A book on the early history of mankind i have been reading named Mesopotamia the first civilisation somewhere around 3500 b.c.
Yet it also tells of a city, Çatal hüyük, with a trade network and religious shrines dating to about 6000 b.c. with an estimated population of 6000.
What Çatal hüyük missing to be called a civilization?
There isn't a fixed or widely accepted definition. In the context of ancient societies, the closest thing is V. Gordon Childe's ten criteria:
Çatalhöyük was very large and impressive settlement for its time, but it doesn't meet very many of these. The population density could probably be described as urban but its total population (3,000–8,000) hardly counts as a city. There is little evidence for craft specialisation at all, never mind full-time specialists; no evidence of an elite or class stratification of any kind; no public buildings; no writing; and no state.
I should stress though that that's very much a historical definition and today few anthropologists or archaeologists would consider the word civilisation to have a technical definition. Although it's probably the most consistent and useful definition anyone's ever come up with, Childe's 'civilisation' doesn't really hold up as a properly scientific type If it was, he would have defined his criteria based on some theoretical principle and then applied it to every society equally in order to classify them as 'civilised' or 'uncivilised'. In reality, he began with the preconception that the early urban societies of Mesopotamia were the first civilisation and created his list from the characteristics he could see there that distinguished them from their contemporaries. So when you're deciding if a society is a civilisation based on Childe's criteria, you're not really comparing them to an objective standard, you're comparing them to Bronze Age Mesopotamia. As a result societies which most people would think of as being equally accomplished as the Sumerians or Egyptians (e.g. Hawaii, Great Zimbabwe, the Xiongnu) fall short because their own historical trajectories didn't take them past arbitrary milestones like writing or "exact and predictive sciences".
Not to mention Childe's is only one of dozens and dozens of definitions of civilisation and it was never applied consistently even within the small world of Anglo-American archaeology. Many archaeologists before and since have understood the word civilisation in the loose, colloquial sense of "a sophisticated and accomplished society" and therefore applied it to everything from the Stone Age down in an attempt to add a bit of glamour to the collection of rock they've been studying for their entire career. As early as 1957 the anthropologist A. L. Kroeber made it clear that he didn't see a compelling reason to distinguish civilisations from any other culture:
There is a widespread usage of the term civilization as meaning advanced or literate or mainly urban culture. With this usage I do not quarrel, but I have tried to choose between the two near synonyms in such a way that the reader would realize in any given situation whether I meant the more general or the more slanted sense.
This is the approach I think most Anglo-American anthropologists and archaeologists today would agree with, because we've long since abandoned the framework of linear social evolution (where societies are seen to inevitably progress from barbarity to civilisation) that this exercise of classification comes from, and because of the unpleasant political implications of calling a culture (especially a living one) "un-civilised".
To complicate matters further, there are lots of completely different definitions floating about. Anthropologists and archaeologists, when they've used it, have tended to look at civilisation as a stage in the development of a society over time. Historians have a completely parallel use of the word civilisation as a concept grouping societies into large cultural blocs. Arthur Toynbee, for example, divided all of world history between just 26 major civilisations. This is the sense that's used in terms like 'Western civilisation', or in games by Sid Meier. Or it can just mean advancement and refinement in general ("we're a long way from civilisation", "this is a very civilised party"). Or be a synonym for culture ("French civilisation"). Classicists might prefer a definition closer to the original sense of the word civitas in Latin – a body of citizens. And I have no doubt that there a hundred other versions of the word in languages other than English.
In short, civilisation is slippery, poorly defined concept that has never really been rigorously applied to ancient societies. The closest thing to a working definition is one that distinguishes urban, state civilisations from smaller scale societies, which is probably what your book was evoking when it left Çatalhöyük out of the club. But the whole idea of classifying societies on the basis of their level of 'advancement' is one that never stood up as good science and is now decidedly outdated. If you want to call Çatalhöyük a civilisation, go for it. It doesn't mean much.
Edit: What's the book, by the way? I'm assuming since it has an up-to-date population estimate for Çatal it can't be that old.