Ideological assumptions are the foundations of the sciences as practiced. They are the bases of the often conflicting theories. The human sciences or social sciences are the most favourable environment for the genesis of ideological assumptions.

One of the best-known ideological assumptions is that the whole Bible's account of creation in Genesis is an unscientific myth. Another ideological assumption is that it had to be replaced by a single model of Darwinism that is a real science. In this controversy, both sides apply their faith in different assumptions.

In the other sciences, often two fierce camps can be distinguished in basic questions of anthropology, ancient history, Biblical studies, or linguistics. Usually one side condemns the theories of the other side as unscholarly, unscientific or ridiculous. The mere mention of these words is sometimes enough to get a final verdict; the advantages or the good logic in the opposing theory does not need to be examined scientifically. This is sometimes an empirical or political solution, and not related to real sciences except insofar as politics is always present in science in its funding and its governance.

A close-knit network of assumptions or axioms has been widely and internationally accepted in every science, as an inheritance from the previous centuries. It is frequently laden with its old racist or supremacist tone and prejudice, sometimes biases.

These axioms are now the cornerstones of the modern social sciences that cannot be revised, double-checked or disturbed, at least not without major career risk. Many of the old cornerstones of the classic philosophers have been omitted and Darwinism has became the strongest pillar of the system. Atheism has got a similar strong mandate, that makes any idea written by a religious scholar suspicious, funny, and unpublishable since its first appearance. Scientism itself, the idea that moral guidance can somehow arise from better understanding of nature and deeper application of mathematics, is present in many theories of human behavior - most notably in the one itself named "behaviorism."

Economics is infamous for accepting the current political economy as some kind of God-given law, and some economists even seek unification of economics with physics, as if the assumptions of both were somehow compatible and complementary. Most economists would acknowledge that at most economics is a rather flawed technology, and not science at all.

Some of the more widely debated "scientific" assumptions in the human sciences are listed here. In most journal papers and peer review processes, such assumptions would pass without comment, while challenges to it would be strongly challenged and investigated with great diligence. Each group of peers in each science tends to form a single epistemic community, at least insofar as they publish in the same journals.

Where recent evidence has cast doubt on the assumption, it is elaborated as a second sentence usually explaining away the evidence, or simply describing it as 'fake'. Where an article explains a given controversy more fully, that article will be one link in the text:

1) The history and sinking of a continent called Atlantis is a fiction invented by Plato. Since his works are purely spiritual and idealized, there is no reason to believe in his ridiculous theories. Atlantis must have been the exploded Greek island of Thera or Santorini.
2) The early human civilizations developed independently. They have never had a common cradle, and none of them has been devastated by a cataclysmic flood. In particular the Black Sea flood which turned it to salt did not happen close enough to the period of recorded history to in fact be the basis of the flood myth.
3) There were no pre-Columbian ethnic, cultural or linguistic ties between the opposite sides of the Atlantic and Pacific Oceans, except some migrations over a land bridge between Asia and Alaska. The theories of pre-Columbian transatlantic contacts are all unscientific. Technology to cross the Atlantic was not available to Vikings or Irish monks. Technology to cross the Pacific was not available in Micronesia.
4) America was discovered by Columbus in 1492 C.E., and earlier claims do not have archaeological support. L'Anse aux Meadows is a fake or more recent settlement.
5) The prehistoric Trojan War waged against Troy by the confederated Greeks belongs to the Greek mythology and not necessarily historic. Ruins of 'Troy' found in Turkey have been misinterpreted.
6) The Bible is not a reliable source for the historians and chronologists, because the numbers and regnal years of those Jewish records are literary devices that do not agree with the unbroken Assyrian eponym lists.
7) The ancestors of the Jews have never lived in Egypt, and the Exodus is a myth. The "standing" of the sun and the moon during Joshua's war does not have any scientific basis. The Babylonian captivity did not last for 70 years as the Jewish records claim.
8) Romulus and Remus were mythical persons. Rome was founded in 753 BCE.
9) The concept of God was created by Man, descendant of apelike animals. Man created god in his likeness, then claimed Man was in God's image to validate his violent dominion over other animals and the Earth in general.
10) Intelligent life does not exist in outer space, because no one has responded to our constant radio broadcasts and systematic signals addressed to them. Those who suggest humans aren't worth talking to, or are too stupid to understand the signals, or are being overly misanthropic or anti-humanist. Those who suggest the signals are being suppressed by authority are paranoid.
11) Should intelligent beings exist anywhere else, they would be unable to visit our planet, since it is scientifically impossible to have the energy and speed to reach Earth from the nearests stars. UFOs are not real.
12) A few millennia ago, most of our ancestors had the constant impulse to invent fictitious stories for their children about their historical experiences. If an account does not fit into our scholarly views, it must be a lie or falsehood. Myth usually has little or no basis in fact.
13) Mankind's myths and legends are literary products, with little or no historical value. They have been created by confused primitive minds, often under the influence of a hallucinogen. In other cases, they are products of the modern colonization. For example, the Cargo Cult with wishful waiting for another ship or airplane laden with goods.
14) The languages of each continent are isolated from each other, and a diffusion never took place. They developed independently, except the Arab, the Madagascan-Malay and Inuit languages. Beyond an indeterminate maximum distance, their apparent similarities are due to coincidence and do not deserve scientific attention. Even an 8% lexicostatistical correspondence of cognates could happen by pure chance.
15) Comparisons between languages (comparative linguistics) must be based on grammatical structure: morphology and syntax. Lexicostatistics is a relatively useless theory.
16) The Romance languages have evolved as provincial dialects of the Roman conquerors' corrupted Latin. Without the Roman Empire, they would not exist.
17) The classification of the languages is objective, scientific and possible. We do not have to worry about dialects and their past. They are only curiosities and not the key issue. They are not tied to ecology, but only to human culture, and thus when culture changes languages may die without ecological disaster. Bioregional democracy has no objective linguistic basis.
18) The Egyptian language is a clearly distinct African language. Any similarities between Egyptian and the European or other distant languages are coincidental, therefore the comparisons are useless.
19) The fictitious story of Robinson Crusoe is the first English novel, written by Defoe. It is based on the story of Alexander Selkirk. It is not a copy of an earlier story of another culture.
20) It is obvious that the Old English language was the direct ancestor of the Middle English. The latter developed from the Old English, a Germanic language, around the twelfth century. It has lost the 85% of its vocabulary since then. This dynamic change is a proof that quick revolutionary changes act in the linguistics, just like in Darwinism or in dialectical materialism.
21) The Roman legend of Lemuria or (continent of) Mu is false. No one lost continent near Asia was the root of all modern civilizations. The Rosetta Stone of the Pacific has no relation to the Greek alphabet - in particular, that alphabet is not a poem in the Mu language. The submerged temple near Okinawa is actually a natural rock formation.
22) Modern Western scientific method is superior as a means of inquiry. Its issues with ethics can be managed as a meta process without fundamentally altering any scientific practice or censoring any experimental reproduction data or conclusions.
23) Social sciences must emulate the methods of natural sciences in particular the acceptance of conclusions or predictions stated using only mathematics.
24) Modern sciences mostly originate in Ancient Greece or Rome, or the Renaissance period in Europe. Muslims did not found the social sciences.
25) Chinese scholars had little or no mathematics as such, and at best practiced a degraded pre-algebraic "folk mathematics."

Many of the above are considered the concern of history and thus some historical practice is assumed to be able to cast light on assumptions such as these. For matters of current concern, a forensic process may be applied. However it is surprisingly common for the outcome of either a historical or forensic process to be mistaken for a 'fact' in the sense of the scientific method, which is impossible even for a correct theory:

An explanation of 'why a plane crashed' or 'who killed Nicole Simpson' or 'whether the Shoah occurred' or 'whether the Ukranian famine was planned' simply cannot have the same objectivity as a falsifiable scientific hypothesis. At best, it is trust in human eyewitnesses, or in a forensic or judicial process, especially an adversarial process in which different points of view explicitly compete to convince judges, which actually determines which such explanation is accepted as truthful.

Concepts of truth and ideology are necessarily subjective when applied beyond the limited domains of aesthetics and simple moral reasoning. Within those domains, objectivity tends to be a matter of common human cognition (some say cognitive bias) and body types. For instance, those of us reading this are all animals, all feel pain, and are all subject to radiation poisoning, so we accept that nuclear weapons should not be used to resolve casual disputes between neighbors. These assumptions may be distincted as the human bodily assumptions.

Whether bodily assumptions are ideolgical is itself an ideological debate.