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Sunday, August 5, 2018

Clovis culture

From Wikipedia, the free encyclopedia
"A Clovis blade with medium to large lanceolate spear-knife points. Side is parallel to convex and exhibit careful pressure flaking along the blade edge. The broadest area is near the midsection or toward the base. The base is distinctly concave with a characteristic flute or channel flake removed from one or, more commonly, both surfaces of the blade. The lower edges of the blade and base is ground to dull edges for hafting. Clovis points also tend to be thicker than the typically thin later stage Folsom points. Length: 4–20 cm/1.5–8 in. Width: 2.5–5 cm/1–2
A Clovis projectile point created using bifacial percussion flaking (that is, each face is flaked on both edges alternately with a percussor)

The Clovis culture is a prehistoric Paleo-Indian culture, named for distinct stone tools found in close association with Pleistocene fauna at Blackwater Locality No. 1 near Clovis, New Mexico, in the 1920s and 1930s. It appears around 11,500–11,000 uncalibrated radiocarbon years before present at the end of the last glacial period, and is characterized by the manufacture of "Clovis points" and distinctive bone and ivory tools. Archaeologists' most precise determinations at present suggest this radiocarbon age is equal to roughly 13,200 to 12,900 calendar years ago. Clovis people are considered to be the ancestors of most of the indigenous cultures of the Americas.

The only human burial that has been directly associated with tools from the Clovis culture included the remains of an infant boy named Anzick-1.[5][6] Researchers from the United States and Europe conducted paleogenetic research on Anzick-1's ancient nuclear, mitochondrial, and Y-chromosome DNA.[7] The results of these analyses reveal that Anzick-1 is closely related to modern Native American populations, which lends support to the Beringia hypothesis for the settlement of the Americas.[8]

The Clovis culture was replaced by several more localized regional societies from the Younger Dryas cold-climate period onward. Post-Clovis cultures include the Folsom tradition, Gainey, Suwannee-Simpson, Plainview-Goshen, Cumberland,and Redstone. Each of these is thought to derive directly from Clovis, in some cases apparently differing only in the length of the fluting on their projectile points. Although this is generally held to be the result of normal cultural change through time,[9] numerous other reasons have been suggested as driving forces to explain changes in the archaeological record, such as the Younger Dryas postglacial climate change which exhibited numerous faunal extinctions.

After the discovery of several Clovis sites in eastern North America in the 1930s, the Clovis people came to be regarded as the first human inhabitants who created a widespread culture in the New World. However, this theory has been challenged, in the opinion of many archaeologists, by several archaeological discoveries, including sites such as Cactus Hill in Virginia, Paisley Caves in the Summer Lake Basin of Oregon, the Topper site in Allendale County, South Carolina, Meadowcroft Rockshelter in Pennsylvania, the Friedkin[10] site in Texas, Cueva Fell in Chile and, especially, Monte Verde, also in Chile.[11] The oldest claimed human archaeological site in the Americas is the Pedra Furada hearths, a site in Brazil that precedes the Clovis culture and the other sites already mentioned by 19,000 to 30,000 years. This claim has become an issue of contention between North American archaeologists and their South American and European counterparts, who disagree on whether it is conclusively proven to be an older human site.[12][13][14]

Description

Clovis points from the Rummells-Maske Cache Site, Iowa

A hallmark of the toolkit associated with the Clovis culture is the distinctively shaped, fluted stone spear point, known as the Clovis point. The Clovis point is bifacial and typically fluted on both sides. Archaeologists do not agree on whether the widespread presence of these artifacts indicates the proliferation of a single people, or the adoption of a superior technology by diverse population groups.[15]

The culture is named after artifacts found between 1932 and 1936 at Blackwater Locality No. 1, an archaeological site between the towns of Clovis and Portales, New Mexico. These finds were deemed especially important due to their direct association with mammoth sp. and the extinct Bison antiquus. The in situ finds of 1936 and 1937 included most of four stone Clovis points, two long bone points with impact damage, stone blades, a portion of a Clovis blade core, and several cutting tools made on stone flakes.[15] Clovis sites have since been identified throughout much of the contiguous United States, as well as Mexico and Central America, and even into northern South America.[16]

Clovis people are generally accepted to have hunted mammoths as well as extinct bison, mastodon, gomphotheres, sloths, tapir, camelops, horse and other smaller animals. More than 125 species of plants and animals are known to have been used by Clovis people in the portion of the Western Hemisphere they inhabited.[17][18]

The oldest Clovis site in North America is believed to be El Fin del Mundo in northwestern Sonora, Mexico, discovered during a 2007 survey. It features occupation dating around 13,390 calibrated years BP.[19] In 2011, remains of gomphotheres were found; the evidence suggests that humans did, in fact, kill two of them there. Also, the Aubrey site in Denton County, Texas, produced an almost identical radiocarbon date.[20]

Disappearance of Clovis

The most commonly held perspective on the end of the Clovis culture is that a decline in the availability of megafauna, combined with an overall increase in a less mobile population, led to local differentiation of lithic and cultural traditions across the Americas.[9][21] After this time, Clovis-style fluted points were replaced by other fluted-point traditions (such as the Folsom culture) with an essentially uninterrupted sequence across North and Central America. An effectively continuous cultural adaptation proceeds from the Clovis period through the ensuing Middle and Late Paleoindian periods.[22]

Whether the Clovis culture drove the mammoth, and other species, to extinction via overhunting – the so-called Pleistocene overkill hypothesis – is still an open, and controversial, question.[23] It has also been hypothesized that the Clovis culture had its decline in the wake of the Younger Dryas cold phase.[24] This 'cold shock', lasting roughly 1500 years, affected many parts of the world, including North America. This appears to have been triggered by a vast amount of meltwater – possibly from Lake Agassiz – emptying into the North Atlantic, disrupting the thermohaline circulation.[25]

The Younger Dryas impact hypothesis or Clovis comet hypothesis originally proposed that a large air burst or earth impact of a comet or comets from outer space initiated the Younger Dryas cold period about 12,900 BP calibrated (10,900 14C uncalibrated) years ago.[26][27][28] The hypothesis has been largely contradicted by research showing that most of the findings cannot be repeated by other scientists, and criticized because of misinterpretation of data and the lack of confirmatory evidence.

Discovery

A cowboy and former slave, George McJunkin, found an ancient bison (Bison antiquus, an extinct relative of the American bison) skeleton in 1908 after a flash flood.[33] The site was first excavated in 1926, near Folsom, New Mexico, under the direction of Harold Cook and Jesse Figgins. On August 29, 1927, they found the first in situ Folsom point with the extinct B. antiquus bones. This confirmation of a human presence in the Americas during the Pleistocene inspired many people to start looking for evidence of early humans.[34]

In 1929, 19-year-old Ridgely Whiteman, who had been closely following the excavations in nearby Folsom in the newspaper, discovered the Clovis site near the Blackwater Draw in eastern New Mexico. Despite several earlier Paleoindian discoveries, the best documented evidence of the Clovis complex was collected and excavated between 1932 and 1937 near Clovis, New Mexico, by a crew under the direction of Edgar Billings Howard until 1935 and later by John Cotter from the Academy of Natural Sciences/University of Pennsylvania. Howard's crew left their excavation in Burnet Cave, New Mexico, (the first truly professionally excavated Clovis site) in August, 1932, and visited Whiteman and his Blackwater Draw site. By November, Howard was back at Blackwater Draw to investigate additional finds from a construction project.[33]

The American Journal of Archaeology (January–March, 1932 V36 #1) in its "Archaeological Notes" mentions E. B. Howard's work in Burnet Cave, including the discovery of extinct fauna and a "Folsom type" point 4 ft below a Basketmaker burial. This brief mention of the Clovis point found in place antedates any work at the Dent Site in Colorado. Reference is made to a slightly earlier article on Burnet Cave in The University Museum Bulletin of November, 1931.

The first report of professional work at the Blackwater Draw Clovis site is in the November 25, 1932, issue of Science News. The publications on Burnet Cave and Blackwater Draw directly contradict statements by several authors (for example see Haynes 2002:56 The Early Settlement of North America) that Dent, Colorado was the first excavated Clovis site. The Dent Site, in Weld County, Colorado, was simply a fossil mammoth excavation in 1932. The first Dent Clovis point was found November 5, 1932, and the in situ point was found July 7, 1933. The in situ Clovis point from Burnet Cave was excavated in late August, 1931 (and reported early in 1932). E. B. Howard brought the Burnet Cave point to the 3rd Pecos Conference, September 1931, and showed it around to several archaeologists interested in early humans (see Woodbury 1983).

Also in 1968, in Montana, a Clovis burial site was found where the remains of a two-year-old child were studied. These remains have been named as Anzick-1 and recently, in 2014, have been used in scientific research.[7]

Clovis Paleo-Indians

Available genetic data show that the Clovis people are the direct ancestors of roughly 80% of all living Native American populations in North and South America, with the remainder descended from ancestors who entered in later waves of migration.[35][36] As reported in February 2014, DNA from the 12,600-year-old remains of Anzick boy, found in Montana, has affirmed this connection to the peoples of the Americas. In addition, this DNA analysis affirmed genetic connections back to ancestral peoples of northeast Asia. This adds weight to the theory that peoples migrated across a land bridge from Siberia to North America.[4]

Clovis First/Single origin hypothesis

Known as "Clovis First", the predominant hypothesis among archaeologists in the latter half of the 20th century had been that the people associated with the Clovis culture were the first inhabitants of the Americas. The primary support for this was that no solid evidence of pre-Clovis human habitation had been found. According to the standard accepted theory, the Clovis people crossed the Beringia land bridge over the Bering Strait from Siberia to Alaska during the period of lowered sea levels during the ice age, then made their way southward through an ice-free corridor east of the Rocky Mountains in present-day Western Canada as the glaciers retreated.[37]

This hypothesis came to be challenged by studies suggesting a pre-Clovis human occupation of the Americas.[38] In 2011, following the excavation of an occupation site at Buttermilk Creek, Texas, a prominent group of scientists claimed to have definitely established the existence "of an occupation older than Clovis."[39][40]

According to researchers Michael Waters and Thomas Stafford of Texas A&M University, new radiocarbon dates place Clovis remains from the continental United States in a shorter time window beginning 450 years later than the previously accepted threshold (13,200 to 12,900 BP).[2]

Recently, the scientific consensus has changed to acknowledge the presence of pre-Clovis cultures in the Americas, ending the "Clovis first" consensus.[41][42][43]

The results of a multiple-author study by Danish, Canadian, and American scientists published in Nature in February 2016 revealed that "the first Americans, whether Clovis or earlier groups in unglaciated North America before 12.6 cal. kyr BP", are "unlikely" to "have travelled to North America from Siberia via the Bering land bridge[44] "via a corridor that opened up between the melting ice sheets in what is now Alberta and B.C. about 13,000 years ago" as many anthropologists have argued for decades.[45] The lead author, Mikkel Pedersen – a PhD student from University of Copenhagen – explained, "The ice-free corridor was long considered the principal entry route for the first Americans ... Our results reveal that it simply opened up too late for that to have been possible."[45] The scientists argued that by 10,000 years ago, the ice-free corridor in what is now Alberta and B.C "was gradually taken over by a boreal forest dominated by spruce and pine trees" and that "Clovis people likely came from the south, not the north, perhaps following wild animals such as bison."[44][45]

Alternatives to Clovis-first

Evidence of human habitation before Clovis

Archaeological sites that antedate Clovis that are well documented include:
Map of the Americas showing pre-Clovis sites

Predecessors of the Clovis people may have migrated south along the North American coastlines, although arguments exist for many migrations along several different routes.[69] Radiocarbon dating of the Monte Verde site in Chile places Clovis-like culture there as early as 18,500 to 14,500 years ago.[56] Remains found at the Channel Islands of California place coastal Paleoindians there 12,500 years ago. This suggests that the Paleoindian migration could have spread more quickly along the Pacific coastline, proceeding south, and that populations that settled along that route could have then begun migrations eastward into the continent.

The Pedra Furada sites in Brazil include a collection of rock shelters, which were used for thousands of years by diverse human populations. The first excavations yielded artifacts with carbon-14 dates of 48,000 to 32,000 years BP. Repeated analyses have confirmed this dating, carrying the range of dates up to 60,000 BP.[70] The best-analyzed archaeological levels are dated between 32,160 ± 1000 years BP and 17,000 ± 400 BP.

In 2004, worked stone tools were found at Topper in South Carolina that have been dated by radiocarbon techniques possibly to 50,000 years ago.[71] But, there is significant scholarly dispute regarding these dates.[72] Scholars agree that evidence of humans at the Topper Site date back to 22,900 cal yr BP.[73]

A more substantiated claim is that of Paisley Caves, Oregon, where rigorous carbon-14 and genetic testing appear to indicate that humans related to modern Native Americans were present in the caves over 1000 14C years before the earliest evidence of Clovis.[74] Traces and tools made by another people, the "Western Stemmed" tradition, were documented.[75]

A study published in Science presents strong evidence that humans occupied sites in Monte Verde, Chile, at the tip of South America, as early as 13,000 years ago.[76] If this is true, then humans must have entered North America long before the Clovis culture – perhaps 16,000 years ago.

The Tlapacoya site in Mexico is located along the base of a volcanic (remnant) hill on the shore of the former Lake Chalco. Seventeen excavations along the base of Tlapacoya Hill between 1956 and 1973 uncovered piles of disarticulated bones of bear and deer that appeared to have been butchered, plus 2,500 flakes and blades presumably from the butchering activities, plus one unfluted spear point. All were found in the same stratum containing three circular hearths filled with charcoal and ash. Bones of many other animal species were also present, including horses and migratory waterfowl. Two uncalibrated radiocarbon dates on carbon from the hearths came in around 24,000 and 22,000 years ago.[77] At another location, a prismatic microblade of obsidian was found in association with a tree trunk radiocarbon dated (uncalibrated) at roughly 24,000 years ago. This obsidian blade has recently been hydration dated by Joaquín García-Bárcena to 22,000 years ago. The hydration results were published in a seminal article that deals with the evidence for pre-Clovis habitation of Mexico.[78]

Coastal migration route

Studies of the mitochondrial DNA of First Nations/Native Americans published in 2007 suggest that the people of the New World may have diverged genetically from Siberians as early as 20,000 years ago, far earlier than the standard theory suggests.[38] According to one alternative theory, the Pacific coast of North America may have been free of ice, allowing the first peoples in North America to come down this route prior to the formation of the ice-free corridor in the continental interior.[79] No evidence has yet been found to support this hypothesis[citation needed] except that genetic analysis of coastal marine life indicates diverse fauna persisting in refugia throughout the Pleistocene ice ages along the coasts of Alaska and British Columbia; these refugia include common food sources of coastal aboriginal peoples, suggesting that a migration along the coastline was feasible at the time.[80] Some early sites on the coast, for example Namu, British Columbia, exhibit maritime focus on foods from an early point with substantial cultural continuity.[81]

In February 2014, researchers reported on their DNA analysis of the remains of Anzick boy (referred to as Anzick-1) of Montana, the oldest skeleton found in the Americas and dated to 12,600 years ago. They found the mtDNA to be D4h3a, "one of the rare lineages associated with Native Americans."[7] This was the same as the mtDNA associated with current coastal populations in North and South America. The study team suggest that finding this genetic evidence so far inland shows that "current distribution of genetic markers are not necessarily indicative of the movement or distribution of peoples in the past."[7] The Y haplotype was found to be Q-L54*(xM3). Further testing found that Anzick-1 was most closely related to Native American populations (see below).[7]

Solutrean hypothesis

The controversial Solutrean hypothesis proposed in 1999 by Smithsonian archaeologist Dennis Stanford and colleague Bruce Bradley (Stanford and Bradley 2002), suggests that the Clovis people could have inherited technology from the Solutrean people who lived in southern Europe 21,000–15,000 years ago, and who created the first Stone Age artwork in present-day southern France.[82] The link is suggested by the similarity in technology between the projectile points of the Solutreans and those found at Clovis (and pre-Clovis) sites. Its proponents point to tools found at various pre-Clovis sites in eastern North America (particularly in the Chesapeake Bay region) as progenitors of Clovis-style tools.[83] The model envisions these people making the crossing in small watercraft via the edge of the pack ice in the North Atlantic Ocean that then extended to the Atlantic coast of France, using skills similar to those of the modern Inuit people, making landfall somewhere around the then-exposed Grand Banks of the North American continental shelf.

In a 2008 study of the relevant paleoceanographic data, Kieran Westley and Justin Dix concluded that "it is clear from the paleoceanographic and paleo-environmental data that the Last Glacial Maximum (LGM) North Atlantic does not fit the descriptions provided by the proponents of the Solutrean Atlantic Hypothesis. Although ice use and sea mammal hunting may have been important in other contexts, in this instance, the conditions militate against an ice-edge-following, maritime-adapted European population reaching the Americas."[84]

University of New Mexico anthropologist Lawrence G. Straus, a primary critic of the Solutrean hypothesis, points to the theoretical difficulty of the ocean crossing, a lack of Solutrean-specific features in pre-Clovis artifacts, as well as the lack of art (such as that found at Lascaux in France) among the Clovis people, as major deficiencies in the Solutrean hypothesis. The 3,000 to 5,000 radiocarbon year gap between the Solutrean period of France and Spain and the Clovis of the New World also makes such a connection problematic.[85] In response, Bradley and Stanford contend that it was "a very specific subset of the Solutrean who formed the parent group that adapted to a maritime environment and eventually made it across the north Atlantic ice-front to colonize the east coast of the Americas" and that this group may not have shared all Solutrean cultural traits.[86]

Genetic evidence of east/west dichotomy

Mitochondrial DNA analysis in 2014 has found that members of some native North American tribes have a maternal ancestry (called haplogroup X) linked to the maternal ancestors of some present-day individuals in western Asia and Europe, albeit distantly. This has also provided some support for pre-Clovis models. More specifically, a variant of mitochondrial DNA called X2a found in many Native Americans has been traced to western Eurasia, while not being found in eastern Eurasia.[87]
Mitochondrial DNA analysis of Anzick-1 concluded that the boy belonged to what is known as haplogroup or lineage D4h3a. This finding is important because the D4h3a line is considered to be a lineage "founder", belonging to the first people to reach the Americas. Although rare in most of today's Native Americans in the US and Canada, D4h3a genes are more common among native peoples of South America, far from the site in Montana where Anzick-1 was buried. This suggests a greater genetic complexity among Native Americans than previously thought, including an early divergence in the genetic lineage 13,000 years ago. One theory suggests that after crossing into North America from Siberia, a group of the first Americans, with the lineage D4h3a, moved south along the Pacific coast and, over thousands of years, into Central and South America, while others may have moved inland, east of the Rocky Mountains.[7] The apparent early divergence between North American and Central plus South American populations may or may not be associated with post-divergence gene flow from a more basal population into North America; however, analysis of published DNA sequences for 19 Siberian populations does not favor the latter scenario.[7]

Spearheads and DNA found at the Paisley Caves site in Oregon suggest that North America was colonized by more than one culture, and that the Clovis culture was not the first. There is evidence to suggest an east/west dichotomy, with the Clovis culture located to the east.[88]

But in 2014, the autosomal DNA of a 12,500+-year-old infant from Montana was sequenced.[7][8][89][90] The DNA was taken from a skeleton referred to as Anzick-1, found in close association with several Clovis artifacts. Comparisons indicate strong affinities with DNA from Siberian sites, and virtually rule out close affinity with European sources (the "Solutrean hypothesis"). The DNA shows strong affinities with all existing Native American populations, which indicated that each of them derives from an ancient population that lived in or near Siberia, the Upper Palaeolithic Mal'ta population. Mal'ta belonged to Y-DNA haplogroup R and mitochrondrial macrohaplogroup U.[7][91]

The data indicate that Anzick-1 is from a population directly ancestral to present South American and Central American Native American populations. This rules out hypotheses which posit that invasions subsequent to the Clovis culture overwhelmed or assimilated previous migrants into the Americas. Anzick-1 is less closely related to present North American Native American populations (including a Yaqui genetic sample), suggesting that the North American populations are basal to Anzick-1 and Central and South American populations.[7] The apparent early divergence between North American and Central plus South American populations might be due to post-divergence gene flow from a more basal population into North America; however, analysis of published DNA sequences of 19 Siberian populations do not suggest this scenario.[7] Anzick-1 belonged to Y-haplogroup Q-L54(xM3)[7], which is by far the largest haplogroup among Native Americans.

Other sites

Mammuthus primigenius "Hebior Mammoth specimen" bearing tool/butcher marks, cast skeleton produced and distributed by Triebold Paleontology Incorporated

In approximate reverse chronological order:
  • Pedra Furada, Serra da Capivara National Park, in the state of Piauí, Brazil. Site with evidence of non-Clovis human remains, a rock painting rupestre art drawings from at least 12,000–6,000 BP. Hearth samples C-14 dates of 48–32,000 BP were reported in a Nature article (Guidon and Delibrias 1986). New hearth samples with ABOX dates of 54,000 BP were reported in the Quaternary Science Reviews.[92] Paleoindian components found here, have been challenged by American researchers such as Meltzer, Adovasio, and Dillehay.
  • The Monte Verde site in Chile, was occupied from 14,800 years BP,[93] with bones and other finds dating on average 12,500 yrs BP.[94] The earliest finds at the site were from between 32,840 and 33,900 years BP, but are controversial.[94]
  • The Bluefish Caves site in Yukon, Canada, contains bones with evidence of human cut-marks which demonstrates a human presence as early as 24,000 yr BP. The Bluefish caves are currently the oldest archaeological site in North America and offers evidence regarding the Beringia Standstill hypothesis, which states a genetically isolated human population remained in the area during the last glacial maximum and then traveled within North America and South America after the glaciers receded.[95]
  • Lagoa Santa, Minas Gerais, Brazil, is erroneously asserted to be Clovis age or even possibly Pre-Clovis in age. The recent discussion of this site (specifically Lapa Vermelha IV) and the Luzia skull, reportedly 11,500 years old by Neves and Hubb, makes it clear that this date is a chronological date in years Before Present and not a raw radiocarbon date[96] in eastern Brazil. Clovis sites mostly date between 11,500 and 11,000 radiocarbon years which means 13,000 years before present at a minimum. "Luzia" is at least 1,000 years younger than Clovis and Lapa Vermelha IV should not be considered a Pre-Clovis site.
  • Cueva del Milodón, in Patagonian Chile[97] dates at least as early as 10,500 BP. This is a site found particularly early in the New World hunt for Early Man, circa 1896, and needs additional basic research, but 10,500 B.P. would be 1,500 years younger than Clovis, or if the dating is 10,500 RCYBP, it would still be roughly 500–700 years younger than Clovis. In either case this should not be considered a Pre-Clovis site.
  • Cueva Fell[98] and Pali Aike Crater sites in Patagonia, with hearths, stone tools and other elements of human habitation dating to at least as early as 11,000 BP.
  • The Big Eddy Site in southwestern Missouri contains several claimed pre-Clovis artifacts or geofacts. In situ artifacts have been found in this well-stratified site in association with charcoal. Five different samples have been AMS dated to between 11,300 and 12,675 BP (Before Present).[citation needed]
  • Taima Taima, Venezuela has cultural material very similar to Monte Verde II, dating to 12,000 years BP.[citation needed] Recovered artifacts of the El Jobo complex in direct association with the butchered remains of a juvenile mastodon. Radiocarbon dates on associated wood twigs indicate a minimum age of 13,000 years before the present for the mastodon kill, a dating significantly older than that of the Clovis complex in North America.[99]
  • A cut mastodon tusk found at Page-Ladson, Jefferson County, Florida on the Aucilla River has been dated to 12,300 years BP near a few in situ artifacts of similar age.[100]
  • The Schaefer and Hebior mammoth sites in Kenosha County, Wisconsin indicate exploitation of this animal by humans. The Schaefer Mammoth site has over 13 highly purified collagen AMS dates and 17 dates on associated wood, dating it to 12,300–12,500 radiocarbon years before the present. Hebior has two AMS dates in the same range. Both animals show conclusive butchering marks and associated non-diagnostic tools.[101]
  • A site in Walker, Minnesota with stone tools, alleged to be from 13,000 to 15,000 years old based on surrounding geology, was discovered in 2006.[102] However, further examination suggests that the site does not represent a human occupation.[103]
  • In a 2011 article[10] in Science, Waters et al. 2011 describe an assemblage of 15,528 lithic artifacts from the Debra L. Friedkin site west of Salado, Texas. These artifacts (including 56 tools, 2,268 macrodebitage and 13,204 microdebitage) define the Buttermilk Creek Complex formation, which stratigraphically underlies a Clovis assemblage. While carbon dating could not be used to directly date the artifacts, 49 samples from the 20 cm Buttermilk floodplain sedimentary clay layer in which the artifacts were embedded were dated using optically stimulated luminescence (OSL). Eighteen OSL ages, ranging from 14,000 to 17,500 ka were obtained from this layer. The authors report "the most conservative estimate" of the age of the Buttermilk clays range from 13,200 to 15,500 ka, based on the minimum age represented by each of the 18 OSL ages.
  • Human coprolites have been found in Paisley Caves in Oregon, carbon dated at 14,300 years ago. Genetic analysis revealed that the coprolites contained mtDNA haplogroups A2 and B2, two of the five major Native American mtDNA haplogroups.[104][105]
  • The Mud Lake site, in Kenosha County, Wisconsin consists of the foreleg of a juvenile mammoth recovered in the 1930s. Over 100 stone tool butchering marks are found on the bones. Several purified collagen AMS dates show the animal to be 13,450 RCYBP with a range of plus or minus 1,500 RCYBP variance.[106]
  • Meadowcroft Rockshelter in southwestern Pennsylvania, excavated 1973–78, with evidence of occupancy dating back from 16,000 to 19,000 years ago.[107]
  • Cactus Hill in southern Virginia, with artifacts such as unfluted bifacial stone tools with dates ranging from c. 15,000 to 17,000 years ago.[108]
  • Sixty-eight stone and bone tools discovered in an orchard in East Wenatchee, Washington in 1987, excavated in 1988 and 1990. Five of the Clovis points are on display at the Wenatchee Valley Museum & Cultural Center.

Graphene sheets allow for very-low-cost diagnostic devices

March 20, 2017
Original link:  http://www.kurzweilai.net/graphene-sheets-allow-for-very-low-cost-diagnostic-devices
A new, very-low-cost diagnostic method. Mild heating of graphene oxide sheets makes it possible to bond particular compounds (blue, orange, purple) to the sheets’ surface, a new study shows. These compounds in turn select and bond with specific molecules of interest, including DNA and proteins, or even whole cells. In this image, the treated graphene oxide on the right has oxygen molecules (red) clustered together, making it nearly twice as efficient at capturing cells (green) as the material on the left. (credit:  the researchers)

A new method developed at MIT and National Chiao Tung University, based on specially treated sheets of graphene oxide, could make it possible to capture and analyze individual cells from a small sample of blood. It could potentially lead to very-low-cost diagnostic devices (less than $5 a piece) that are mass-producible and could be used almost anywhere for point-of-care testing, especially in resource-constrained settings.

A single cell can contain a wealth of information about the health of an individual. The new system could ultimately lead to a variety of simple devices that could perform a variety of sensitive diagnostic tests, even in places far from typical medical facilities, for cancer screening or treatment follow-up, for example.

How to capture DNA, proteins, or even whole cells for analysis

The material (graphene oxide, or GO) used in this research is an oxidized version of the two-dimensional form of pure carbon known as graphene. The key to the new process is heating the graphene oxide at relatively mild temperatures.

This low-temperature annealing, as it is known, makes it possible to bond particular compounds to the material’s surface that can be used to capture molecules of diagnostic interest.

Schematic showing oxygen clustering, resulting in improved ability to recognize foreign molecules (credit: Neelkanth M. Bardhan et al./ACS Nano)

The heating process changes the material’s surface properties, causing oxygen atoms to cluster together, leaving spaces of bare graphene between them. This leaves room to attach other chemicals to the surface, which can be used to select and bond with specific molecules of interest, including DNA and proteins, or even whole cells. Once captured, those molecules or cells can then be subjected to a variety of tests.*

Nanobodies

The new research demonstrates how that basic process could potentially enable a suite of low-cost diagnostic systems.

For this proof-of-concept test, the team used molecules that can quickly and efficiently capture specific immune cells that are markers for certain cancers. They were able to demonstrate that their treated graphene oxide surfaces were almost twice as effective at capturing such cells from whole blood, compared to devices fabricated using ordinary, untreated graphene oxide.

They did this by enzymatically coating the treated graphene oxide surface with peptides called “nanobodies” — subunits of antibodies, which can be cheaply and easily produced in large quantities in bioreactors and are highly selective for particular biomolecules.**

The new process allows for rapid capture and assessment of cells or biomolecules within about 10 minutes and without the need for refrigeration of samples or incubators for precise temperature control. And the whole system is compatible with existing large-scale manufacturing methods.

The researchers believe many different tests could be incorporated on a single device, all of which could be placed on a small glass slide like those used for microscopy. The basic processing method could also make possible a wide variety of other applications, including solar cells and light-emitting devices.

The findings are reported in the journal ACS Nano. Authors include Angela Belcher, the James Mason Crafts Professor in biological engineering and materials science and engineering at MIT and a member of the Koch Institute for Integrative Cancer Research; Jeffrey Grossman, the Morton and Claire Goulder and Family Professor in Environmental Systems at MIT; Hidde L. Ploegh, a professor of biology and member of the Whitehead Institute for Biomedical Research; Guan-Yu Chen, an assistant professor in biomedical engineering at National Chiao Tung University in Taiwan; and Zeyang Li, a doctoral student at the Whitehead Institute.

“Efficiency is especially important if you’re trying to detect a rare event,” Belcher says. “The goal of this was to show a high efficiency of capture.” The next step after this basic proof of concept, she says, is to try to make a working detector for a specific disease model.

The work was supported by the Army Research Office Institute for Collaborative Biotechnologies and MIT’s Tata Center and Solar Frontiers Center.

* Other researchers have been trying to develop diagnostic systems using a graphene oxide substrate to capture specific cells or molecules, but these approaches used just the raw, untreated material. Despite a decade of research, other attempts to improve such devices’ efficiency have relied on external modifications, such as surface patterning through lithographic fabrication techniques, or adding microfluidic channels, which add to the cost and complexity. Those methods for treating graphene oxide for this purpose require high-temperature treatments or the use of harsh chemicals; the new system, which the group has patented, requires no chemical pretreatment and an annealing temperature of just 50 to 80 degrees Celsius (122 to 176 F).

** The researchers found that increasing the annealing time steadily increased the efficiency of cell capture: After nine days of annealing, the efficiency of capturing cells from whole blood went from 54 percent, for untreated graphene oxide, to 92 percent for the treated material. The team then performed molecular dynamics simulations to understand the fundamental changes in the reactivity of the graphene oxide base material. The simulation results, which the team also verified experimentally, suggested that upon annealing, the relative fraction of one type of oxygen (carbonyl) increases at the expense of the other types of oxygen functional groups (epoxy and hydroxyl) as a result of the oxygen clustering. This change makes the material more reactive, which explains the higher density of cell capture agents and increased efficiency of cell capture.



Abstract of Enhanced Cell Capture on Functionalized Graphene Oxide Nanosheets through Oxygen Clustering

With the global rise in incidence of cancer and infectious diseases, there is a need for the development of techniques to diagnose, treat, and monitor these conditions. The ability to efficiently capture and isolate cells and other biomolecules from peripheral whole blood for downstream analyses is a necessary requirement. Graphene oxide (GO) is an attractive template nanomaterial for such biosensing applications. Favorable properties include its two-dimensional architecture and wide range of functionalization chemistries, offering significant potential to tailor affinity toward aromatic functional groups expressed in biomolecules of interest. However, a limitation of current techniques is that as-synthesized GO nanosheets are used directly in sensing applications, and the benefits of their structural modification on the device performance have remained unexplored. Here, we report a microfluidic-free, sensitive, planar device on treated GO substrates to enable quick and efficient capture of Class-II MHC-positive cells from murine whole blood. We achieve this by using a mild thermal annealing treatment on the GO substrates, which drives a phase transformation through oxygen clustering. Using a combination of experimental observations and MD simulations, we demonstrate that this process leads to improved reactivity and density of functionalization of cell capture agents, resulting in an enhanced cell capture efficiency of 92 ± 7% at room temperature, almost double the efficiency afforded by devices made using as-synthesized GO (54 ± 3%). Our work highlights a scalable, cost-effective, general approach to improve the functionalization of GO, which creates diverse opportunities for various next-generation device applications.

Introduction to genetics

From Wikipedia, the free encyclopedia

Genetics is the study of heredity and variations. Heredity and variations are controlled by genes—what they are, what they do, and how they work. Genes inside the nucleus of a cell are strung together in such a way that the sequence carries information: that information determines how living organisms inherit various features (phenotypic traits). For example, offspring produced by sexual reproduction usually look similar to each of their parents because they have inherited some of each of their parents' genes. Genetics identifies which features are inherited, and explains how these features pass from generation to generation. In addition to inheritance, genetics studies how genes are turned on and off to control what substances are made in a cell—gene expression; and how a cell divides—mitosis or meiosis.

Some phenotypic traits can be seen, such as eye color while others can only be detected, such as blood type or intelligence. Traits determined by genes can be modified by the animal's surroundings (environment): for example, the general design of a tiger's stripes is inherited, but the specific stripe pattern is determined by the tiger's surroundings. Another example is a person's height: it is determined by both genetics and nutrition.

Chromosomes are tiny packages which contain one DNA molecule and its associated proteins. Humans have 46 chromosomes (23 pairs). This number varies between species—for example, many primates have 24 pairs. Meiosis creates special cells, sperm in males and eggs in females, which only have 23 chromosomes. These two cells merge into one during the fertilization stage of sexual reproduction, creating a zygote. In a zygote, a nucleic acid double helix divides, with each single helix occupying one of the daughter cells, resulting in half the normal number of genes. By the time the zygote divides again, genetic recombination has created a new embryo with 23 pairs of chromosomes, half from each parent. Mating and resultant mate choice result in sexual selection. In normal cell division (mitosis) is possible when the double helix separates, and a complement of each separated half is made, resulting in two identical double helices in one cell, with each occupying one of the two new daughter cells created when the cell divides.

Chromosomes all contain DNA made up of four nucleotides, abbreviated C (cytosine), G (guanine), A (adenine), or T (thymine), which line up in a particular sequence and make a long string. There are two strings of nucleotides coiled around one another in each chromosome: a double helix. C on one string is always opposite from G on the other string; A is always opposite T. There are about 3.2 billion nucleotide pairs on all the human chromosomes: this is the human genome. The order of the nucleotides carries genetic information, whose rules are defined by the genetic code, similar to how the order of letters on a page of text carries information. Three nucleotides in a row—a triplet—carry one unit of information: a codon.

The genetic code not only controls inheritance: it also controls gene expression, which occurs when a portion of the double helix is uncoiled, exposing a series of the nucleotides, which are within the interior of the DNA. This series of exposed triplets (codons) carries the information to allow machinery in the cell to "read" the codons on the exposed DNA, which results in the making of RNA molecules. RNA in turn makes either amino acids or microRNA, which are responsible for all of the structure and function of a living organism; i.e. they determine all the features of the cell and thus the entire individual. Closing the uncoiled segment turns off the gene.

Heritability means the information in a given gene is not always exactly the same in every individual in that species, so the same gene in different individuals does not give exactly the same instructions. Each unique form of a single gene is called an allele; different forms are collectively called polymorphisms. As an example, one allele for the gene for hair color and skin cell pigmentation could instruct the body to produce black pigment, producing black hair and pigmented skin; while a different allele of the same gene in a different individual could give garbled instructions that would result in a failure to produce any pigment, giving white hair and no pigmented skin: albinismMutations are random changes in genes creating new alleles, which in turn produce new traits, which could help, harm, or have no new effect on the individual's likelihood of survival; thus, mutations are the basis for evolution.

Inheritance in biology

Genes and inheritance


A section of DNA; the sequence of the plate-like units (nucleotides) in the center carries information.
Red hair is a recessive trait.

Genes are pieces of DNA that contain information for synthesis of ribonucleic acids (RNAs) or polypeptides. Genes are inherited as units, with two parents dividing out copies of their genes to their offspring. This process can be compared with mixing two hands of cards, shuffling them, and then dealing them out again. Humans have two copies of each of their genes, and make copies that are found in eggs or sperm—but they only include one copy of each type of gene. An egg and sperm join to form a complete set of genes. The eventually resulting offspring has the same number of genes as their parents, but for any gene one of their two copies comes from their father, and one from their mother.[1]

The effects of this mixing depend on the types (the alleles) of the gene. If the father has two copies of an allele for red hair, and the mother has two copies for brown hair, all their children get the two alleles that give different instructions, one for red hair and one for brown. The hair color of these children depends on how these alleles work together. If one allele dominates the instructions from another, it is called the dominant allele, and the allele that is overridden is called the recessive allele. In the case of a daughter with alleles for both red and brown hair, brown is dominant and she ends up with brown hair.[2]

Although the red color allele is still there in this brown-haired girl, it doesn't show. This is a difference between what you see on the surface (the traits of an organism, called its phenotype) and the genes within the organism (its genotype). In this example you can call the allele for brown "B" and the allele for red "b". (It is normal to write dominant alleles with capital letters and recessive ones with lower-case letters.) The brown hair daughter has the "brown hair phenotype" but her genotype is Bb, with one copy of the B allele, and one of the b allele.

Now imagine that this woman grows up and has children with a brown-haired man who also has a Bb genotype. Her eggs will be a mixture of two types, one sort containing the B allele, and one sort the b allele. Similarly, her partner will produce a mix of two types of sperm containing one or the other of these two alleles. When the transmitted genes are joined up in their offspring, these children have a chance of getting either brown or red hair, since they could get a genotype of BB = brown hair, Bb = brown hair or bb = red hair. In this generation, there is therefore a chance of the recessive allele showing itself in the phenotype of the children—some of them may have red hair like their grandfather.[2]

Many traits are inherited in a more complicated way than the example above. This can happen when there are several genes involved, each contributing a small part to the end result. Tall people tend to have tall children because their children get a package of many alleles that each contribute a bit to how much they grow. However, there are not clear groups of "short people" and "tall people", like there are groups of people with brown or red hair. This is because of the large number of genes involved; this makes the trait very variable and people are of many different heights.[3] Despite a common misconception, the green/blue eye traits are also inherited in this complex inheritance model.[4] Inheritance can also be complicated when the trait depends on interaction between genetics and environment. For example, malnutrition does not change traits like eye color, but can stunt growth.[5]

Inherited diseases

Some diseases are hereditary and run in families; others, such as infectious diseases, are caused by the environment. Other diseases come from a combination of genes and the environment.[6] Genetic disorders are diseases that are caused by a single allele of a gene and are inherited in families. These include Huntington's disease, Cystic fibrosis or Duchenne muscular dystrophy. Cystic fibrosis, for example, is caused by mutations in a single gene called CFTR and is inherited as a recessive trait.[7]

Other diseases are influenced by genetics, but the genes a person gets from their parents only change their risk of getting a disease. Most of these diseases are inherited in a complex way, with either multiple genes involved, or coming from both genes and the environment. As an example, the risk of breast cancer is 50 times higher in the families most at risk, compared to the families least at risk. This variation is probably due to a large number of alleles, each changing the risk a little bit.[8] Several of the genes have been identified, such as BRCA1 and BRCA2, but not all of them. However, although some of the risk is genetic, the risk of this cancer is also increased by being overweight, drinking a lot of alcohol and not exercising.[9] A woman's risk of breast cancer therefore comes from a large number of alleles interacting with her environment, so it is very hard to predict.

How genes work

Genes make proteins

The function of genes is to provide the information needed to make molecules called proteins in cells.[1] Cells are the smallest independent parts of organisms: the human body contains about 100 trillion cells, while very small organisms like bacteria are just one single cell. A cell is like a miniature and very complex factory that can make all the parts needed to produce a copy of itself, which happens when cells divide. There is a simple division of labor in cells—genes give instructions and proteins carry out these instructions, tasks like building a new copy of a cell, or repairing damage.[10] Each type of protein is a specialist that only does one job, so if a cell needs to do something new, it must make a new protein to do this job. Similarly, if a cell needs to do something faster or slower than before, it makes more or less of the protein responsible. Genes tell cells what to do by telling them which proteins to make and in what amounts.

Genes are expressed by being transcribed into RNA, and this RNA then translated into protein.

Proteins are made of a chain of 20 different types of amino acid molecules. This chain folds up into a compact shape, rather like an untidy ball of string. The shape of the protein is determined by the sequence of amino acids along its chain and it is this shape that, in turn, determines what the protein does.[10] For example, some proteins have parts of their surface that perfectly match the shape of another molecule, allowing the protein to bind to this molecule very tightly. Other proteins are enzymes, which are like tiny machines that alter other molecules.[11]

The information in DNA is held in the sequence of the repeating units along the DNA chain.[12] These units are four types of nucleotides (A,T,G and C) and the sequence of nucleotides stores information in an alphabet called the genetic code. When a gene is read by a cell the DNA sequence is copied into a very similar molecule called RNA (this process is called transcription). Transcription is controlled by other DNA sequences (such as promoters), which show a cell where genes are, and control how often they are copied. The RNA copy made from a gene is then fed through a structure called a ribosome, which translates the sequence of nucleotides in the RNA into the correct sequence of amino acids and joins these amino acids together to make a complete protein chain. The new protein then folds up into its active form. The process of moving information from the language of RNA into the language of amino acids is called translation.[13]
 
DNA replication. DNA is unwound and nucleotides are matched to make two new strands.

If the sequence of the nucleotides in a gene changes, the sequence of the amino acids in the protein it produces may also change—if part of a gene is deleted, the protein produced is shorter and may not work any more.[10] This is the reason why different alleles of a gene can have different effects in an organism. As an example, hair color depends on how much of a dark substance called melanin is put into the hair as it grows. If a person has a normal set of the genes involved in making melanin, they make all the proteins needed and they grow dark hair. However, if the alleles for a particular protein have different sequences and produce proteins that can't do their jobs, no melanin is produced and the person has white skin and hair (albinism).[14]

Genes are copied

Genes are copied each time a cell divides into two new cells. The process that copies DNA is called DNA replication.[12] It is through a similar process that a child inherits genes from its parents, when a copy from the mother is mixed with a copy from the father.
DNA can be copied very easily and accurately because each piece of DNA can direct the creation of a new copy of its information. This is because DNA is made of two strands that pair together like the two sides of a zipper. The nucleotides are in the center, like the teeth in the zipper, and pair up to hold the two strands together. Importantly, the four different sorts of nucleotides are different shapes, so for the strands to close up properly, an A nucleotide must go opposite a T nucleotide, and a G opposite a C. This exact pairing is called base pairing.[12]

When DNA is copied, the two strands of the old DNA are pulled apart by enzymes; then they pair up with new nucleotides and then close. This produces two new pieces of DNA, each containing one strand from the old DNA and one newly made strand. This process is not predictably perfect as proteins attach to a nucleotide while they are building and cause a change in the sequence of that gene. These changes in DNA sequence are called mutations.[15] Mutations produce new alleles of genes. Sometimes these changes stop the functioning of that gene or make it serve another advantageous function, such as the melanin genes discussed above. These mutations and their effects on the traits of organisms are one of the causes of evolution.[16]

Genes and evolution

Mice with different coat colors

A population of organisms evolves when an inherited trait becomes more common or less common over time.[16] For instance, all the mice living on an island would be a single population of mice: some with white fur, some gray. If over generations, white mice became more frequent and gray mice less frequent, then the color of the fur in this population of mice would be evolving. In terms of genetics, this is called an increase in allele frequency.

Alleles become more or less common either by chance in a process called genetic drift, or by natural selection.[17] In natural selection, if an allele makes it more likely for an organism to survive and reproduce, then over time this allele becomes more common. But if an allele is harmful, natural selection makes it less common. In the above example, if the island were getting colder each year and snow became present for much of the time, then the allele for white fur would favor survival, since predators would be less likely to see them against the snow, and more likely to see the gray mice. Over time white mice would become more and more frequent, while gray mice less and less.

Mutations create new alleles. These alleles have new DNA sequences and can produce proteins with new properties.[18] So if an island was populated entirely by black mice, mutations could happen creating alleles for white fur. The combination of mutations creating new alleles at random, and natural selection picking out those that are useful, causes adaptation. This is when organisms change in ways that help them to survive and reproduce. Many such changes, studied in evolutionary developmental biology, affect the way the embryo develops into an adult body.

Genetic engineering

Since traits come from the genes in a cell, putting a new piece of DNA into a cell can produce a new trait. This is how genetic engineering works. For example, rice can be given genes from a maize and a soil bacteria so the rice produces beta-carotene, which the body converts to Vitamin A.[19] This can help children suffering from Vitamin A deficiency. Another gene being put into some crops comes from the bacterium Bacillus thuringiensis; the gene makes a protein that is an insecticide. The insecticide kills insects that eat the plants, but is harmless to people.[20] In these plants, the new genes are put into the plant before it is grown, so the genes are in every part of the plant, including its seeds.[21] The plant's offspring inherit the new genes, which has led to concern about the spread of new traits into wild plants.[22]
The kind of technology used in genetic engineering is also being developed to treat people with genetic disorders in an experimental medical technique called gene therapy.[23] However, here the new gene is put in after the person has grown up and become ill, so any new gene is not inherited by their children. Gene therapy works by trying to replace the allele that causes the disease with an allele that works properly.

Infrared-light-based Wi-Fi network is 100 times faster

March 22, 2017
Original link:  http://www.kurzweilai.net/infrared-light-based-wi-fi-network-is-100-times-faster
Schematic of a beam of white light being dispersed by a prism into different wavelengths, similar in prinicple to how a new near-infrared WiFi system works (credit: Lucas V. Barbosa/CC)

A new infrared-light WiFi network can provide more than 40 gigabits per second (Gbps) for each user* — about 100 times faster than current WiFi systems — say researchers at Eindhoven University of Technology (TU/e) in the Netherlands.

The TU/e WiFi design was inspired by experimental systems using ceiling LED lights (such as Oregon State University’s experimental WiFiFO, or WiFi Free space Optic, system), which can increase the total per-user speed of WiFi systems and extend the range to multiple rooms, while avoiding interference from neighboring WiFi systems. (However, WiFiFo is limited to 100 Mbps.)

Experimental Oregon State University system uses LED lighting to boost the bandwidth of Wi-Fi systems and extend range (credit: Thinh Nguyen/Oregon State University)

Near-infrared light

Instead of visible light, the TU/e system uses invisible near-infrared light.** Supplied by a fiber optic cable, a few central “light antennas” (mounted on the ceiling, for instance) each use a pair of ”passive diffraction gratings” that radiate light rays of different wavelengths at different angles.

That allows for directing the light beams to specific users. The network tracks the precise location of every wireless device, using a radio signal transmitted in the return direction.***

The TU/e system uses infrared light with a wavelength of 1500 nanometers (a frequency of 200 terahertz, or 40,000 times higher than 5GHz), allowing for significantly increased capacity. The system has so far used the light rays only for downloading; uploads are still done using WiFi radio signals, since much less capacity is usually needed for uploading.

The researchers expect it will take five years or more for the new technology to be commercially available. The first devices to be connected will likely be high-data devices like video monitors, laptops, and tablets.

* That speed is 67 times higher than the current 802.11n WiFi system’s max theoretical speed of 600Mbps capacity — which has to be shared between users, so the ratio is actually about 100 times, according to TU/e researchers. That speed is also 16 times higher than the 2.5 Gbps performance with the best (802.11ac) Wi-Fi system — which also has to be shared (so actually lower) — and in addition, uses the 5GHz wireless band, which has limited range. “The theoretical max speed of 802.11ac is eight 160MHz 256-QAM channels, each of which are capable of 866.7Mbps, for a total of 6,933Mbps, or just shy of 7Gbps,” notes Extreme Tech. “In the real world, thanks to channel contention, you probably won’t get more than two or three 160MHz channels, so the max speed comes down to somewhere between 1.7Gbps and 2.5Gbps. Compare this with 802.11n’s max theoretical speed, which is 600Mbps.”

** The TU/e system was designed by Joanne Oh as a doctoral thesis and part of the wider BROWSE project headed up by professor of broadband communication technology Ton Koonen, with funding from the European Research Council, under the auspices of the noted TU/e Institute for Photonic Integration.


*** According to TU/e researchers, a few other groups are investigating network concepts in which infrared-light rays are directed using movable mirrors. The disadvantage here is that this requires active control of the mirrors and therefore energy, and each mirror is only capable of handling one ray of light at a time. The grating used the and Oh can cope with many rays of light and, therefore, devices at the same time.

Functional programming

From Wikipedia, the free encyclopedia https://en.wikipedia.org/wiki/Functional_programming In computer sc...