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During 2010, fossilised animal bones bearing marks from stone tools were found in the Lower Awash Valley in Ethiopia. Discovered by an international team led by Shannon McPherron, at 3.4 million years old they are the oldest evidence of stone tool use ever found anywhere in the world.

The oldest known stone tools have been excavated from several sites at Gona, Ethiopia, on the sediments of the paleo-Awash River, which serve to date them. All the tools come from the Busidama Formation, which lies above a disconformity, or missing layer, which would have been from 2.9 to 2.7 mya. The oldest sites containing tools are dated to 2.6–2.55 mya.One of the most striking circumstances about these sites is that they are from the Late Pliocene, where previous to their discovery tools were thought to have evolved only in the Pleistocene. Rogers and Semaw, excavators at the locality, point out that:

The excavators are confident that more tools will be found elsewhere from 2.9 mya. The species who made the Pliocene tools remains unknown. Fragments of Australopithecus garhi, Australopithecus aethiopicus and Homo, possibly Homo habilis, have been found in sites near the age of the oldest tools.

Innovation of the technique of smelting ore ended the Stone Age and began the Bronze Age. The first most significant metal manufactured was bronze, an alloy of copper and tin, each of which was smelted separately. The transition from the Stone Age to the Bronze Age was a period during which modern people could smelt copper, but did not yet manufacture bronze, a time known as the Copper Age, or more technically the Chalcolithic, "copper-stone" age. The Chalcolithic by convention is the initial period of the Bronze Age and is unquestionably part of the Age of Metals. The Bronze Age was followed by the Iron Age. During this entire time stone remained in use in parallel with the metals for some objects, including those also used in the Neolithic, such as stone pottery.

The transition out of the Stone Age occurred between 6000 BCE and 2500 BCE for much of humanity living in North Africa and Eurasia. The first evidence of human metallurgy dates to between the 5th and 6th millennium BCE in the archaeological sites of Majdanpek, Yarmovac and Pločnik (a copper axe from 5500 BCE belonging to the Vinca culture), though not conventionally considered part of the Chalcolithic or "Copper Age", this provides the earliest known example of copper metallurgy. and the Rudna Glava mine in Serbia. Ötzi the Iceman, a mummy from about 3300 BCE carried with him a copper axe and a flint knife.

In regions such as Subsaharan Africa, the Stone Age was followed directly by the Iron Age. The Middle East and southeastern Asian regions progressed past Stone Age technology around 6000 BCE. Europe, and the rest of Asia became post–Stone Age societies by about 4000 BCE. The proto-Inca cultures of South America continued at a Stone Age level until around 2000 BCE, when gold, copper and silver made their entrance, the rest following later. Australia remained in the Stone Age until the 17th century. Stone tool manufacture continued. In Europe and North America, millstones were in use until well into the 20th century, and still are in many parts of the world.

The terms was never meant to suggest that advancement and time periods in prehistory are only measured by the type of tool material, rather than, for example, social organization, food sources exploited, adaptation to climate, adoption of agriculture, cooking, settlement and religion. Like pottery, the typology of the stone tools combined with the relative sequence of the types in various regions provide a chronological framework for the evolution of man and society. They serve as diagnostics of date, rather than characterizing the people or the society.

Lithic analysis is a major and specialised form of archaeological investigation. It involves the measurement of the stone tools to determine their typology, function and the technology involved. It includes scientific study of the lithic reduction of the raw materials, examining how the artifacts were made. Much of this study takes place in the laboratory in the presence of various specialists. In experimental archaeology, researchers attempt to create replica tools, to understand how they were made. Flintknappers are craftsmen who use sharp tools to reduce flintstone to flint tool.

In addition to lithic analysis, the field prehistorian utilizes a wide range of techniques derived from multiple fields. The work of the archaeologist in determining the paleocontext and relative sequence of the layers is supplemented by the efforts of the geologic specialist in identifying layers of rock over geologic time, of the paleontological specialist in identifying bones and animals, of the palynologist in discovering and identifying plant species, of the physicist and chemist in laboratories determining dates by the carbon-14, potassium-argon and other methods. Study of the Stone Age has never been mainly about stone tools and archaeology, which are only one form of evidence. The chief focus has always been on the society and the physical people who belonged to it.

Useful as it has been, the concept of the Stone Age has its limitations. The date range of this period is ambiguous, disputed, and variable according to the region in question. While it is possible to speak of a general 'stone age' period for the whole of humanity, some groups never developed metal-smelting technology, so remained in a 'stone age' until they encountered technologically developed cultures. The term was innovated to describe the archaeological cultures of Europe. It may not always be the best in relation to regions such as some parts of the Indies and Oceania, where farmers or hunter-gatherers used stone for tools until European colonisation began.

The archaeologists of the late 19th and early 20th centuries CE, who adapted the three-age system to their ideas, hoped to combine cultural anthropology and archaeology in such a way that a specific contemporaneous tribe can be used to illustrate the way of life and beliefs of the people exercising a specific Stone-Age technology. As a description of people living today, the term stone age is controversial. The Association of Social Anthropologists discourages this use, asserting:

"To describe any living group as 'primitive' or 'Stone Age' inevitably implies that they are living representatives of some earlier stage of human development that the majority of humankind has left behind. For some, this could be a positive description, implying, for example, that such groups live in greater harmony with nature .... For others, ... 'primitive' is a negative characterisation. For them, 'primitive' denotes irrational use of resources and absence of the intellectual and moral standards of 'civilised' human societies.... From the standpoint of anthropological knowledge, both these views are equally one-sided and simplistic."

In the 1920s, South African archaeologists organizing the stone tool collections of that country observed that they did not fit the newly detailed Three-Age System. In the words of J. Desmond Clark,

"It was early realized that the threefold division of culture into Stone, Bronze and Iron Ages adopted in the nineteenth century for Europe had no validity in Africa outside the Nile valley."

Consequently they proposed a new system for Africa, the Three-stage System. Clark regarded the Three-age System as valid for North Africa; in sub-Saharan Africa, the Three-stage System was best. In practice, the failure of African archaeologists either to keep this distinction in mind, or to explain which one they mean, contributes to the considerable equivocation already present in the literature. There are in effect two Stone Ages, one part of the Three-age and the other constituting the Three-stage. They refer to one and the same artifacts and the same technologies, but vary by locality and time.

The Three-stage System was proposed in 1929 by Astley John Hilary Goodwin, a professional archaeologist, and Clarence van Riet Lowe, a civil engineer and amateur archaeologist, in an article titled "Stone Age Cultures of South Africa" in the journal Annals of the South African Museum. By then, the dates of the Early Stone Age, or Paleolithic, and Late Stone Age, or Neolithic (neo = new), were fairly solid and were regarded by Goodwin as absolute. He therefore proposed a relative chronology of periods with floating dates, to be called the Earlier and Later Stone Age. The Middle Stone Age would not change its name, but it would not mean Mesolithic.

The duo thus reinvented the Stone Age. In Sub-Saharan Africa, however, it was ended by the intrusion of the Iron Age from the north. The Neolithic and the Bronze Age never occurred. Moreover, the technologies included in those 'stages', as Goodwin called them, were not exactly the same. Since then, the original relative terms have become identified with the technologies of the Paleolithic and Mesolithic, so that they are no longer relative. Moreover, there has been a tendency to drop the comparative degree in favor of the positive: resulting in two sets of Early, Middle and Late Stone Ages of quite different content and chronologies.

By voluntary agreement, archaeologists respect the decisions of the Pan-African Congress of Prehistory, which meets every four years to resolve archaeological business brought before it. Delegates are actually international; the organization takes its name from the topic. Louis Leakey hosted the first one in Nairobi in 1947. It adopted Goodwin and Lowe's 3-stage system at that time, the stages to be called Early, Middle and Later.

The problem of the transitions in archaeology is a branch of the general philosophic continuity problem, which examines how discrete objects of any sort that are contiguous in any way can be presumed to have a relationship of any sort. In archaeology, the relationship is one of causality. If Period B can be presumed to descend from Period A, there must be a boundary between A and B, the A–B boundary. The problem is in the nature of this boundary. If there is no distinct boundary, then the population of A suddenly stopped using the customs characteristic of A and suddenly started using those of B, an unlikely scenario in the process of evolution. More realistically, a distinct border period, the A/B transition, existed, in which the customs of A were gradually dropped and those of B acquired. If transitions do not exist, then there is no proof of any continuity between A and B.

The Stone Age of Europe is characteristically in deficit of known transitions. The 19th and early 20th-century innovators of the modern three-age system recognized the problem of the initial transition, the "gap" between the Paleolithic and the Neolithic. Louis Leakey provided something of an answer by proving that man evolved in Africa. The Stone Age must have begun there to be carried repeatedly to Europe by migrant populations. The different phases of the Stone Age thus could appear there without transitions. The burden on African archaeologists became all the greater, because now they must find the missing transitions in Africa. The problem is difficult and ongoing.

After its adoption by the First Pan African Congress in 1947, the Three-Stage Chronology was amended by the Third Congress in 1955 to include a First Intermediate Period between Early and Middle, to encompass the Fauresmith and Sangoan technologies, and the Second Intermediate Period between Middle and Later, to encompass the Magosian technology and others. The chronologic basis for definition was entirely relative. With the arrival of scientific means of finding an absolute chronology, the two intermediates turned out to be will-of-the-wisps. They were in fact Middle and Lower Paleolithic. Fauresmith is now considered to be a facies of Acheulean, while Sangoan is a facies of Lupemban.[13] Magosian is "an artificial mix of two different periods."

Once seriously questioned, the intermediates did not wait for the next Pan African Congress two years hence, but were officially rejected in 1965 (again on an advisory basis) by Burg Wartenstein Conference #29, Systematic Investigation of the African Later Tertiary and Quaternary, a conference in anthropology held by the Wenner-Gren Foundation, at Burg Wartenstein Castle, which it then owned in Austria, attended by the same scholars that attended the Pan African Congress, including Louis Leakey and Mary Leakey, who was delivering a pilot presentation of her typological analysis of Early Stone Age tools, to be included in her 1971 contribution to Olduvai Gorge, "Excavations in Beds I and II, 1960–1963."

However, although the intermediate periods were gone, the search for the transitions continued.