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Archive for the ‘World History’ Category

Most Ancient Case of Tuberculosis Found In 500,000-Year-Old Human

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Evidence Suggests Vitamin D Deficiency Endangers Migrating Populations

Although most scientists believe tuberculosis emerged only several thousand years ago, new research from The University of Texas at Austin reveals the most ancient evidence of the disease has been found in a 500,000-year-old human fossil from Turkey.

The discovery of the new specimen of the human species, Homo erectus, suggests support for the theory that dark-skinned people who migrate northward from low, tropical latitudes produce less vitamin D, which can adversely affect the immune system as well as the skeleton.

Professor John Kappelman holds a plaster cast replica of the cranium of the newly discovered young male Homo erectus specimen<br /> from western Turkey

Professor John Kappelman of The University of Texas at Austin holds a plaster cast replica of the cranium of the newly discovered young male Homo erectus specimen from western Turkey. The fossil is 500,000 years old and was recovered from a block of travertine stone as it was being sawed into tiles for the building stone market.

Prior to this discovery in western Turkey, which helps scientists fill a temporal and geographical gap  in human evolution, the oldest evidence of tuberculosis in humans was found in mummies from Egypt and Peru that date to several thousand years ago.

Paleontologists spent decades prospecting in Turkey for remains of Homo erectus, widely believed to be the first human species to migrate out of Africa. After moving north, the species had to adapt to increasingly seasonal climates.

The researchers identified this specimen of Homo erectus as a young male based on aspects of the cranial suture closure, sinus formation and the size of the ridges of the brow. They also found a series of small lesions etched into the bone of the cranium whose shape and location are characteristic of the Leptomeningitis tuberculosa, a form of tuberculosis that attacks the meninges of the brain.

After reviewing the medical literature on the disease that has reemerged as a global killer, the researchers found that some groups of people demonstrate a higher than average rate of infection, including Gujarati Indians who live in London, and Senegalese conscripts who served with the French army during World War I.

The research team identified two shared characteristics in the communities: a path of migration from low, tropical latitudes to northern temperate regions and darker skin color.

People with dark skin produce less vitamin D because the skin pigment melanin blocks ultraviolet light. And, when they live in areas with lower ultraviolet radiation such as Europe, their immune systems can be compromised.

John Kappelman, professor of anthropology at The University of Texas at Austin, is part of an international team of researchers from the United States, Turkey and Germany who have published their findings in the Dec. 7 issue of the American Journal of Physical Anthropology.

It is likely that Homo erectus had dark skin because it evolved in the tropics, Kappelman explained. After the species moved north, it had to adapt to more seasonal climates. The researchers hypothesize the young male’s body produced less vitamin D and this deficiency weakened his immune system, opening the door to tuberculosis.

“Skin color represents one of biology’s most elegant adaptations,” Kappelman said. “The production of vitamin D in the skin serves as one of the body’s first lines of defenses against a whole host of infections and diseases. Vitamin D deficiencies are implicated in hypertension, multiple sclerosis, cardiovascular disease and cancer.”

Before antibiotics were invented, doctors typically treated tuberculosis by sending patients to sanatoria where they were prescribed plenty of sunshine and fresh air.

“No one knew why sunshine was integral to the treatment, but it worked,” Kappelman said. “Recent research suggests the flush of ultraviolet radiation jump-started the patients’ immune systems by increasing the production of vitamin D, which helped to cure the disease.”

View of the inside of a plaster cast of the skull of the newly discovered young male Homo erectus from western Turkey
View of the inside of a plaster cast of the skull of the newly discovered young male Homo erectus from western Turkey. The stylus points to tiny lesions 1-2 mm in size found along the rim of bone just behind the right eye orbit. The lesions were formed by a type of tuberculosis that infects the brain and, at 500,000 years in age, represents the most ancient case

American Journal of Physical Anthropology 7 Dec 2007 Early View DOI 10.1002/ajpa.20739
Brief Communication
First Homo erectus from Turkey and implications for migrations into temperate Eurasia
John Kappelman 1 *, Mehmet Cihat Alçiçek 2, Nizamettin Kazanc 3 4, Michael Schultz 5, Mehmet Özkul 2 4, evket en 6
1Department of Anthropology, The University of Texas, Austin, TX
2Department of Geological Engineering, Engineering Faculty, Pamukkale University, Denizli, Turkey
3Department of Geological Engineering, Engineering Faculty, Ankara University, Ankara, Turkey
4JEMIRKO, Turkish Association for Protection of Geological Heritage, Ankara, Turkey
5Zentrum Anatomie der Georg-August-Universität, Göttingen, Germany D-37075
6Laboratoire de Paléontologie du Muséum National d’Histoire Naturelle, Paris, France
email: John Kappelman (jkappelman@mail.utexas.edu)

*Correspondence to John Kappelman, The University of Texas at Austin, Anthrop and Archeol, 1 University Station C3200, Austin, TX 78712-0303, USA

Abstract
Remains of fossil hominins from temperate regions of the Old World are rare across both time and space, but such specimens are necessary for understanding basic issues in human evolution including linkages between their adaptations and early migration patterns. We report here the remarkable circumstances surrounding the discovery of the first fossil hominin calvaria from Turkey. The specimen was found in the Denizli province of western Turkey and recovered from within a solid block of travertine stone as it was being sawed into tile-sized slabs for the commercial natural stone building market. The new specimen fills an important geographical and temporal gap and displays several anatomical features that are shared with other Middle Pleistocene hominins from both Africa and Asia attributed to Homo erectus. It also preserves an unusual pathology on the endocranial surface of the frontal bone that is consistent with a diagnosis of Leptomeningitis tuberculosa (TB), and this evidence represents the most ancient example of this disease known for a fossil human. TB is exacerbated in dark-skinned peoples living in northern latitudes by a vitamin D deficiency because of reduced levels of ultraviolet radiation (UVR). Evidence for TB in the new specimen supports the thesis that reduced UVR was one of the many climatic variables presenting an adaptive challenge to ancient hominins during their migration into the temperate regions of Europe and Asia. Am J Phys Anthropol, 2007. © 2007 Wiley-Liss, Inc.

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American Journal of Physical Anthropology Volume 134, Issue S45 , Pages 85 – 105

Research Article

Human pigmentation variation: Evolution, genetic basis, and implications for public health

Esteban J. Parra
Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada L5L 1C6

email: Esteban J. Parra (esteban.parra@utoronto.ca) Correspondence to Esteban J. Parra, Department of Anthropology, University of Toronto at Mississauga, 3559 Mississauga Road North, Room 212 North Building, Mississauga, ON, Canada L5L 1C6

Pigmentation, which is primarily determined by the amount, the type, and the distribution of melanin, shows a remarkable diversity in human populations, and in this sense, it is an atypical trait. Numerous genetic studies have indicated that the average proportion of genetic variation due to differences among major continental groups is just 10-15% of the total genetic variation. In contrast, skin pigmentation shows large differences among continental populations. The reasons for this discrepancy can be traced back primarily to the strong influence of natural selection, which has shaped the distribution of pigmentation according to a latitudinal gradient. Research during the last 5 years has substantially increased our understanding of the genes involved in normal pigmentation variation in human populations. At least six genes have been identified using genotype/phenotype association studies and/or direct functional assays, and there is evidence indicating that several additional genes may be playing a role in skin, hair, and iris pigmentation. The information that is emerging from recent studies points to a complex picture where positive selection has been acting at different genomic locations, and for some genes only in certain population groups. There are several reasons why elucidating the genetics and evolutionary history of pigmentation is important. 1) Pigmentation is a trait that should be used as an example of how misleading simplistic interpretations of human variation can be. It is erroneous to extrapolate the patterns of variation observed in superficial traits such as pigmentation to the rest of the genome. It is similarly misleading to suggest, based on the average genomic picture, that variation among human populations is irrelevant. The study of the genes underlying human pigmentation diversity brings to the forefront the mosaic nature of human genetic variation: our genome is composed of a myriad of segments with different patterns of variation and evolutionary histories. 2) Pigmentation can be very useful to understand the genetic architecture of complex traits. The pigmentation of unexposed areas of the skin (constitutive pigmentation) is relatively unaffected by environmental influences during an individual’s lifetime when compared with other complex traits such as diabetes or blood pressure, and this provides a unique opportunity to study gene-gene interactions without the effect of environmental confounders. 3) Pigmentation is of relevance from a public health perspective, because of its critical role in photoprotection and vitamin D synthesis. Fair-skinned individuals are at higher risk of several types of skin cancer, particularly in regions with high UVR incidence, and dark-skinned individuals living in high latitude regions are at higher risk for diseases caused by deficient or insufficient vitamin D levels. Yrbk Phys Anthropol 50:85-105, 2007. © 2007 Wiley-Liss, Inc.

Written by huehueteotl

December 9, 2007 at 12:56 pm

Americans Are Siberians By Provenance

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 What GWB’s manners do suggest, seems highly likely in the light of genetic research: Americans are Siberians by provenance. 😉 Native Americans should not feel offended by this, we all know, that the Bush Clan is not native to the Americas. Seriously now, did a relatively small number of people from Siberia who trekked across a Bering Strait land bridge some 12,000 years ago give rise to the native peoples of North and South America?

The U-M study, which analyzed genetic data from 29 Native American populations, suggests a Siberian origin is much more likely than a South Asian or Polynesian origin. (Credit: University of Michigan)

Or did the ancestors of today’s native peoples come from other parts of Asia or Polynesia, arriving multiple times at several places on the two continents, by sea as well as by land, in successive migrations that began as early as 30,000 years ago?

The questions — featured on magazine covers and TV specials — have agitated anthropologists, archaeologists and others for decades.

University of Michigan scientists, working with an international team of geneticists and anthropologists, have produced new genetic evidence that’s likely to hearten proponents of the land bridge theory. The study, published online in PLoS Genetics, is one of the most comprehensive analyses so far among efforts to use genetic data to shed light on the topic.

The researchers examined genetic variation at 678 key locations or markers in the DNA of present-day members of 29 Native American populations across North, Central and South America. They also analyzed data from two Siberian groups. The analysis shows:

o genetic diversity, as well as genetic similarity to the Siberian groups, decreases the farther a native population is from the Bering Strait — adding to existing archaeological and genetic evidence that the ancestors of native North and South Americans came by the northwest route.

o a unique genetic variant is widespread in Native Americans across both American continents — suggesting that the first humans in the Americas came in a single migration or multiple waves from a single source, not in waves of migrations from different sources. The variant, which is not part of a gene and has no biological function, has not been found in genetic studies of people elsewhere in the world except eastern Siberia.

The researchers say the variant likely occurred shortly prior to migration to the Americas, or immediately afterwards.

“We have reasonably clear genetic evidence that the most likely candidate for the source of Native American populations is somewhere in east Asia,” says Noah A. Rosenberg, Ph.D., assistant professor of human genetics and assistant research professor of bioinformatics at the Center for Computational Medicine and Biology at the U-M Medical School and assistant research professor at the U-M Life Sciences Institute.

“If there were a large number of migrations, and most of the source groups didn’t have the variant, then we would not see the widespread presence of the mutation in the Americas,” he says.

Rosenberg has previously studied the same set of 678 genetic markers used in the new study in 50 populations around the world, to learn which populations are genetically similar and what migration patterns might explain the similarities. For North and South America, the current research breaks new ground by looking at a large number of native populations using a large number of markers.

The pattern the research uncovered — that as the founding populations moved south from the Bering Strait, genetic diversity declined — is what one would expect when migration is relatively recent, says Mattias Jakobsson, Ph.D., co-first author of the paper and a post-doctoral fellow in human genetics at the U-M Medical School and the U-M Center for Computational Medicine and Biology. There has not been time yet for mutations that typically occur over longer periods to diversify the gene pool.

In addition, the study’s findings hint at supporting evidence for scholars who believe early inhabitants followed the coasts to spread south into South America, rather than moving in waves across the interior.

“Assuming a migration route along the coast provides a slightly better fit with the pattern we see in genetic diversity,” Rosenberg says.

The study also found that:

  • Populations in the Andes and Central America showed genetic similarities.
  • Populations from western South America showed more genetic variation than populations from eastern South America.
  • Among closely related populations, the ones more similar linguistically were also more similar genetically.

PLoS Genet 3(11): e185 doi:10.1371/journal.pgen.0030185

Genetic Variation and Population Structure in Native Americans. 

Wang S, Lewis Jr. CM, Jakobsson M, Ramachandran S, Ray N, et al. (2007) 

 We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.

Author Summary

Studies of genetic variation have the potential to provide information about the initial peopling of the Americas and the more recent history of Native American populations. To investigate genetic diversity and population relationships in the Americas, we analyzed genetic variation at 678 genome-wide markers genotyped in 29 Native American populations. Comparing Native Americans to Siberian populations, both genetic diversity and similarity to Siberians decrease with geographic distance from the Bering Strait. The widespread distribution of a particular allele private to the Americas supports a view that much of Native American genetic ancestry may derive from a single wave of migration. The pattern of genetic diversity across populations suggests that coastal routes might have been important during ancient migrations of Native American populations. These and other observations from our study will be useful alongside archaeological, geological, and linguistic data for piecing together a more detailed description of the settlement history of the Americas.

 

Is The Beauty Of A Sculpture In The Brain Of The Beholder?

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Is there an objective biological basis for the experience of beauty in art? Or is aesthetic experience entirely subjective? This question has been addressed in a new article by Cinzia Di Dio, Emiliano Macaluso and Giacomo Rizzolatti. The researchers used fMRI scans to study the neural activity in subjects with no knowledge of art criticism, who were shown images of Classical and Renaissance sculptures.

Brain activations in the contrasts “judged-as-beautiful vs. judged-as-ugly” and “judged-as-ugly vs. judged-as-beautiful” stimuli. Statistical parametric maps rendered onto the MNI brain template showing activity within left somatomotor cortex in the contrast of ugly vs. beautiful stimuli averaged across the three conditions. (Credit: Di Dio C, Macaluso E, Rizzolatti G,Image courtesy of PLoS One)

The ‘objective’ perspective was examined by contrasting images of Classical and Renaissance sculptures of canonical proportions, with images of the same sculptures whose proportions were altered to create a comparable degraded aesthetic value. In terms of brain activations, this comparison showed that the presence of the “golden ratio” in the original material activated specific sets of cortical neurons as well as (crucially) the insula, a structure mediating emotions. This response was particularly apparent when participants were only required to observe the stimuli; that is, when the brain reacted most spontaneously to the images presented.

persee-florence.jpg

The ‘subjective’ perspective was evaluated by contrasting beautiful vs. ugly sculptures, this time as judged by each participant who decided whether or not the sculpture was aesthetic. The images judged to be beautiful selectively activated the right amygdala, a structure that responds tolearned incoming information laden with emotional value.

These results indicate that, in observers naïve to art criticism, the sense of beauty is mediated by two non-mutually exclusive processes: one is based on a joint activation of sets of cortical neurons, triggered by parameters intrinsic to the stimuli, and the insula (objective beauty); the other is based on the activation of the amygdala, driven by one’s own emotional experiences (subjective beauty). The researchers conclude that both objective and subjective factors intervene in determining our appreciation of an artwork.

The history of art is replete with the constant tension between objective values and subjective judgments. This tension is deepened when artists discover new aesthetic parameters that may appeal for various reasons, be they related to our biological heritage, or simply to fashion or novelty. Still, the central question remains: when the fashion and novelty expire, could their work ever become a permanent patrimony of humankind without a resonance induced by some biologically inherent parameters?

PLoS ONE 2(11): e1201. doi:10.1371/journal.pone.0001201

The Golden Beauty: Brain Response to Classical and Renaissance Sculptures.

Di Dio C, Macaluso E, Rizzolatti G (2007)

Abstract

Is there an objective, biological basis for the experience of beauty in art? Or is aesthetic experience entirely subjective? Using fMRI technique, we addressed this question by presenting viewers, naïve to art criticism, with images of masterpieces of Classical and Renaissance sculpture. Employing proportion as the independent variable, we produced two sets of stimuli: one composed of images of original sculptures; the other of a modified version of the same images. The stimuli were presented in three conditions: observation, aesthetic judgment, and proportion judgment. In the observation condition, the viewers were required to observe the images with the same mind-set as if they were in a museum. In the other two conditions they were required to give an aesthetic or proportion judgment on the same images. Two types of analyses were carried out: one which contrasted brain response to the canonical and the modified sculptures, and one which contrasted beautiful vs. ugly sculptures as judged by each volunteer. The most striking result was that the observation of original sculptures, relative to the modified ones, produced activation of the right insula as well as of some lateral and medial cortical areas (lateral occipital gyrus, precuneus and prefrontal areas). The activation of the insula was particularly strong during the observation condition. Most interestingly, when volunteers were required to give an overt aesthetic judgment, the images judged as beautiful selectively activated the right amygdala, relative to those judged as ugly. We conclude that, in observers naïve to art criticism, the sense of beauty is mediated by two non-mutually exclusive processes: one based on a joint activation of sets of cortical neurons, triggered by parameters intrinsic to the stimuli, and the insula (objective beauty); the other based on the activation of the amygdala, driven by one’s own emotional experiences (subjective beauty).

Emergence Of Life On Earth – Primordial Soup Real?

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Tiny DNA Molecules Show Liquid Crystal Phases, Pointing Up New Scenario For First Life On Earth

A team led by the University of Colorado at Boulder and the University of Milan has discovered some unexpected forms of liquid crystals of ultrashort DNA molecules immersed in water, providing a new scenario for a key step in the emergence of life on Earth

A colorful microscope image showing that a solution of tiny DNA molecules has formed a liquid-crystal phase. The DNA molecules pair to form DNA double helices, which, in turn stack end-to-end to make rod-shaped aggregates that orient parallel to one another. (Credit: Michi Nakata)

CU-Boulder physics Professor Noel Clark said the team found that surprisingly short segments of DNA, life’s molecular carrier of genetic information, could assemble into several distinct liquid crystal phases that “self-orient” parallel to one another and stack into columns when placed in a water solution. Life is widely believed to have emerged as segments of DNA- or RNA-like molecules in a prebiotic “soup” solution of ancient organic molecules.

Since the formation of molecular chains as uniform as DNA by random chemistry is essentially impossible, Clark said, scientists have been seeking effective ways for simple molecules to spontaneously self-select, “chain-up” and self-replicate. The new study shows that in a mixture of tiny fragments of DNA, those molecules capable of forming liquid crystals selectively condense into droplets in which conditions are favorable for them to be chemically linked into longer molecules with enhanced liquid crystal-forming tendencies, he said.

“We found that even tiny fragments of double helix DNA can spontaneously self-assemble into columns that contain many molecules,” Clark said. “Our vision is that from the collection of ancient molecules, short RNA pieces or some structurally related precursor emerged as the molecular fragments most capable of condensing into liquid crystal droplets, selectively developing into long molecules.”

Liquid crystals — organic materials related to soap that exhibit both solid and liquid properties — are commonly used for information displays in computers, flat-panel televisions, cell phones, calculators and watches. Most liquid crystal phase molecules are rod-shaped and have the ability to spontaneously form large domains of a common orientation, which makes them particularly sensitive to stimuli like changes in temperature or applied voltage.

RNA and DNA are chain-like polymers with side groups known as nucleotides, or bases, that selectively adhere only to specific bases on a second chain. Matching, or complementary base sequences enable the chains to pair up and form the widely recognized double helix structure. Genetic information is encoded in sequences of thousands to millions of bases along the chains, which can be microns to millimeters in length.

Such DNA polynucleotides had previously been shown to organize into liquid crystal phases in which the chains spontaneously oriented parallel to each other, he said. Researchers understand the liquid crystal organization to be a result of DNA’s elongated molecular shape, making parallel alignment easier, much like spaghetti thrown in a box and shaken would be prone to line up in parallel, Clark said.

A paper on the subject was published in the Nov. 23 issue of Science. The paper was authored by Clark, Michi Nakata and Christopher Jones from CU-Boulder, Giuliano Zanchetta and Tommaso Bellini of the University of Milan, Brandon Chapman and Ronald Pindak of Brookhaven National Laboratory and Julie Cross of Argonne National Laboratory. Nakata died in September 2006.

The CU-Boulder and University of Milan team began a series of experiments to see how short the DNA segments could be and still show liquid crystal ordering, said Clark. The team found that even a DNA segment as short as six bases, when paired with a complementary segment that together measured just two nanometers long and two nanometers in diameter, could still assemble itself into the liquid crystal phases, in spite of having almost no elongation in shape.

Structural analysis of the liquid crystal phases showed that they appeared because such short DNA duplex pairs were able to stick together “end-to-end,” forming rod-shaped aggregates that could then behave like much longer segments of DNA. The sticking was a result of small, oily patches found on the ends of the short DNA segments that help them adhere to each other in a reversible way — much like magnetic buttons — as they expelled water in between them, Clark said.

A key characterization technique employed was X-ray microbeam diffraction combined with in-situ optical microscopy, carried out with researchers from Argonne and Brookhaven National Laboratories. The team using a machine called the Argonne Advanced Photon Source synchrotron that enabled probing of the “nano DNA” molecular organization in single liquid crystal orientation domains only a few microns in size. The experiments provided direct evidence for the columnar stacking of the nano DNA pieces in a fluid liquid crystal phase.

“The key observation with respect to early life is that this aggregation of nano DNA strands is possible only if they form duplexes,” Clark said. “In a sample of chains in which the bases don’t match and the chains can’t form helical duplexes, we did not observe liquid crystal ordering.”

Subsequent tests by the team involved mixed solutions of complementary and noncomplementary DNA segments, said Clark. The results indicated that essentially all of the complementary DNA bits condensed out in the form of liquid crystal droplets, physically separating them from the noncomplementary DNA segments.

“We found this to be a remarkable result,” Clark said. “It means that small molecules with the ability to pair up the right way can seek each other out and collect together into drops that are internally self-organized to facilitate the growth of larger pairable molecules.

“In essence, the liquid crystal phase condensation selects the appropriate molecular components, and with the right chemistry would evolve larger molecules tuned to stabilize the liquid crystal phase. If this is correct, the linear polymer shape of DNA itself is a vestige of formation by liquid crystal order.”
Science 23 November 2007:Vol. 318. no. 5854, pp. 1276 – 1279 DOI: 10.1126/science.1143826


End-to-End Stacking and Liquid Crystal Condensation of 6– to 20–Base Pair DNA Duplexes

Michi Nakata,1*{dagger} Giuliano Zanchetta,2* Brandon D. Chapman,3 Christopher D. Jones,1 Julie O. Cross,4 Ronald Pindak,3 Tommaso Bellini,2{ddagger} Noel A. Clark1{ddagger}

Short complementary B-form DNA oligomers, 6 to 20 base pairs in length, are found to exhibit nematic and columnar liquid crystal phases, even though such duplexes lack the shape anisotropy required for liquid crystal ordering. Structural study shows that these phases are produced by the end-to-end adhesion and consequent stacking of the duplex oligomers into polydisperse anisotropic rod-shaped aggregates, which can order into liquid crystals. Upon cooling mixed solutions of short DNA oligomers, in which only a small fraction of the DNA present is complementary, the duplex-forming oligomers phase-separate into liquid crystal droplets, leaving the unpaired single strands in isotropic solution. In a chemical environment where oligomer ligation is possible, such ordering and condensation would provide an autocatalytic link whereby complementarity promotes the extended polymerization of complementary oligomers.

1 Department of Physics and Liquid Crystal Materials Research Center, University of Colorado, Boulder, CO 80309–0390, USA.
2 Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università di Milano, Milano, Italy.
3 National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA.
4 Advanced Photon Source, Argonne National Laboratory, Argonne, IL60439, USA.

* These authors contributed equally to this work.

{dagger} Deceased.

{ddagger} To whom correspondence should be addressed. E-mail: tommaso.bellini@unimi.it

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MULTIPLE LIQUID CRYSTAL PHASES
OF DNA AT HIGH CONCENTRATIONS

Teresa E. Strzelecka
Michael W. Davidson & Randolph L. Rill

Department of Chemistry
and Institute of Molecular Biophysics
The Florida State University
Tallahassee, Florida 32306-3006, USA

DNA packaging in vivo is very tight, with volume concentrations approaching 70% w/v in sperm heads, virus capsids and bacterial nucleoids1-3. The packaging mechanisms adopted may be related to the natural tendency of semi-rigid polymers to form liquid crystalline phases in concentrated solutions4-8. We find that DNA forms at least three distinct liquid crystalline phases at concentrations comparable to those in vivo, with phase transitions occurring over relatively narrow ranges of DNA concentration. A weakly birefringent, dynamic, `precholesteric’ mesophase with microscopic textures intermediate between those of a nematic and a true cholesteric phase forms at the lowest concentrations required for phase separation. At slightly higher DNA concentrations, a second mesophase forms which is a strongly birefringent, well-ordered cholesteric phase with a concentration-dependent pitch varying from 2 to 10 µm. At the highest DNA concentrations, a phase forms which is two-dimensionally ordered and resembles smectic phases of thermotropic liquid crystals observed with small molecules.

Although specialized proteins are involved in many DNA packaging processes descriptions of mechanisms of DNA packaging must also consider the intrinsic tendency of the stiff DNA chain to fold when confined to a small volume. Stiff nonelectrolyte polymers form highly ordered, liquid crystalline phases above a critical concentration dependent on the persistence length4-8. Formation of nematic or cholesteric liquid crystalline phases by semi-rigid polymers, such as polybenzyl-L-glutamate, in organic solvents has been studied in detail7,8, and was predicted theoretically by Onsager4, Flory5,6 and others. Much less is known about the behavior of semi-rigid polyelectrolytes. Because DNA, fibrous proteins and certain polysaccharides are polyelectrolytes involved in numerous supramolecular associations in vivo, an understanding of the phase behavior of these biopolymers is of fundamental biological importance.

Ordering of semi-rigid polymers at high concentrations occurs spontaneously to minimize the macromolecular excluded volume4-8. Semi-rigid polyelectrolyte behavior is complicated by charge-shielding requirements. A strong polyelectrolyte is surrounded by a counterion layer, which determines the effective axial ratio and excluded volume9-13. Because polymer phase behavior depends on the effective polymer dimensions, the critical concentration for DNA ordering is a sensitive function if ionic strength and counterion type.

Figure 1. Dependence of solid state 31P NMR linewidth on DNA concentration suggesting multiple phase transitions. DNA fragments of average length 146 base pairs (~500 Å) and with a narrow distribution about this length were prepared by digestion with micrococcal nuclease of calf-thymus chromatin previously depleted of histone H1, and by subsequent deproteinization16. Short DNA molecules are studied as a preliminary step to understanding the natural behavior of DNA at in vivo concentrations. Such defined samples are useful because effects of relative molecular mass heterogeneity are minimized and phase transitions are sharp and kinetically rapid. Using DNA fragments of this size is appropriate because the driving forces are the same for ordering of high axial ratio, rod-like molecules and long semi-flexible polymers of identical composition5,6. Open circles: data taken at 30ºC; filled circles: data taken at 50ºC. Spectra were obtained on non-spinning samples at a phosphorus frequency of 61.3 MHz on the `Seminole’, an in-house constructed multinuclear Fourier transform (FT) spectrometer equipped with wide-bore superconducting solenoid and quadrature detection, modified for solid-state applications. Sweep width was ±25 kHz, pulse repetition times were 3 s, and 600 scans were added for each spectrum. Gated proton decoupling was applied during data acquisition.

Previous studies demonstrated that aqueous solutions of persistence length DNA (~500 Å), with 0.3 M NaCl as the supporting electrolyte, form biphasic liquid crystalline solutions containing spherulites at DNA concentrations (CDs) of 130-170 mg DNA ml-1 at room temperature, and become fully liquid crystalline at higher CD (refs 14-16). Phase transition boundaries were in good agreement with predicted rigid rod behavior when DNA was treated as a scaled rod with an effective radius of 21.5 Å at this ionic strength16. Here we report the phase behavior when DNA solutions over a range of CDs from 100 to 350 mg DNA ml-1, as determined by solid-state 31P NMR spectroscopy, polarized light microscopy and by electron microscopy.Solutions showed a uniform liquid crystalline phase at CDs from 170 to 220 mg ml-1. A CD of 170-mg ml-1 corresponds to an effective DNA volume fraction of 0.76, assuming 21.5 Å for the effective DNA radius16. Extrapolation to higher CDs yields an apparent effective volume fraction > 1.0 for CDs exceeding ~230 mg ml-1. As DNA solutions were prepared with CDs over 300-mg ml-1, there must be mechanisms for reducing the effective DNA volume fraction.Three potential mechanisms for reducing the effective DNA volume are evident: (1) a change to a more ordered phase, (2) a contraction of the counterion layer, or (3) a change in DNA confirmation/hydration. A phase change above CDs of 220-mg ml-1 was indicated by a change in 31P resonance linewidth and shape(Fig. 1). At lower CDs, in the biphasic region, the resonance linewidth increased progressively with CD until the solution became fully liquid-crystalline, then dramatically sharpened. Concurrently, the lineshape changed from lorenzian to an asymmetric form excepted from an aligned sample with some rotational averaging. Magnetic alignment of liquid crystalline DNA phases with the long molecular axes perpendicular to the field was reported eviously16,17.

Figure 2(a&b)

Figure 2(c&d)

Figure 2(e&f)

Fig. 2 Multiple liquid crystalline DNA phases observed by polarized light microscopy. A sample of 100-mg ml-1 DNA in 0.25-M ammonium acetate was placed on a slider under a partially sealed coverslip so that slow evaporation created a continuous concentration gradient. Samples were observed through crossed polarizers with a Nikon Optiphot-Pol microscope under 3,200 K tungsten-halide illumination and photographed on Fujichrome 64-T professional film. a,c, Low magnification views illustrating sharp transition zones between precholesteric and cholesteric domains (a) and between cholesteric and smectic-like domains(c). Magnification ~ x 40. b,d-f, Higher magnification views of the three major phases. b, Weakly birefringent, diffuse ring texture of `precholesteric’ phase. d, Highly birefringent, fringe or chevron texture of magnetically aligned cholesteric phase. e, Focal-conic-fan texture of smectic-like phase. f, `Pleated ribbon’ texture of most concentrated smectic-like phase near open end of coverslip. Magnifications ~ x 100 in b,e,f; x 200 in d

Magnetic alignment of the mesophase in a biphasic solution is prevented because surface tension restricts the mesophase to spherulites in which DNA molecules are oriented tangentially to the spherical surface18. By analogy, we attribute lineshape changes at CDs slightly above 220-mg ml-1 to formation of a biphasic solution in which two liquid-crystalline phases coexist. Magnetic alignment may be ineffective because of dynamic exchange of molecules between phases with different alignment properties. This conclusion was enforced by the behavior at yet higher CDs (Fig 1). The resonance remained broad at CDs from 229 to 240 mg ml-1, then narrowed again at CDs of 250 and 275-mg ml-1, suggesting formation of a second uniform, aligned phase. Resonance broadening indicative of another phase transition was again observed at a CD of 309-mg ml-1.Interpretations of lineshape changes in terms of phase transitions were supported by microscope examination. Liquid-crystalline phases are traditionally characterized by their microscopic textures as observed through crossed polarizers19-21. Cholesteric liquid crystals, in which the long axes of the molecules lie in pseudo-planes that are slightly twisted with respect to each other, have periodic variations in refractive index and fringe patterns with spacing of P/2, where P is the cholesteric pitch. Many smectic liquid crystals show focal-conic fan textures due to ordering in a second dimension, and can be easily distinguished from nematic or cholesteric forms20,21.Three distinct phases were observed simultaneously by placing a 100mg DNA ml-1 sample on a slide and partially sealing the coverslip, allowing slow evaporation to create a gradient in CD across the slide (Fig. 2 a,c). The low CD mesophase was weakly birefringent and gave roughly circular patterns of broad alternating light and dark lines when viewed through crossed polarizers (Fig. 2 a,b). Rapid, small-scale changes in birefringence due to fluctuations in the nematic director were noted at high magnification (x400). The weak birefringence and director fluctuations imply a dynamic character of this phase. Thicker specimens of this phase had an `oily streak’ texture and could be magnetically aligned, but were easily perturbed when removed from the field.

Figure 3(a&b)

Figure 3(c)

Fig. 3 Evolution of the smectic-like phase. A 350-mg DNA ml-1 sample in 0.25-M ammonium acetate, when first applied to a slide and coverslipped exhibited a mottled planar texture typical of a homoeotropic alignment. Small batonnets formed within 1-h (a) and enlarged (b), eventually merging to form a classical focal-conic-fan texture (c). Microscopy and photography as in Fig. 2. Magnification ~ x 125.

We tentatively refer to the first mesophase as a `precholesteric’ phase. A weakly birefringent precholesteric mesophase in moderately concentrated samples of high relative molecular mass DNA was recently reported19. The textures of the latter phase were attributed to a three-dimensional helicoidal arrangement of DNA molecules somewhat analogous to the molecular arrangement in blue phases of small molecules. Microscopic textures we observed for the precholesteric phase of short DNA were unlike those reported19, suggesting that evolution of DNA phases may be molecular-length dependent.The periodic fringe and `oily streak’ textures of the first mesophase are reminiscent of a cholesteric phase, but they differed significantly from the classical cholesteric textures of the intermediate DNA mesophase, which was highly birefringent with very regular, finely spaced fringe patterns and was extensively aligned in a magnetic field (Fig. 2d). Freeze-fracture-etch electron microscopy and optical diffraction studies have confirmed that this intermediate phase is, in fact, cholesteric (M.W. Davidson and R. L. Rill, manuscript in preparation).Smectic phases have two-dimensional order, with the molecules arranged in planes at a defined angle to the preferred orientation direction of the long molecular axes. There are two common `natural’ textures of smectic a and several other smectic phases-a uniform, homeotropic texture with molecules oriented nearly perpendicular to the slide surface, and the focal-conic fan texture20,21. Focal-conic and striated fan textures were observed for the highest concentration mesophase (s) in controlled drying experiments (Fig. 2 c,e, and f). Close examination of a 350 mg DNA ml-1 sample confirmed that DNA forms a mesophase with molecular layering resembling that found in smectic phases of small molecules.Specimens observed immediately after placement on a slide usually exhibited a nearly uniform homeotropic texture. Batonnets initiated after a few hours, enlarged, and eventually merged to yield a classical focalconic fan texture (Fig. 3). Examination in the electron microscope of freeze-fracture-etch replicas confirmed that DNA molecules were arranged in layers, and that the long molecular axes were approximately perpendicular to the layer planes (Fig. 4). More definitive data are required to unambiguously relate this DNA phase to conventional smectics.

Figure 4

Fig. 4 Freeze-fracture-etch electron microscopy illustrating the layered structure of the smectic-like, high concentration DNA phase. Low magnification view shows cleavage `steps’ (scale bar, 1µm). The direction of shadowing is indicated by the arrow. DNA molecules appear to lie `end-on’ to the viewer and approximately perpendicular to the layer planes, as expected for a smectic phase. The `end-on’ view is readily distinguished from `side-on’ views obtained on examination of cholesteric phases, which tend to shear across cholesteric planes (M.W. Davidson and R. L. Rill, unpublished observations). Samples were placed on gold grids, quick frozen between gold planchets using propane jets, fractured at -120ºC, etched at-100ºC for 2 min, and platinum-carbon shadowed at 45ºC (Balzers BAE 360). Micrographs of replicas were obtained on a Jeol 100CX in transmission mode at 80 kV acceleration voltage.

Using light and electron microscopy we observed several other textures in samples of ~300-400 mg ml-1 (for example, compare Fig. 2 e,f), suggesting the existence of other higher-order phases. As DNA is chiral and packs hexagonally in crystals22, chiral phases could form which are analogous to the chiral smectic C phase, or to more ordered chiral hexatic phases of small molecules (for example, chiral smectic G or I (refs 20,21). These observations demonstrate that DNA in vitro can assume multiple-packing arrangements, which can be readily altered over small ranges of concentration. We expect that the phase behavior of DNA in vitro will also be a sensitive function of the ionic environment. Significant modulation of DNA packing in vivo may be accomplished by small changes in DNA concentration of counterion atmosphere. Similar principles may apply to the ordering of other biological polyelectrolytes.We thank Dr. Henry Aldrich of the University of Florida for assistance with freeze-fracture-etch methods and Drs. David Van Winkle and Francoise Livolant for advice on liquid crystal theory. This work was supported in part by the NIH.

REFERENCES

1. Du Praw, E.J. DNA and Chromosomes (Holt, Rinehart & Winston, New York, 1970).

2. Earnshaw, W.C. & Casjens, S.R. Cell 21, 319-331 (1980).

3. Sipski, W. & Wagner, T.E. Biopolymers 16, 573-582 (1977).

4. Onsager, L. Ann. N.Y. Acad. Sci.51, 627-659 (1949).

5. Flory, P.J. Proc. R. Soc. A234, 60-89 (1956).

6. Flory, P.J. in Polymer Liquid Crystals (eds. Ciferri, A., Krigbaum, W.R. & Meyer, R.B.) 103-112 (Academic, New York, 1982).

7. Robinson, C. Trans Faraday Soc. 52, 571-592 (1956).

8. Miller, W.A. Rev. Biophys. 29, 519-535 (1979).

9. Manning, G.S.Q. Rev. Biophys. 11, 170-246 (1978).

10. Stigter, D. Biopolymers 16, 1435-1448 (1977).

11. Stigter, D. J. phys. Chem. 82, 1603-1606 (1978).

12. Brian, A.A., Frisch, H.L. & Lerman, L. S. Biopolymers 20, 1305-1328 (1981).

13. LeBret, M. & Zimm, B. H. Biopolymers 23, 271-285 & 286-312 (1984).

14. Rill, R. L., Hilliard, P.R. & Levy, G.C. J. biol. Chem. 258, 250-256 (1983).

15. Rill, R.L. Proc. natn. Acad. Sci. U.S.A. 83, 342-346 (1986).

16. Strzelecka, T. E. & Rill, R. L. J. Am. chem. Soc. 109, 4513-4518 (1987).

17.. Brandes, R. & Kearns, E. R. Biochemistry 25, 5890-5895 (1986).

18. Lerman, L.S. Cold Spring Harbor Symp. quant. Biol. 38, 59-74 (1974).

19. Livolant, F. J. Physique 48, 1051-1066 (1987).

20. Demus, D. & Richter, L. Textures of Liquid Crystals (Verlag Chemie, New York, 1978).

21.Gray, G.W. & Goodby, J.W.G. Smectic Liquid Crystals (Heyden, Philadelphia, 1984).

22. Lerman, L.S. Wilkerson, L.S., Venable, J.H. J. molec. Biol. 108, 271-293 (1976).

‘Noah’s Flood’ Kick-started European Farming?

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The flood believed to be behind the Noah’s Ark myth kick-started European agriculture, according to new research by the Universities of Exeter, UK and Wollongong, Australia. New research assesses the impact of the collapse of the North American (Laurentide) Ice Sheet, 8000 years ago. The results indicate a catastrophic rise in global sea level led to the flooding of the Black Sea and drove dramatic social change across Europe.

noahsark1.jpg

Photo: According to press materials supplied by Shamrock — The Trinity Corporation, this satellite view shows Noah’s Ark jutting out from the snow on Mt. Ararat. Image Courtesy of Digital Globe Satellite photos of Mount Aratat, Turkey taken by commercial imaging satellite company Digital Globe released today are said to contain proof of the existence of the biblical Noah’s Ark.

The research team argues that, in the face of rising sea levels driven by contemporary climate change, we can learn important lessons from the past.

The collapse of the Laurentide Ice Sheet released a deluge of water that increased global sea levels by up to 1.4 metres and caused the largest North Atlantic freshwater pulse of the last 100,000 years. Before this time, a ridge across the Bosporus Strait dammed the Mediterranean and kept the Black Sea as a freshwater lake. With the rise in sea level, the Bosporus Strait was breached, flooding the Black Sea.

This event is now widely believed to be behind the various folk myths that led to the biblical Noah’s Ark story. Archaeological records show that around this time there was a sudden expansion of farming and pottery production across Europe, marking the end of the Mesolithic hunter-gatherer era and the start of the Neolithic. The link between rising sea levels and such massive social change has previously been unclear.

The researchers created reconstructions of the Mediterranean and Black Sea shoreline before and after the rise in sea levels. They estimated that nearly 73,000 square km of land was lost to the sea over a period of 34 years. Based on our knowledge of historical population levels, this could have led to the displacement of 145,000 people. Archaeological evidence shows that communities in southeast Europe were already practising early farming techniques and pottery production before the Flood. With the catastrophic rise in water levels it appears they moved west, taking their culture into areas inhabited by hunter-gatherer communities.

Professor Chris Turney of the University of Exeter, lead author of the paper, said: “People living in what is now southeast Europe must have felt as though the whole world had flooded. This could well have been the origin of the Noah’s Ark story. Entire coastal communities must have been displaced, forcing people to migrate in their thousands. As these agricultural communities moved west, they would have taken farming with them across Europe. It was a revolutionary time.”


Quaternary Science Reviews Volume 26, Issues 17-18, September 2007, Pages 2036-2041
doi:10.1016/j.quascirev.2007.07.003

Catastrophic early Holocene sea level rise, human migration and the Neolithic transition in Europe

Chris S.M. Turneya, b, Corresponding Author Contact Information, E-mail The Corresponding Author and Heidi Brown
aSchool of Geography, Archaeology and Earth Resources, University of Exeter, Exeter, EX4 4RJ, UK
bGeoQuEST Research Centre, School of Earth and Environmental Sciences, University of Wollongong, Wollongong, NSW 2522, Australia

Abstract

The collapse of the Laurentide Ice Sheet and release of freshwater 8740–8160 years ago abruptly raised global sea levels by up to 1.4 m. The effect on human populations is largely unknown. Here we constrain the time of the main sea level rise and investigate its effect on the onset of the Neolithic across Europe. An analysis of radiocarbon ages and palaeoshoreline reconstruction supports the hypothesis that flooding of coastal areas led to the sudden loss of land favoured by early farmers and initiated an abrupt expansion of activity across Europe, driven by migrating Neolithic peoples.
The rise in global sea levels 8000 years ago is in-line with current estimates for the end of the 21st century. Professor Chris Turney continued: “This research shows how rising sea levels can cause massive social change. 8,000 years on, are we any better placed to deal with rising sea levels? The latest estimates suggest that by AD 2050, millions of people will be displaced each year by rising sea levels. For those people living in coastal communities, the omen isn’t good.”

Written by huehueteotl

November 20, 2007 at 3:30 pm

Altruism And Hostility Not Contradicting, But Evolved Together

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SFI researcher Samuel Bowles and colleague Jung-Kyoo Choi of Kyungpook National University in South Korea suggest that the altruistic and warlike aspects of human nature may have a common origin.

Altruism–benefiting fellow group members at a cost to oneself–and parochialism–hostility toward individuals not of one’s own ethnic, racial, or other group–are common to human nature, but we don’t immediately think of them as working together hand in hand. In fact the unexpected combination of these two behaviors may have enabled the survival of each trait according to Bowles and Choi.

They show that the two behaviors–which they term “parochial altruism”– may have in fact coevolved. On the face of it joining parochialism to altruism is puzzling from an evolutionary perspective because both behaviors reduce one’s payoffs by comparison to what one would gain by avoiding them.

Aggression consumes resources and risks death; altruism, particularly toward those with whom we have no direct relationship, has the effect of helping other genes advance at our expense. But parochial altruism could have evolved if parochialism promoted intergroup hostilities and the combination of altruism and parochialism contributed to the success of these conflicts.

Using game theoretic analysis and agent-based simulations Bowles and Choi show that under conditions likely to have been experienced by late Pleistocene and early Holocene humans neither parochialsim nor altruism would have been viable singly, but by promoting group conflict, they could have evolved jointly.

“But even if a parochial form of altruism may be our legacy,” said Bowles, “it need not be our fate.” He pointed to the many examples of contemporary altruism extending beyond group boundaries, and the fact that hostility toward outsiders is often redirected or eliminated entirely in a matter of years.

Science. 2007 Oct 26;318(5850):636-640.

The Coevolution of Parochial Altruism and War.

Choi JK, Bowles S.

School of Economics and Trade, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701, Korea.

Altruism-benefiting fellow group members at a cost to oneself-and parochialism-hostility toward individuals not of one’s own ethnic, racial, or other group-are common human behaviors. The intersection of the two-which we term “parochial altruism”-is puzzling from an evolutionary perspective because altruistic or parochial behavior reduces one’s payoffs by comparison to what one would gain by eschewing these behaviors. But parochial altruism could have evolved if parochialism promoted intergroup hostilities and the combination of altruism and parochialism contributed to success in these conflicts. Our game-theoretic analysis and agent-based simulations show that under conditions likely to have been experienced by late Pleistocene and early Holocene humans, neither parochialism nor altruism would have been viable singly, but by promoting group conflict, they could have evolved jointly.

see also:

Altruistic Rats: First Evidence For Generalized Reciprocal Cooperation In Non-humans

 

Written by huehueteotl

October 29, 2007 at 4:22 pm

Irregular Verbs – Fossils of Linguistic And Social Rules

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How ‘holp’ became ‘helped’

Studies link frequency of word use to how fast words evolve.

People talkingWhat did you say? Infrequently-used words have a habit of changing.Getty

The less often a word is said, the faster it will change over time, whereas more-often uttered words are resistant to change. In this week’s Nature, two groups publish analyses of this trend, which quantify it and compare it with biological evolution.

The idea that aspects of culture might ‘evolve’ in in a similar way as biological organisms dates back to Darwin himself. The notion was given a big push forwards in 1976, when Richard Dawkins introduced the concept of ‘memes’ — aspects of culture or fashion that “propagate themselves … by leaping from brain to brain”. That idea proved to be a successful meme in itself, becoming often-referenced in the literature. But, as Tecumseh Fitch, a psychologist at the University of St Andrews in Scotland, points out “not much has been done” to quantify the effect.

“There is this general idea that culture evolves, but it is more of a metaphor than something that has teeth — that obeys precise mathematical rules,” says Erez Lieberman, a specialist in evolutionary maths at Harvard University. “I wondered: can you make this metaphor be real? Can you show a process like natural selection that is affecting ideas or language?”

I getted it

Lieberman was struck by this idea when he learned that the ten most common verbs in English (be, have, do, go, say, can, will, see, take, get) are all irregular. Instead of their past tenses ending in ‘-ed’, as do 97% of English verbs, they take the peculiar forms of was, had, did, went, said, could, would, saw, took and got.

Researchers suppose that this is because often-used irregulars are easy to remember and get right. Seldom-used irregulars, on the other hand, are more likely to be forgotten, so speakers often mistakenly apply the ‘-ed’ rule. The most commonly used word that they found this happened to was the verb ‘to help’ – the past tense used to be ‘holp’, but is now ‘helped’.

This could be seen as analogous to the way that crucially needed genes tend to stay the same throughout biological evolution, whereas those for less-often-used or specialist traits have more freedom to evolve.

Lieberman wondered whether he could quantify the effect. He and his team looked at 177 verbs with varying frequencies of use that were irregular in Old English, and examined how many had been regularized into the ‘-ed’ past tense by the eras of Middle and Modern English. They found that an irregular verb used 100 times less frequently is regularized 10 times as fast. For the more mathematically inclined, this can be expressed as: ‘The half-life of irregular verbs is proportional to the square root of their frequency.

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At the same time, a different group led by evolutionary bio-informaticist Mark Pagel of the University of Reading, UK, looked at 200 basic words across different Indo-European languages, to estimate their rates of evolution.

Some words sound very similar, or can be traced back to a common origin by linguists, throughout many of the languages, which suggests these words were resistant to evolution. The English word ‘water’, for example, is similar to the now-extinct European Gothic word ‘wato’, along with words in many other modern European languages. Other words were markedly different across languages, suggesting they had evolved separately and more quickly (see Table 1).

When Pagel’s team plotted frequency of word use against rate of evolution for four languages (Greek, Spanish, English and Russian), they too found that less-frequently-used words evolved faster, and that frequency can explain half of the rate of evolution.2

“The easiest way to think about it is that changes to the higher-frequency words are less likely to be accepted,” says Pagel. “If I say there are two guys coming over the hill to kill us, and in fact there are 20, we might end up dead.”

The meaning of it all

Both papers were written by teams with evolutionary biology backgrounds, and both call attention to the similarities between language change and the evolution of species. Leiberman even refers to early English as a “primordial soup” of verb forms in his paper.

Brian Joseph, a historical linguist at Ohio State University in Columbus and the editor of the journal Language, says that’s going too far. Early English, he says, was “just as regular and rule-based” as modern language – it just had more complicated rules.

“The analogy with darwinian evolution is crude, although not useless,” says Stephen Pinker, a language and cognition specialist at Harvard. “Some portion of the variance can be accounted for by a quantitative variable such as frequency, but much more remains unexplained. You can’t understand language change without looking at the cognitive psychology of the human brains that learn and transmit the words.”

Nature 449, 713-716 (11 October 2007) | doi:10.1038/nature06137; Received 20 March 2007; Accepted 27 July 2007

Quantifying the evolutionary dynamics of language

Erez Lieberman1,2,3,5, Jean-Baptiste Michel1,4,5, Joe Jackson1, Tina Tang1 & Martin A. Nowak1

  1. Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics,
  2. Department of Applied Mathematics, Harvard University, Cambridge, Massachusetts 02138, USA
  3. Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
  4. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
  5. These authors contributed equally to this work

Correspondence to: Erez Lieberman1,2,3,5 Correspondence and requests for materials should be addressed to E.L. (Email: erez@erez.com).

Human language is based on grammatical rules1, 2, 3, 4. Cultural evolution allows these rules to change over time5. Rules compete with each other: as new rules rise to prominence, old ones die away. To quantify the dynamics of language evolution, we studied the regularization of English verbs over the past 1,200 years. Although an elaborate system of productive conjugations existed in English’s proto-Germanic ancestor, Modern English uses the dental suffix, ‘-ed’, to signify past tense6. Here we describe the emergence of this linguistic rule amidst the evolutionary decay of its exceptions, known to us as irregular verbs. We have generated a data set of verbs whose conjugations have been evolving for more than a millennium, tracking inflectional changes to 177 Old-English irregular verbs. Of these irregular verbs, 145 remained irregular in Middle English and 98 are still irregular today. We study how the rate of regularization depends on the frequency of word usage. The half-life of an irregular verb scales as the square root of its usage frequency: a verb that is 100 times less frequent regularizes 10 times as fast. Our study provides a quantitative analysis of the regularization process by which ancestral forms gradually yield to an emerging linguistic rule.

also:

 

Nature 449, 717-720 (11 October 2007) | doi:10.1038/nature06176; Received 30 April 2007; Accepted 17 August 2007

Frequency of word-use predicts rates of lexical evolution throughout Indo-European history

Mark Pagel1,2, Quentin D. Atkinson1 & Andrew Meade1

  1. School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, RG6 6AS, UK
  2. Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA

Correspondence to: Mark Pagel1,2 Correspondence and requests for materials should be addressed to M.P. (Email: m.pagel@reading.ac.uk).

Greek speakers say “omicronupsilonrhoUnfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com“, Germans “schwanz” and the French “queue” to describe what English speakers call a ‘tail’, but all of these languages use a related form of ‘two’ to describe the number after one. Among more than 100 Indo-European languages and dialects, the words for some meanings (such as ‘tail’) evolve rapidly, being expressed across languages by dozens of unrelated words, while others evolve much more slowly—such as the number ‘two’, for which all Indo-European language speakers use the same related word-form1. No general linguistic mechanism has been advanced to explain this striking variation in rates of lexical replacement among meanings. Here we use four large and divergent language corpora (English2, Spanish3, Russian4 and Greek5) and a comparative database of 200 fundamental vocabulary meanings in 87 Indo-European languages6 to show that the frequency with which these words are used in modern language predicts their rate of replacement over thousands of years of Indo-European language evolution. Across all 200 meanings, frequently used words evolve at slower rates and infrequently used words evolve more rapidly. This relationship holds separately and identically across parts of speech for each of the four language corpora, and accounts for approximately 50% of the variation in historical rates of lexical replacement. We propose that the frequency with which specific words are used in everyday language exerts a general and law-like influence on their rates of evolution. Our findings are consistent with social models of word change that emphasize the role of selection, and suggest that owing to the ways that humans use language, some words will evolve slowly and others rapidly across all languages.

 

Written by huehueteotl

October 11, 2007 at 11:53 am