1970s, a system of Five Kingdoms had come to be accepted as the model by which all living things could be classified. At a more fundamental level, a distinction was made between the prokaryotic bacteria and the four eukaryotic kingdoms (plants, animals, fungi, and protists). The distinction recognizes the common traits that eukaryotic organisms share, such as nuclei, cytoskeletons, and internal membranes. (More)
**Info on the Axial Volcano:
Axial Volcano rises 700 meters above the mean level of the ridge crest and is the most magmatically robust and seismically active site on the Juan de Fuca Ridge between the Blanco Fracture Zone and the Cobb offset. It represents the product of intense volcanic activity from the Cobb-Eikelberg hotspot juxtaposed on the extensional field of the spreading center. Axial Volcano was first studied in the late 1970s and then mapped in greater detail by NOAA/VENTS with SeaBeam in the early 1980s. Following the initial discovery of venting in the northern portion of the caldera in 1983, a concentrated mapping and sampling effort was made in the mid-late 1980s.The summit of Axial Volcano is marked by an unusual rectangular shaped caldera (3 x 8 km) that lies between the two rift zones. (More)
Friday, December 15, 2006
An open access/free PLoS Biology article by the science writer Tabitha M. Powledge**.
Citation: Powledge TM (2006) What Is the Hobbit? PLoS Biol 4(12): e440 DOI: 10.1371/journal.pbio.0040440
Who - or what - is Homo floresiensis? (Wiki) The tiny hominid bones, which a joint Australian-Indonesian team unearthed in 2003 on the Indonesian island of Flores, have quickly become as celebrated (and derided) as any find in the tempestuous history of human paleontology. The mystery that shrouds these ancient skeletons, nicknamed hobbits after the diminutive characters in J. R. R. Tolkien's novels, seems to deepen with every study published. Two main camps have emerged, each certain they can settle the question. But many other paleoanthropologists confess they still have no idea.
H. floresiensis Discovered
The discovery team declared their find a new human species, H. floresiensis, based primarily on a single near-complete skeleton of one very small individual with a very small brain, known as LB1. Compared to H. sapiens, LB1, whose age was estimated from tooth wear at about 30 years, was only one meter tall - about the size of a 4-year-old H. sapiens child - with a brain the size of a newborn's. Although there are also fragments of eight other small individuals, they provide no information about brain size, nor is much skeleton preserved. Nonetheless, they possess a combination of features never before seen in human fossils, which makes it credible that a previously unknown population of people smaller than today's pygmies lived on Flores between 90,000 and 12,000 years ago.
Stone tools found at the site raise the possibility that hobbits had culture, even though LB1's brain size would make a chimpanzee sneer. H. floresiensis, the discovery team claimed, could be the first human example of island dwarfing. This phenomenon, thought to be evolution's response to limited resources, is known for other mammals, including dwarf elephants from Flores itself. But this is not the only possible conclusion. A long-awaited paper*, which appeared online in Proceedings of the National Academy of Sciences of the United States of America (PNAS) on August 23, 2006, offers a radically different interpretation of these skeletal remains.
Continued at "What Is the Hobbit?"
*An open access/free paper. Full text (pdf) available via the Abstract link:
"Pygmoid Australomelanesian Homo sapiens skeletal remains from Liang Bua, Flores: Population affinities and pathological abnormalities"
Liang Bua 1 (LB1) exhibits marked craniofacial and postcranial asymmetries and other indicators of abnormal growth and development. Anomalies aside, 140 cranial features place LB1 within modern human ranges of variation, resembling Australomelanesian populations. Mandibular and dental features of LB1 and LB6/1 either show no substantial deviation from modern Homo sapiens or share features (receding chins and rotated premolars) with Rampasasa pygmies now living near Liang Bua Cave. We propose that LB1 is drawn from an earlier pygmy H. sapiens population but individually shows signs of a developmental abnormality, including microcephaly. Additional mandibular and postcranial remains from the site share small body size but not microcephaly.
The discovery of an unusual human skeleton has broad implications
When a team of Indonesian and Australian palaeontologists discovered a nearly complete but very strange 18,000-year-old human skeleton in an Indonesian cave in 2003, the find provoked questions about modern human origins. Do these ancient bones belong to a new human species? Are they, as many have claimed, the most important find in hominid palaeontology for decades? Or is this creature - indelibly christened 'the Hobbit' because it is so tiny - simply one of an isolated people who suffered from a deforming malady? The huge stakes in this competitive, caustic debate can be summed up succinctly: money and fame. But Hobbit investigations may eventually have less impact on the study of human evolution than they do on the standing of palaeoanthropology, and on the continuing crusade against the Darwinian account of how life on Earth evolved.
A team of scientists found a new class of organics in comet dust captured from comet Wild 2 in 2004 by NASA's Stardust spacecraft.
The discovery is described in a technical paper, 'Organics Captured from Comet Wild 2 by the Stardust Spacecraft,'* in the December 15 issue of Science Express, the online edition of the journal Science.
In January 2004, the Stardust spacecraft flew through comet dust and captured specks of it in a very light, low-density substance called aerogel. Stardust's return capsule parachuted to the Utah Test and Training Range on Jan. 15, 2006, after a seven-year mission. The science canister containing the comet particles and interstellar dust particles arrived at Johnson Space Center on Jan. 17. From there, the cometary samples have been processed and distributed to about 150 scientists worldwide who are using a variety of techniques to determine the properties of the cometary grains.
'A portion of the organic material in the samples is unlike anything seen before in extraterrestrial materials,' said Scott Sandford, the study's lead author and a scientist from NASA's Ames Research Center in California's Silicon Valley. 'Capturing the particles in aerogel was a little bit like collecting BBs by shooting them into Styrofoam.'
The comet organics collected by the Stardust spacecraft are more 'primitive' than those seen in meteorites and may have formed by processes in nebulae, either in space clouds between the stars, or in the disk-shaped cloud of gas and dust from which our solar system formed, the study's authors found. [Astrobiology]
Continued at "NASA Study Finds New Kind of Organics in Stardust Mission"
*A Science Special Online Collection: Stardust includes:
1) Organics Captured from Comet 81P/Wild 2 by the Stardust Spacecraft
Organics found in comet 81P/Wild 2 samples show a heterogeneous and unequilibrated distribution in abundance and composition. Some organics are similar, but not identical, to those in interplanetary dust particles and carbonaceous meteorites. A class of aromatic-poor organic material is also present. The organics are rich in oxygen and nitrogen compared with meteoritic organics. Aromatic compounds are present, but the samples tend to be relatively poorer in aromatics than are meteorites and interplanetary dust particles. The presence of deuterium and nitrogen-15 excesses suggest that some organics have an interstellar/protostellar heritage. Although the variable extent of modification of these materials by impact capture is not yet fully constrained, a diverse suite of organic compounds is present and identifiable within the returned samples.
2) Isotopic Compositions of Cometary Matter Returned by Stardust
Hydrogen, carbon, nitrogen, and oxygen isotopic compositions are heterogeneous among comet 81P/Wild 2 particle fragments; however, extreme isotopic anomalies are rare, indicating that the comet is not a pristine aggregate of presolar materials. Nonterrestrial nitrogen and neon isotope ratios suggest that indigenous organic matter and highly volatile materials were successfully collected. Except for a single 17O-enriched circumstellar stardust grain, silicate and oxide minerals have oxygen isotopic compositions consistent with solar system origin. One refractory grain is 16O-enriched, like refractory inclusions in meteorites, suggesting that Wild 2 contains material formed at high temperature in the inner solar system and transported to the Kuiper belt before comet accretion.
3) There is a video (or rather, 5 videos) presentation here
Also see "Astrobiology and Stardust"
Carl Sagan once said "We are all star stuff." But how? What does that really mean? One of the fundamental questions of astrobiology, how does life originate and evolve?, provides a structure in which to examine the relationship between life and the cosmos. Everywhere life has been found on Earth, which is essentially every place in which it has been sought, life's intimate connection with water has also been found. Within the framework of contemplating life's cosmic origins, one must also ask about the history of water on Earth. NASA's Stardust mission has provided the opportunity for astrobiologists to gain deeper insight into this history.
Many scientists from the NASA Astrobiology Institute** (NAI) have been involved in the Stardust mission, spearheaded by none other than Stardust PI Don Brownlee at the University of Washington. The list also includes Scott Sanford of the NAI NASA Ames Team, lead author of one of the papers in this week's Science, and George Cody of the NAI Carnegie Institution of Washington Team.
"Comets are important to the understanding of the origin of life," said Brownlee, "we have always considered Stardust an astrobiology mission." Results from analysis of the Stardust samples have brought new insight to bear on the relationship between the inner and outer solar system. "The samples we've obtained from Stardust have helped us understand both the origin of water and other volatiles, as well as their delivery mechanisms to the early Earth," said Brownlee.
-------**From "About the NAI":
"Astrobiology is devoted to the scientific study of life in the universe - its origin, evolution, distribution, and future. This multidisciplinary field brings together the physical and biological sciences to address some of the most fundamental questions of the natural world: How do living systems emerge? How do habitable worlds form and how do they evolve? Does life exist on worlds other than Earth? How could terrestrial life potentially survive and adapt beyond our home planet?
Scientists now realize that the origin and evolution of life itself cannot be fully understood unless viewed from a larger perspective than just our own Earth. Biologists are working with astronomers to describe the formation of life's chemical precursors, to discover new planets, and to determine their habitability; with chemists to understand the transition from molecular interaction to life itself; with geologists to search for evidence of water and key minerals on other planets; with paleontologists and evolutionary molecular biologists to look for and comprehend the earliest forms of life, as well as with climatologists, planetary scientists, and researchers from nearly every field of science.
In 1998 NASA established the NASA Astrobiology Institute (NAI) as one element of its research program in astrobiology. The NAI is currently composed of 12 Lead Teams, which together represent over 700 investigators across the United States, and it has international partnerships with astrobiology research organizations around the world.
The major research themes of astrobiology are described in detail in the NASA Astrobiology Roadmap."
Thursday, December 14, 2006
Adapted from an open access/free PLoS Biology paper:
Balancing Robustness and Evolvability*
Richard E. Lenski, Jeffrey E. Barrick, Charles Ofria
Citation: Lenski RE, Barrick JE, Ofria C (2006) Balancing Robustness and Evolvability. PLoS Biol 4(12): e428 doi:10.1371/journal.pbio.0040428
One of the most important features of biology is the ability of organisms to persist in the face of changing conditions. Consider the remarkable fact that every organism alive today is the product of billions of generations in which its progenitors, without fail, managed to produce progeny that survived to reproduce. To achieve this consistency, organisms must have a balance between robustness and evolvability, that is, between resisting and allowing change in their own internal states [1, 2**, 3]. Moreover, they must achieve this balance on multiple time scales, including physiological responses to changes over an individual life and evolutionary responses, in which a population of genomes continually updates its encoded information about past environments and how future generations should respond given that record.
Examples of robust biological systems are found at many scales, from biochemical to ecological. At each scale, robustness may reflect the properties of individual elements or, alternatively, the dynamic feedbacks between interacting elements. The expression of some metabolic function, for example, may be robust in the face of temperature change, because an enzyme maintains its shape and specificity across a range of temperatures or because an interconnected network of reactions sustains the supply of product, even when some enzyme fails. A genome may be robust because it encodes proofreading and repair systems that reduce replication errors or because it is organized such that many mutations have little effect on its phenotype. An ecosystem might be robust if it resists the extinction of some keystone species or, if extinction does occur, because surviving species can compensate over physiological, demographic, or evolutionary time scales.
One important question is whether there exists a single unifying mathematical framework that can encompass such diverse examples of biological robustness. Might new insights come from such a conceptual unification, or will future understanding require detailed analyses of specific cases? Across the different scales, recurring mechanisms for achieving robustness - including redundancy of component parts and negative feedbacks - might serve as organizing principles. Yet, similarities in mechanism could mask important differences in the evolutionary origins of those mechanisms. At the level of genes in genomes or of cells in multicellular organisms, it is reasonable to suggest that redundancy evolved by natural selection to maintain some functional capacity in the face of perturbation . But whereas species redundancy could also be critical for robustness of ecosystem functions, differences in redundancy might be an emergent property rather than an ecosystem-level adaptation, because selection generally acts at lower levels (but see  for another view).
And if robustness has evolved to maintain performance, what prevents systems from becoming ever more robust? We will focus on genomic robustness to mutations, because it provides a concrete example, although many ideas are speculative and much work is needed to formalize and test them. Two mechanisms that could make a genome more robust are genetic redundancy, so that many otherwise deleterious mutations are masked, and proofreading during replication, so that fewer mutations occur. Redundancy imposes a cost of replicating the additional gene copies , whereas proofreading entails costs of encoding and expressing that function .
Mutational robustness can also arise in more subtle ways. Populations evolving at high mutation rates may settle in regions of genotypic space where mutations are less deleterious, on average, than those regions that attract populations that experience low mutation rates. The idea is that evolution at low mutation rates favors populations that achieve high fitness peaks, even if they are surrounded by steep cliffs, because mutations that push progeny off those cliffs are rare. By contrast, at high mutation rates, most offspring carry mutations, and selection favors populations that find lower fitness peaks surrounded by less precipitous mutational chasms. Experiments with digital organisms (self-replicating computer programs) provide direct support for "survival of the flattest" at high mutation rates . RNA viruses also have very high mutation rates, and a recent experiment implicated the importance of mutational robustness for them, in this case, by showing the loss of robustness in viruses that evolved at high multiplicities of infection, where co-infecting particles guaranteed redundancy and allowed their native robustness to decay .
But generalizing to other organisms presents some difficulties. The strength of selection for robustness should be weaker in larger genomes if the advantage to a mutation that increases robustness locally is correspondingly smaller. According to one alternate hypothesis, mutational robustness is not so much a directly evolved property as it is a correlated benefit of selection for robustness in the face of variable environments . The essential ideas here are that environmental change is a pervasive feature of nature, and those physiological mechanisms that allow organisms to adjust to changing environments, such as by regulating gene expression, will also compensate for the effects of many mutations . Robustness might also evolve to minimize internal noise in biochemical systems. The genetic code itself, once viewed as a frozen accident from the early history of life, has been shown to be remarkably well designed for minimizing the production of proteins that, owing to translational errors, have the amino acids most likely to disrupt protein function . Individual proteins, too, have been strongly selected for robustness to translational errors .
Two recent studies with evolving computational systems have shown, unexpectedly, that sexual reproduction promotes the evolution of mutational robustness [13,14]. The evolutionary value of sex is a fascinating old problem. According to one hypothesis, the advantage of sex depends on negative interactions between deleterious mutations, such that two mutations combined tend to be worse, on average, than expected from their individual effects . In that case, sex helps to purge them and provides a kind of robustness to multiple mutations. But these new studies found that sexual populations became more robust, on average, to the effects of single mutations, even though they evolved at the same mutation rate as asexual controls. Sex bombards genomes with mutant alleles that arose in other genetic backgrounds, which evidently promotes a kind of "survival of the flattest" similar to that seen at high mutation rates.
Another important issue revolves around the tension between robustness and evolvability. Are genomes that are more robust to mutations less evolvable in the face of changing environments? In other words, does canalizing the phenotype to minimize perturbations - including biochemical and environmental as well as mutational - lead to an evolutionary conservatism that inhibits the discovery of new adaptive solutions? Some mechanisms of robustness, such as proofreading and repair, must inhibit evolvability because they reduce the production of new beneficial mutations. But are robustness and evolvability inversely correlated more generally? In the case of redundancy, the presence of multiple gene copies might mask the beneficial effects of some new mutations, thus suppressing evolvability. But redundancy can also promote adaptation by allowing duplicated genes to evolve distinct functions [16,17].
Evolving populations can also become robust by finding regions of genotypic space that are flat because they contain a high proportion of neutral mutations . As shown schematically for RNA secondary structures in Figure 1, the resulting neutral network might provide evolutionary paths to new adaptations by random drift, in effect allowing populations to search wider regions of genotypic space for rare beneficial mutations . If so, robustness and evolvability might again be positively, rather than negatively, correlated. However, deleterious mutations can also serve as stepping stones to adaptations . Although deleterious mutations tend to be removed by selection and have shorter half-lives than neutral mutations, they are not instantly eliminated. Moreover, deleterious mutations may lead to genetic neighborhoods that are more promising, from the perspective of adaptation, than neutral mutations. In other words, neutral mutations are neutral precisely because they are isolated from important phenotypes, whereas deleterious ones must be connected to phenotypes that matter for fitness. It is unclear, therefore, whether neutral or deleterious mutations are more important for evolvability, and whether robustness associated with increased neutrality will promote or impede evolvability.
Figure 1. A Neutral Network of Four RNA Secondary Structures, with One Member Connected to Two Sequences outside the Network, One with Lower, and One with Higher Fitness
Colored positions show mutations, whereas the scale to the left of each sequence shows its relative fitness. (Figure credit: Jeffrey E. Barrick, Michigan State University, East Lansing, Michigan, United States)
Theoretical population genetics has historically emphasized models with one or two loci, whereas quantitative genetics has relied on a sort of statistical mechanics that ignores underlying detail. Richer mathematical representations of genotypic spaces and fitness landscapes may be required to understand the balance between robustness and evolvability. Meanwhile, empiricists must push ahead to obtain data about evolvability and robustness. Experimental evolution, in which populations are monitored while they evolve under defined conditions, offers the potential to observe changes in these properties as a function of environmental and genetic manipulations . For example, one could ask how robustness and evolvability change depending on whether evolution occurs in constant or variable environments . Or one might instead manipulate an organism's regulatory networks to investigate how that affects these properties. As new insights are achieved into the tension between genomic robustness and evolvability, perhaps the findings can inform investigations into robustness at other levels, from cells to ecosystems, as biologists seek to understand the constancy of change.
References available via citation
*Info on Evolvability:
Evolvability is a concept that relates to the ability of a particular genotype to evolve new adaptive changes. For instance, the class of mutator genotypes is sometimes selectively favoured relative to more conservative genotypes because its members can produce new mutations more quickly, and hence evolve faster. However, as organisms continue to adapt to stable environments, it is believed that mutator genotypes are selected against as they produce an increasing fraction of maladaptive progeny. Hence, evolvability is a critical topic in the evolution of pathogens.
**Evolvability is a selectable trait by David J. Earl, and Michael W. Deem
Published online before print August 2, 2004, 10.1073/pnas.0404656101
PNAS | August 10, 2004 | vol. 101 | no. 32 | 11531-11536
OPEN ACCESS ARTICLE
Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, because of the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object of Darwinian selection, emphasizing the collective nature of the process. We quantify our theory with computer simulations of protein evolution. These simulations demonstrate that rapid or dramatic environmental change leads to selection for greater evolvability. The selective pressure for large-scale genetic moves such as DNA exchange becomes increasingly strong as the environmental conditions become more uncertain. Our results demonstrate that evolvability is a selectable trait and allow for the explanation of a large body of experimental results.
Pay a visit to the Biologic Institute* and you are liable to get a chilly reception. 'We only see people with appointments,' states the man who finally responds to my persistent knocks. Then he slams the door on me.
I am standing on the ground floor of an office building in Redmond, Washington, the Seattle suburb best known as home town to Microsoft. What I'm trying to find out is whether the 1-year-old institute is the new face of another industry that has sprung up in the area - the one that has set out to try to prove evolution is wrong.
This is my second attempt to engage in person with scientists at Biologic. At the institute's other facility in nearby Fremont, researchers work at benches lined with fume hoods, incubators and microscopes - a typical scene in this up-and-coming biotech hub. Most of them there proved just as reluctant to speak with a New Scientist reporter.
The reticence cloaks an unorthodox agenda. 'We are the first ones doing what we might call lab science in intelligent design,' says George Weber, the only one of Biologic's four directors who would speak openly with me. 'The objective is to challenge the scientific community on naturalism.' Weber is not a scientist but a retired professor of business and administration at the Presbyterian Whitworth College in Spokane, Washington. He heads the Spokane chapter of Reasonstobelieve.org, a Christian organisation that seeks to challenge Darwinism.
...While researching protein structure at various institutes in the UK, Douglas Axe, now at the Biologic Institute in Redmond, Washington, published two peer-reviewed papers** that are cited by anti-evolutionists as evidence that intelligent design is backed by serious science.
Continued at "Intelligent Design: The God Lab"
*See the New York Times article "In Explaining Life's Complexity, Darwinists and Doubters Clash" (Page 2):
..."If we've defined science such that it cannot get to the true answer, we've got a pretty lame definition of science," said Douglas D. Axe, a molecular biologist and the director of research at the Biologic Institute, a new research center in Seattle that looks at the organization of biological systems, including intelligent design issues. Dr. Axe said he had received "significant" financing from the Discovery Institute, but he declined to give any other details about the institute or its financing...
**1) "Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors" Journal of Molecular Biology, vol 301, p 585.
Mutagenesis studies and alignments of homologous sequences have demonstrated that protein function typically is compatible with a variety of amino-acid residues at most exterior non-active-site positions. These observations have led to the current view that functional constraints on sequence are minimal at these positions. Here, it is shown that this inference assumes that the set of acceptable residues at each position is independent of the overall sequence context. Two approaches are used to test this assumption. First, highly conservative replacements of exterior residues, none of which would cause significant functional disruption alone, are combined until roughly one in five have been changed. This is found to cause complete loss of function in vivo for two unrelated monomeric enzymes: barnase (a bacterial RNase) and TEM-1 beta-lactamase. Second, a set of hybrid sequences is constructed from the 50 %-identical TEM-1 and Proteus mirabilis beta-lactamases. These hybrids match the TEM-1 sequence except for a region at the C-terminal end, where they are random composites of the two parents. All of these hybrids are biologically inactive. In both experiments, complete loss of activity demonstrates the importance of sequence context in determining whether substitutions are functionally acceptable. Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular. Homologues sharing less than about two-thirds sequence identity should probably be viewed as distinct designs with their own sets of optimising features.
2) "Estimating the prevalence of protein sequences adopting functional enzyme folds." Journal of Molecular Biology 2004 Aug 27;341(5):1295-315.
Proteins employ a wide variety of folds to perform their biological functions. How are these folds first acquired? An important step toward answering this is to obtain an estimate of the overall prevalence of sequences adopting functional folds. Since tertiary structure is needed for a typical enzyme active site to form, one way to obtain this estimate is to measure the prevalence of sequences supporting a working active site. Although the immense number of sequence combinations makes wholly random sampling unfeasible, two key simplifications may provide a solution. First, given the importance of hydrophobic interactions to protein folding, it seems likely that the sample space can be restricted to sequences carrying the hydropathic signature of a known fold. Second, because folds are stabilized by the cooperative action of many local interactions distributed throughout the structure, the overall problem of fold stabilization may be viewed reasonably as a collection of coupled local problems. This enables the difficulty of the whole problem to be assessed by assessing the difficulty of several smaller problems. Using these simplifications, the difficulty of specifying a working beta-lactamase domain is assessed here. An alignment of homologous domain sequences is used to deduce the pattern of hydropathic constraints along chains that form the domain fold. Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10(64) signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences.
Wednesday, December 13, 2006
From BBC News (UK): Mammals took to the skies at least 70 million years earlier than previously thought, scientists say.
A fossil uncovered in China suggests mammals were trying out flight at about the same time - or even earlier - than birds, the team reports in Nature.
The researchers said the squirrel-sized animal, which lived at least 125 million years ago, used a fur-covered skin membrane to glide through the air.
The creature was so unusual, they said, it belonged to a new order of mammals.
The US-Chinese team said Volaticotherium antiquus, which means 'ancient gliding beast', belonged to a now extinct ancestral line and was not related to modern day flying mammals, such as bats or flying marsupials.
Continued at "Earliest flying mammal discovered"
Based on the jounal Nature paper:
"A Mesozoic gliding mammal from northeastern China"
by Jin Meng*, Yaoming Hu, Yuanqing Wang, Xiaolin Wang and Chuankui Li
Gliding flight has independently evolved many times in vertebrates. Direct evidence of gliding is rare in fossil records and is unknown in mammals from the Mesozoic era**. Here we report a new Mesozoic mammal from Inner Mongolia, China, that represents a previously unknown group characterized by a highly specialized insectivorous dentition and a sizable patagium (flying membrane) for gliding flight. The patagium is covered with dense hair and supported by an elongated tail and limbs; the latter also bear many features adapted for arboreal life. This discovery extends the earliest record of gliding flight for mammals to at least 70 million years earlier in geological history, and demonstrates that early mammals were diverse in their locomotor strategies and lifestyles; they had experimented with an aerial habit at about the same time as, if not earlier than, when birds endeavoured to exploit the sky.
*From Jin Meng's homepage:
"I am interested in morphology, systematics and evolution of mammals in general and early mammals in particular. My past research concerned several mammal groups such as didymoconids, multituberculates, and gliriforms (rodents, lagomorphs and their early kin). Current research focuses on higher-level phylogeny of Glires (Rodentia + Lagomorpha): their morphology, relationships, distributions, function and evolution. In addition to teeth, I have been working on cranium, ear region and enamel microstructure of teeth as sources of data to address phylogenic and evolutionary issues of those taxa." [More]
**Info on the Mesozoic (comprising the Triassic, Jurassic, and Cretaceous):
The Mesozoic Era is one of three geologic eras of the Phanerozoic eon. The division of time into eras dates back to Giovanni Arduino, in the 18th century, although his original name for the era now called the 'Mesozoic' was 'Secondary' (making the modern era the 'Tertiary'). Lying between the Paleozoic and the Cenozoic, Mesozoic means 'middle animals', derived from Greek prefix meso- for 'between' and zoon- meaning animal or 'living being'. It is often called the 'Age of Medieval Life' or the 'Age of the Dinosaurs', after the dominant fauna of the era.
The Mesozoic was a time of tectonic, climatic and evolutionary activity. The continents gradually shifted from a state of connectedness into their present configuration, this rifting providing for speciation and other important evolutionary developments. The climate was exceptionally warm throughout the period, also playing an important role in the evolution and diversification of new animal species. By the end of the era, the basis of modern life was in place.
Harrisburg, Pennysylvania. - A federal judge who barred a Pennsylvania school district from teaching 'intelligent design' virtually copied findings suggested by the winning side in a key section of the landmark ruling, according to a Seattle think tank that promotes the concept and has criticized the decision.
But legal experts say it is common for judges in civil cases to rely heavily on findings proposed by lawyers when they write their opinions, and there is nothing wrong with copying those findings if the legal briefs have been well-prepared.
The Discovery Institute on Tuesday released a study* in which it compared the December 2005 ruling by U.S. District Judge John E. Jones III with findings proposed by lawyers for eight families who sued to have intelligent design removed from the Dover Area School District's biology curriculum. The decision equated intelligent design, which attributes the complexity of living organisms to an unidentified intelligent cause, with creationism.
Continued at "Dover: 'Intelligent design' ruling relied too much on plaintiffs"
In December of 2005, critics of the theory of intelligent design (ID) hailed federal judge John E. Jones' ruling in Kitzmiller v. Dover, which declared unconstitutional the reading of a statement about intelligent design in public school science classrooms in Dover, Pennsylvania. Since the decision was issued, Jones' 139-page judicial opinion has been lavished with praise as a "masterful decision" based on careful and independent analysis of the evidence. However, a new analysis of the text of the Kitzmiller decision reveals that nearly all of Judge Jones' lengthy examination of "whether ID is science" came not from his own efforts or analysis but from wording supplied by ACLU attorneys. In fact, 90.9% (or 5,458 words) of Judge Jones' 6,004- word section on intelligent design as science was taken virtually verbatim from the ACLU's proposed "Findings of Fact and Conclusions of Law" submitted to Judge Jones nearly a month before his ruling. Judge Jones even copied several clearly erroneous factual claims made by the ACLU. The finding that most of Judge Jones' analysis of intelligent design was apparently not the product of his own original deliberative activity seriously undercuts the credibility of Judge Jones' examination of the scientific validity of intelligent design.
See Memorandum Opinion:
Introduction: On October 18, 2004, the Defendant Dover Area School Board of Directors passed by a 6-3 vote the following resolution:
Students will be made aware of gaps/problems in Darwin's theory and of other theories of evolution including, but not limited to, intelligent design. Note: Origins of Life is not taught.
On November 19, 2004, the Defendant Dover Area School District announced by press release that, commencing in January 2005, teachers would be required to read the following statement to students in the ninth grade biology class at Dover High School:
The Pennsylvania Academic Standards require students to learn about Darwin's Theory of Evolution and eventually to take a standardized test of which evolution is a part.
Because Darwin's Theory is a theory, it continues to be tested as new evidence is discovered. The Theory is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations.
Intelligent Design is an explanation of the origin of life that differs from Darwin's view. The reference book, Of Pandas and People**, is available for students who might be interested in gaining an understanding of what Intelligent Design actually involves.
With respect to any theory, students are encouraged to keep an open mind. The school leaves the discussion of the Origins of Life to individual students and their families. As a Standards-driven district, class instruction focuses upon preparing students to achieve proficiency on Standards-based assessments.
**Of Pandas and People: The Central Question of Biological Origins by Percival Davis, Dean H. Kenyon
Of Pandas and People gives evidence for intelligent design from origin-of-life studies, biochemistry, genetics, homology, and paleontology. In a unique manner, Of Pandas and People gives the pros and cons of both the biological-evolution theory and the intelligent-design concept. Pandas promotes a widely recognized goal of science education by fostering a questioning, skeptical and scrutinizing mindset. This supplemental biology textbook provides an extensive index, glossary, references, and suggested reading and resources to help familarize the reader with the material. Pandas is enhanched by the use of numerous diagrams, charts, illustrations and full-color pictures.
From the New Scientist: Fossil bones of a mouse-sized creature that died between 16 million and 19 million years ago have been discovered on the South Island of New Zealand. It is the first hard evidence that the islands once had their own indigenous land mammals.
Today the only land mammals that live in New Zealand are animals like Australian possums - which have arrived since human settlement - although the country does have its own species of bats, seals and sea lions.
The find, by Trevor Worthy* of Adelaide University, Australia, and colleagues, includes two jawbones, and one thigh bone, from at least two of the creatures, says team member Suzanne Hand. "The amazing thing is, it is unlike any other fossil mammal found anywhere else," she says.
The shape of the fossil bones suggest a very primitive mammal that would have evolved before the mammal-line split into placental mammals and marsupials, 125 million years ago, says Hand of the University of New South Wales in Sydney, Australia. As the fossil bones are only around 16 million to 19 million years old, it appears the mammal managed to survive for at least 100 million years before going extinct.
Continued at "Fossils reveal New Zealand's indigenous 'mouse'"
Based on the open access/free Proceedings of the National Academy of Sciences (PNAS) paper:
"Miocene mammal reveals a Mesozoic ghost lineage on insular New Zealand, southwest Pacific"
Abstract (Full Text available at same link)
New Zealand (NZ) has long been upheld as the archetypical example of a land where the biota evolved without nonvolant terrestrial mammals. Their absence before human arrival is mysterious, because NZ was still attached to East Antarctica in the Early Cretaceous when a variety of terrestrial mammals occupied the adjacent Australian portion of Gondwana. Here we report discovery of a nonvolant mammal from Miocene (19-16 Ma) sediments of the Manuherikia Group near St Bathans (SB) in Central Otago, South Island, NZ. A partial relatively plesiomorphic femur and two autapomorphically specialized partial mandibles represent at least one mouse-sized mammal of unknown relationships. The material implies the existence of one or more ghost lineages, at least one of which (based on the relatively plesiomorphic partial femur) spanned the Middle Miocene to at least the Early Cretaceous, probably before the time of divergence of marsupials and placentals >125 Ma. Its presence in NZ in the Middle Miocene and apparent absence from Australia and other adjacent landmasses at this time appear to reflect a Gondwanan vicariant event and imply persistence of emergent land during the Oligocene marine transgression of NZ. Nonvolant terrestrial mammals disappeared from NZ some time since the Middle Miocene, possibly because of late Neogene climatic cooling.
*Trevor Worthy was also involved in finding New Zealand's first snake fossil:
"Geologists have found a fossil bonanza in Central Otago - including the first evidence that New Zealand once had snakes.
The treasure-trove of animal and bird fossils was unearthed in the Manuherikia Valley, about 100km northwest of Dunedin.
The remains, dated at between 18 and 14 million years old, include tiny jaw and teeth of a python-like snake, fish, birds, and fragments from an ancient crocodile.
The find is the first evidence of a land snake living in New Zealand. It is particularly significant because it had long been thought that New Zealand did not have snakes," said palaeontologist Craig Jones of the GNS Science Limited (GNS).
GNS, Alan Tennyson of Te Papa, moa specialist Trevor Worthy, and James McNamara from the South Australian Museum combined forces in the project."
Tuesday, December 12, 2006
Scientists at Manchester University (UK) have discovered that a dinosaur traditionally regarded as one of the most violent actually used its giant razor-sharp claw to climb trees.
The velociraptor* was immortalised in Steven Speilberg's 1993 film Jurassic Park, where it was depicted as a vicious hunter that slashed open its prey's intestine with its sickle-shaped claw.
But palaeontologist Dr Phillip Manning from Manchester University and scientists from the National History Museum in London have discovered this fearsome-looking appendage was of little use for this purpose.
The researchers found a replica claw attached to the end of a robotic arm was better at hooking on to flesh than slashing it during a simulated attack.
They also replicated the dinosaur's hind leg motion and this led to the discovery it was better suited to climbing.
Full article at "Dinosaur claws used for climbing - research"
A related Natural History Museum report from 2005:
Scientists at the University of Manchester and the Natural History Museum have been studying the large foot claw found on small meat-eating dinosaurs such as Velociraptor and Deinonychus . These dinosaurs both belong to a group called dromaeosaurs.
The study has found that instead of slicing through flesh and disembowelling prey, as previously thought, the dinosaur primarily used its foot claw as a tool to hold on to and perhaps clamber over its victims.
The dromaeosaur's sharp serrated teeth would then tear into the flesh of its prey whilst clinging tightly to its victim. This is similar to the hunting techniques of modern day big cats, which use their protracted claws to cling onto their prey as their powerful jaws deliver the killer blow. (Continued)
*Info on Velociraptors:
Velociraptor (meaning "swift thief") is a genus of dromaeosaurid theropod dinosaur that existed approximately 83 to 70 million years ago during the later part of the Cretaceous Period. There is only one universally recognized species, V. mongoliensis, although others have been attributed in the past. Fossils of this species have been found in central Asia, from both Inner and Outer Mongolia.
Smaller than other dromaeosaurids like Deinonychus and Achillobator, the turkey-sized Velociraptor nevertheless shared many of the same anatomical features. It was a bipedal carnivore with a long, stiffened tail and had an enlarged, sickle-shaped claw on each hindfoot, which is thought to have been used to kill its prey. Velociraptor can be distinguished from other dromaeosaurids by its long and low skull, with an upturned snout.
Due in large part to its prominent role in Michael Crichton's novel Jurassic Park and the subsequent motion picture series, Velociraptor (commonly shortened to 'raptor') is one of the dinosaur genera most familiar to the general public. It is also well-known to paleontologists, with over a dozen recovered fossil skeletons - the most of any dromaeosaurid. One particularly famous specimen shows a Velociraptor locked in combat with a Protoceratops.
3-D Animations of a Velociraptor and Protoceratops engaging in combat from the American Museum of Natural History.
Louisiana University Professor Discovers New Lizard Species
Chris Austin (Austin Lab), assistant curator of herpetology at LSU's Museum of Natural Science, or LSUMNS, and adjunct professor in biological sciences, recently discovered a new species of lizard while conducting field research in Borneo.
Austin, along with colleague Indraneil Das from the Institute of Biodiversity and Environmental Conservation at the Universiti Malaysia Sarawak, will publish their findings and photos of the new species in the prestigious Journal of Herpetology. The article, which will contain the currently embargoed scientific name of the species, is slated for publication in March 2007.
'We actually found four specimens at once,' said Austin. 'One of the best methods for finding lizards in the rainforest is to look under logs. We found two individuals of the new species under one log and two more under another.' With more than 15 years of fieldwork experience behind him, Austin knew immediately that he had found a new species. After collecting the lizards, he and Das began the difficult work of proving what they already knew.
'Determining that a species is new to science is a long and laborious process,' said Austin. 'Natural history museums and their invaluable collections are critical in that they allow scientists to examine known biodiversity in order to determine a species is new.' He and Das examined specimens from a slew of museums around the world.
Natural history collections, such as the more than 80,000 specimens in the LSUMNS reptile and amphibian collection, are important because taxonomy - the science of describing, naming and classifying organisms - has implications for basic and applied fields of science. 'We can't conserve what we don't know we have. It is imperative that we know what species exist in order to preserve them for future generations,' said Austin.
He used the cutting-edge molecular genetics lab at the LSUMNS to decipher the genetic code of the lizards. "We sequenced the DNA of this new species and several other closely related species in order to help our diagnosis," he said. "Using DNA to help describe new species is becoming one of the most important tools for scientists to use in documenting and describing biodiversity." The global decline of biodiversity has become a major public issue recently, and the use of modern molecular methods is proving to be fundamental in gaining a better understanding of the situation.
The new species is distinguishable from its closest cousin, a type of skink found in the southern Philippines, in several distinct ways:
* different color patterns
* its structure and shape, or morphology
* differences in scale count, which is one of the basic ways scientists distinguish between species
* and significant genetic variations.
These traits combined to confirm the original hypothesis that the lizard was, in fact, an entirely new species.
Austin spent the entire summer of 2006 in New Guinea, his geographical area of expertise, conducting fieldwork with graduate students. He is currently working on research funded by the National Science Foundation to understand why New Guinea, called a megadiverse region, has such a high level of biodiversity.
"While we were there, we collected what we think is a new species of snake, a new species of lizard and probably two or three new species of frogs," he said. "But the process of certifying a new species takes so long that it will be awhile before we're certain."
Austin has been at LSU since 2003, coming from post-doctoral positions in Australia and Japan. "What attracted me to the university the most was LSUMNS and its international reputation for excellence," he said. Access to the LSUMNS genetics lab makes that aspect of identifying a new species much easier, giving Austin and his graduate students at-home resources that many other researchers have to travel to reach.
Source: Louisiana State University PR December 11 2006
Chris Austin is author of the Nature paper:
Lizards took express train to Polynesia
Christopher C Austin
Nature 397, 113-114 (14 January 1999) | doi:10.1038/16365
The pattern of human colonization of the islands of the central and eastern Pacific is contentious. Two models have been widely considered: the 'express train to Polynesia' and the 'entangled bank' hypotheses. Here I analyse the mitochondrial DNA sequences of the lizard Lipinia noctua, which lives alongside humans on these Pacific islands, with a view to distinguishing between these two hypotheses. From a phylogenetic analysis of mitochondrial DNA sequence variation, I find that these lizards colonized the central and eastern Pacific as a result of human-mediated dispersal, presumably as stowaways on early Polynesian canoes. The extreme genetic similarity between the different colonies indicates rapid colonization from a single source, which I take as support of the express-train hypothesis.
Monday, December 11, 2006
Amid 70-mile-an-hour winds and freezing Antarctic conditions, an American-Argentine research team has recovered the well-preserved fossil skeleton of a juvenile plesiosaur (general info) --a marine reptile that swam the waters of the Southern Ocean roughly 70 million years ago.
The fossil remains represent one of the most-complete plesiosaur skeletons ever found and is thought to be the best-articulated fossil skeleton ever recovered from Antarctica. The creature would have inhabited Antarctic waters during a period when the Earth and oceans were far warmer than they are today.
James E. Martin (homepage), curator of vertebrate paleontology and coordinator of the paleontology program at the South Dakota School of Mines and Technology's Museum of Geology, announced today the plesiosaur bones will be unveiled at the museum on December 13, 2006.
The long-necked, diamond-finned plesiosaurs are probably most familiar as the legendary inhabitants of Scotland's Loch Ness*, although scientific evidence indicates the marine carnivores have been extinct for millions of years. But when the creatures were alive, their paddle-like fins would have allowed them to "fly through the water" in a motion very similar to modern-day penguins.
Martin, an expert on fossil marine reptiles, co-led the 2005 expedition to Antarctica that recovered the plesiosaur. Judd Case, of Eastern Washington University, and Marcelo Reguero of the Museo de La Plata, Argentina, were also co- leaders.
The National Science Foundation (NSF) and the Instituto Antártico Argentino, directed by Sergio Marenssi, funded the expedition. The Argentine Air Force provided helicopter support.
NSF manages the U.S Antarctic Program, which coordinates all U.S. research on the southernmost continent. The White House has designated NSF as the lead federal agency for the International Polar Year, a 2-year global research campaign in the polar regions that begins in March 2007.
Preserved by a volcanic blast?
After it was prepared in the United States, Martin said, the specimen was discovered tobe the 5-foot-long (1.5 meters) skeleton of a long-necked (elasmosaurid) plesiosaur. An adult specimen could reach over 32 feet (10 meters) in length. Most of the bones of the baby plesiosaur had not developed distinct ends due to the youth of the specimen, he said.
But the animal's stomach area was spectacularly preserved. Stomach ribs (gastralia) span the abdomen, and rather than being long, straight bones like those of most plesiosaurs, these are forked, sometimes into three prongs. Moreover, numerous small, rounded stomach stones (gastroliths) are concentrated within the abdominal cavity, indicating stomach stones were ingested even by juvenile plesiosaurs to help maintain buoyancy or to aid digestion.
The skeleton is nearly perfectly articulated as it would have been in life, but the skull has eroded away from the body. Extreme weather at the excavation site on Vega Island off the Antarctic Peninsula and lack of field time prevented further exploration for the eroded skull.
The researchers speculate volcanism similar to the massive eruption of Mt. St. Helens in Washington in 1980, may have caused the animal's death. Excavation turned up volcanic ash beds layered within the shallow marine sands at the site, and chunks of ash were found with plant material inside. That suggests a major blow-down of trees as was observed when Mt. St. Helens erupted. Either the blast or ash dumped into the ocean, the scientists say, may have caused the baby's demise. Moreover, silica released from the ash allowed spectacular preservation of the skeleton.
High winds, freezing water, hard work
As with the find of a new species of dinosaur Martin and Case made in Antarctica several years ago, the weather and the harsh Antarctic climate made collecting the plesiosaur specimen exceedingly difficult. Weeks of winds exceeding 70 miles an hour hindered the excavation. At the end of the work, icy temperatures turned water to slush before plaster could be mixed to encase the fossil for transportation. The ground was so frozen a digging tool snapped in half during the excavation. Finally, a jackhammer had to be carried up to the site in backpacks along with gasoline, plaster, and water.
The resulting package of plesiosaur remains encased in a protective plaster jacket was too large to carry, so the Argentine air force brought helicopters to the rescue. It took five men to lift the specimen into the chopper, which delivered the cargo to the tent camp on the shores of Herbert Sound. The specimen was later picked up by the Laurence M. Gould, an NSF-chartered research vessel.
At the Museum of Geology, the reptile was prepared by Michelle Pinsdorf and replicated by Shawna Johnson, both master's degree students of paleontology at the South Dakota School of Mines.
A prehistoric nursery?
J. Foster Sawyer, of the South Dakota Geological Survey and the School of Mines, found the skeleton while working with Martin at an elevation of 650 feet (200 meters) on Vega Island. Sawyer found vertebrae exposed by wind from the ancient sandy seabed. The bones were embedded in rocks and associated with marine shellfish that suggest the area was a shallow-water marine environment roughly 70 million years ago. Two other partial plesiosaurs were also collected, as well as finds of very advanced shore birds.
Since 1998, expeditions by the American-Argentine team to the area--in part to compare the ancient climates of South Dakota and Antarctica--have secured numerous isolated elements of juvenile plesiosaurs and mosasaurs, a giant marine reptile that looked like an alligator with fins. Martin and his colleagues believe the site may have been a shallow-water area where marine reptiles had their young, and where the young remained until they were of sufficient size and ability to survive in open waters.
Whether plesiosaurs gave live birth has not been proved, but numerous bones and partial skeletons of larger plesiosaurs were found in the same area as the young. Given the long history of plesiosaurs, evolution would have had ample time for them to develop a form of live birth.
The juvenile plesiosaur appears to be related to one discovered in New Zealand in 1874. That plesiosaur was named Mauisaurus and is characterized by a rounded end of the major paddle bone. It was confined to the southern oceans where it existed more than 5 million years. [End]
A "News Conference to Discuss Discovery of Unique Juvenile Plesiosaur Fossil" was held today (Monday, December 11, 2006) and a video of the event will eventually appear on this page.
Humans may have evolved altruistic traits as a result of a cultural 'tax' we paid to each other early in our evolution, a new study suggests.
The research also changes what we knew about the genetic makeup of our hunter-gatherer ancestors.
The origin of human altruism has puzzled evolutionary biologists for many years (see Survival of the nicest).
In every society, humans make personal sacrifices for others with no expectation that it will be reciprocated. For example, we donate to charity, or care for the sick and disabled. This trait is extremely rare in the natural world, unless there is a family relationship or later reciprocation.
One theory to explain how human altruism evolved involves the way we interacted as groups early in our evolution. Towards the end of the Pleistocene period – about 12,000 years ago - humans foraged for food as hunter-gatherers. These groups competed against each other for survival.
Continued at "Why altruism paid off for our ancestors"
Based on the journal Science paper "Group Competition, Reproductive Leveling, and the Evolution of Human Altruism" by Samuel Bowles*
Science 8 December 2006:
Vol. 314. no. 5805, pp. 1569 - 1572
Humans behave altruistically in natural settings and experiments. A possible explanation - that groups with more altruists survive when groups compete - has long been judged untenable on empirical grounds for most species. But there have been no empirical tests of this explanation for humans. My empirical estimates show that genetic differences between early human groups are likely to have been great enough so that lethal intergroup competition could account for the evolution of altruism. Crucial to this process were distinctive human practices such as sharing food beyond the immediate family, monogamy, and other forms of reproductive leveling. These culturally transmitted practices presuppose advanced cognitive and linguistic capacities, possibly accounting for the distinctive forms of altruism found in our species.
*Info on Samuel Bowles:
My research focuses on two areas (much of it conducted jointly with Herbert Gintis). The first concerns the co-evolution of preferences, institutions and behavior, with emphasis on the modeling and empirical study of cultural evolution, the importance and evolution of non-self-regarding motives in explaining behavior, and applications of these studies to policy areas such as intellectual property rights, the economics of education and the politics of government redistributive programs. Included are agent-based modeling and other studies of what I term "property rights revolutions." Much of this research is carried out as part of the MacArthur Research Network on Preferences and in conjunction with the Behavioral Sciences Program at the Santa Fe Institute.
Study Detects Recent Instance of Human Evolution
A discovery by an international team led by University of Maryland researcher Sarah Tishkoff* identifies, for the first time, genetic mutations in East Africans that are associated with the ability to digest milk as adults.
Tishkoff's study of DNA, described in the journal Nature Genetics , found that the mutations evolved at the time in history when some Africans were beginning to raise cattle, and they evolved independently from the mutation that regulates milk digestion in Europeans.
The findings are not only evidence of how genes and culture co-evolve, says Tishkoff, associate professor of biology at Maryland, "they reveal one of the most striking genetic footprints of natural selection ever observed in humans."
Lactose Intolerant Humans
Human adults were not designed to digest milk. It took a genetic mutation to enable humans to tolerate lactose (see lactose intolerance), the main sugar found in milk. But not everyone has the mutation. Most northern Europeans, whose ancestors domesticated cattle, do. Descendants of cultures that did not raise cattle for milk - many southern Europeans, most Asians and many Africans - do not have the mutation and can't digest milk products.
Then there is the mystery of why some African people who raise cattle and successfully digest milk do not have the mutation that allows Europeans to digest milk.
Tishkoff's study appears to have solved that mystery. By resequencing DNA samples that her team collected from a number of different ethnic groups in remote regions of Africa and testing whether genetic variation is associated with the ability to digest lactose, Tishkoff discovered that, indeed, a distinct genetic mutation to allow digestion of milk occurred in Africa independently from the European mutation and arose at the time that African populations started raising cattle.
The mutation has gone undetected until now because it appears to be in a different location than the European mutation, and appears to be restricted to East African populations that herd cattle.
When humans were hunter-gatherers, before some began to domesticate cattle, they were able to digest milk only until they were about four years old. Lactase-phlorizin hydrolase (LPH), the enzyme that lets humans digest lactose, the main carbohydrate in milk, works in the small intestine to help the body absorb the sugars found in lactose. But LPH levels decrease rapidly after weaning and are at low levels in adults
When milk became a human food source, evolution went to work. Says Tishkoff, "The ability to digest milk as adults, called lactase persistence, appears to be an excellent example of gene-culture co-evolution. In this case, it is the development of technology - raising cattle - and the genetic mutation - the ability to digest milk - that becomes common."
By looking at the rate of decay of association of genetic variants over a three-million base pair region, Tishkoff and collaborators were able to estimate when these genetic mutations occurred in human history. The mutation for lactose tolerance began to show up in Northern Europeans at about the same time they began to raise milk cattle, around 9,000 years ago. A distinct mutation for lactose tolerance became common in East Africa beginning around 7,000 years ago. These dates correlate with archeological evidence for the origins of cattle domestication in these regions.
For Tishkoff, who has been doing genetics research on disease and human origins among African populations for more than ten years, there were clues that some groups of Africans had adapted due to a distinct genetic mutation for lactase persistence- they have a history of cattle domestication, they consume milk- yet they don't have the mutation associated with lactase persistence in Europeans.
"Archeological evidence suggests that cattle domestication originated in southern Egypt as early as 9,000 years ago," said Tishkoff. "The ability to digest milk as adults was likely to be adaptive, because of the nutritional benefits from milk, and also because milk is an important source of water in arid regions. During the dry season, many pastoralist populations are fully milk-dependent."
Tishkoff's group selected specific African ethnic groups to study, those with and without a history of cattle domestication. Driving across rugged terrain in Land Cruisers, traveling to remote villages, and setting up collection stations under trees, they collected DNA samples from almost every major pastoralist population and some hunter-gatherers in regions where no one else had looked before: the Arusha and Dodoma provinces of Tanzania; Rift Valley, Eastern, and Nyanza provinces of Kenya; and the Khartoum and Kasala provinces of the Sudan.
The researchers also asked volunteers to consume lactose, then measured their blood sugar levels to determine if they were able to digest the lactose found in milk. "This ability was then compared to the specific genetic variants found in these individuals to identify the genetic basis for the ability to digest milk," says Tishkoff.
Location, Location, Location
Five hundred field samples of DNA went to Dr. Panos Deloukas' lab at the Sanger Institute in Cambridge, England, for genotyping of the new African variants identified by the Tishkoff lab. The lab also did genotyping of 123 genetic differences over a three-million-base pair region of chromosome 2, which encompasses the gene that regulates lactose digestion.
It was on that chromosome, near the gene coding for the enzyme"lactase" that the genetic variations for milk digestion in the African populations turned up - not just one, but three distinct mutations that evolved at different times, in different geographic regions. The most significant variant, the C-14010 allele, was common in East Africans. Two other mutations, not as common, were G-13907 and G-13915, found among Beja (North Sudan) and North Kenyan populations.
Studies of gene expression in small intestine cell lines that contained these new mutations, led by Dr. Greg Wray at Duke University in collaboration with the Tishkoff study, also indicated that these mutations regulate expression of the enzyme "lactase," that enables digestion of lactose.
Based on computer simulations of the strength and age of selection, done in collaboration with Dr. Jonathan Pritchard and Benjamin Voight at the University of Chicago, they estimate the most common mutation, C-14010, evolved over a 7,000-year time span, when different groups of Africans were moving from being hunter-gatherer to pastoral cultures.
"If a mutation provides a strong benefit, it will become common in the population," says Tishkoff. "This mutation was so important for adaptation that it rapidly swept to high frequency in East Africa.
"Furthermore, positive selection was so strong that a huge region of chromosome 2 near this mutation rapidly swept to high frequency as well," Tishkoff said. "The area of the chromosome affected by this adaptive event, more than two million nucleotides, is larger then any region ever reported in any human population, making this one of the most striking examples of recent natural selection in humans."
Implications for Disease
"Without resequencing, we wouldn't have found this," said Tishkoff. "Our results point to the importance of studying genetic variation in different ethnic groups. Even though we weren't looking for disease mutations, it demonstrates that mutations, including those that result in disease, can be geographically restricted."
Other University of Maryland researchers involved with this study include NIH postdoctoral research fellow Floyd Reed and graduate students Alessia Ranciaro, Holly Mortensen, Kweli Powell and Jibril B. Hirbo.
Source (Adapted): University of Maryland PR "UMd-Led Team Discovers Gene Mutation for Milk Tolerance in Africans" December 5 2006
 Convergent adaptation of human lactase persistence in Africa and Europe
Sarah A Tishkoff et al.
Nature Genetics - 39, 31 - 40 (2006)
Published online: 10 December 2006; | doi:10.1038/ng1946
A SNP (single nucleotide polymorphism) in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenotype association study in 470 Tanzanians, Kenyans and Sudanese and identified three SNPs (G/C-14010, T/G-13915 and C/G-13907) that are associated with lactase persistence and that have derived alleles that significantly enhance transcription from the LCT promoter in vitro. These SNPs originated on different haplotype backgrounds from the European C/T-13910 SNP and from each other. Genotyping across a 3-Mb region demonstrated haplotype homozygosity extending greater than 2.0 Mb on chromosomes carrying C-14010, consistent with a selective sweep over the past approx 7,000 years. These data provide a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits - animal domestication and adult milk consumption.
*Excerpt from Sarah Tishkoff's webpage about the African Genetic Diversity Project:
"Despite the fact that Africa plays a central role in human evolution, African populations have been greatly underrepresented in the study of human genetic diversity. Our goal is to establish a large database of genetic diversity among geographically, linguistically, and culturally diverse African populations. The study of African genetic diversity will be important for reconstructing modern human origins as well as recent African and African American population histories. The study of African genetic diversity will also be important for the identification of the genetic basis of diseases prevalent in African and African American populations (e.g. hypertension, diabetes, prostate cancer).
To achieve this goal, we and our collaborators have made several field expeditions to Africa to collect 9ml blood samples from greater than 4000 individuals from greater than 80 ethnic groups (most previously un-sampled) originating from Nigeria, Cameroon, Tanzania, the Sudan, and Kenya, from which we have extracted DNA."