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I know that when two bodies of different temperature are kept in contact "heat" flows from hotter body to colder. But how did anyone know that it is the "hotness" that flows, one could have said that the "coldness" flows from colder body to hotter one. Why was heat given a preference as both cases were equally possible.

I think that the theory that hotness flows from one body to another came long before the kinetic energy theory of energy transfer as heat. Also the caloric theory was given long before kinetic energy theory. In a way everyone knew that it was heat that is flowing and coldness is absence of heat. But how did they know it?

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    $\begingroup$ Quite possibly in part because up until the invention of various engines in the 19th century, there was no way to "create" cold while it was dead obvious that, e.g., wood is consumed by fire as it generates heat. The wood was as "cold" as the local environment until burned. $\endgroup$ – Carl Witthoft Dec 10 '19 at 13:50
  • $\begingroup$ In addition to the references given in the answers: if I remember right, some of the long history of this topic is told in Jennifer Coopersmith, Energy, the Subtle Concept: The discovery of Feynman's blocks from Leibniz to Einstein (Oxford University Press 2010, revised edition 2015). $\endgroup$ – Calum Gilhooley Dec 14 '19 at 23:52
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In a way everyone knew that it was heat that is flowing and coldness is absence of heat. But how did they know it?

The answer, quite simply, is that they didn't know it. Coldness was frequently measured in degrees just as heat was, and terms like degrees of frost were in common use even into the early 20th century. Alternative temperature scales like the Delisle scale and the original Celsius scale that increased with degrees of cold were widely recognized historically.

In the book Inventing Temperature, Hasok Chang includes an in-depth discussion of historical theories of cold, which the following summary is derived from. Chang begins (p. 160):

Practical thermometry achieved a good deal of reliability and precision before people could say with any confidence what it was that thermometers measured. A curious fact in the history of meteorology gives us a glimpse into that situation. The common attribution of the centigrade thermometer to the Swedish astronomer Anders Celsius (1701-1744) is correct enough, but his scale had the boiling point of water as 0° and the freezing point as 100°. In fact, Celsius was not alone in adopting such an "upside-down" thermometric scale. [...] These "upside-down" scales were in serious scientific use up to the middle of the eighteenth century.

Chang goes on to give plenty of examples of such scales of "coldness," tracing the history of the concept over time (p. 162).

There have been a number of perfectly capable philosophers and scientists through the ages who regarded cold as real as heat--starting with Aristotle, who took cold and hot as opposite qualities on an equal footing, as two of the four fundamental qualities in the terrestrial world. [...] Although many of [the mechanical philosophers of the seventeenth century] subscribed to theories that understood heat as motion and cold as the lack of it, the mechanical philosophy did not rule out giving equal ontological status to heat and cold.

Francis Bacon viewed cold as a type of contractive motion, the opposite of the expansive motion of heat. Robert Boyle tried to rule out the reality of positive cold, but admitted he couldn't do it conclusively. Pierre Gassendi postulated "frigorific atoms" that were the equivalent of the "calorific atoms" that supposedly caused heating.

Thomas Thomson (1773-1852), an early historian of chemistry, claimed that the general opinion of philosophers (i.e., scientists) in the early eighteenth century was that cold was a "positive something, of a peculiar body endowed with specific qualities. [...] According to [these philosophers], cold is a substance of a saline nature, very much resembling nitre, constantly floating in the air, and wafted about by the wind in very minute corpuscles, to which they gave the name of frigorific particles."

Even in the late 1700s, this question had not been settled, as the Encyclopaedia Britannica reported in 1778 that there was no consensus on this question, and came down on the side of the existence of cold as a separate force/entity of some sort. Experiments in the late 1700s and early 1800s seemed to confirm the existence of independent cold of some sort. It would be a bit involved to try to describe these here, but suffice it to say that there was considerable evidence marshaled by some scientists even into the 1800s for the concept of positive cold. One of the last prominent theories of this type was promoted by Count Rumford (1753-1814), who argued for a type of "frigorific radiation" that was a kind of analogue to radiant heat.

In the end, Chang argues that positive cold didn't go away because it was conclusively debunked at the time, but rather because the caloric theory of heat became so systematized and clearly articulated that it made it difficult to retain a place for positive cold within it.

As for the reason why "upside-down" thermometers gradually fell into disuse even before this time, there's no clear rationale given in historical treatises. But one might theorize that the fact that thermometers had scales with a rising expanding liquid might naturally tend toward having a scale marked to indicate the increasing volume by increasing numbers. Again, note that this trend began likely as a matter of computational and theoretical convenience before any consensus had been reached on whether or not cold existed as an independent entity. And, as pointed out in a comment, it is much easier to practically measure the effects of added heat, but much more difficult to create "added cold." Scientists certainly tried to do the latter too, but it's likely the bias of experimentation involving heat sources led to the caloric theory focusing on heat rather than cold, which ultimately led to the demise of the notion of independent coldness.

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It makes no difference for either measuring temperature, or calculating heat flow, what flows there, if anything. So experimental basis for measuring temperature was established long before the nature of what was measured became clear. As Fowler writes in Early Attempts to Understand Heat:

"By the late 1700’s, the experiments of Fahrenheit, Black and others had established a systematic, quantitative way of measuring temperatures, heat flows and heat capacities — but this didn’t really throw any new light on just what was flowing".

The situation was somewhat similar to electricity, which was also analogized to fluid(s) at the time, but there were competing theories with one and two fluids. In contrast, there never was a two-fluid theory of heat, or a theory with a cold fluid. Both Stahl's phlogiston (1703) and Lavoisier's caloric (1787) were carrying heat, not cold, see What are the major flaws of the “caloric” theory of heat? Indeed, when heated materials usually expand, which suggests something being added. Fowler explains more of the intuitive motivation in Lavoiser's case:

"However, in contrast to electricity, which had no noticeable effect on the appearance of a charged object, when heat was added to a solid things changed considerably. First the material expanded, then it changed to a liquid and finally to a gas, if sufficient heat could be delivered. Further heating expanded the gas, or increased its pressure if it was held in a fixed container.

To interpret this sequence of events in terms of a caloric fluid being fed into the material, one could imagine the fluid flowing between the atoms of the solid and lessening their attraction for each other, until the solid melted into a liquid, whereupon the caloric continued to accumulate around the atoms until they were pushed apart into a gas. It was thought that in the gas each atom or molecule was surrounded by a ball of caloric, like a springy ball of wool, and these balls were packed in a container like oranges in a crate, except that the caloric balls could expand indefinitely as heat was poured in."

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