Various contributors to the subreddit have written fairly extensively on Guns, Germs and Steel over the years, and to summarise: it isn't a very well-composed book from a historian's point of view:

https://www.reddit.com/r/AskHistorians/wiki/historians_views#wiki_historians.27_views_of_jared_diamond.27s_.22guns.2C_germs.2C_and_steel.22

The primary problem with it, which ultimately results in Diamond's thesis of environmental determinism, is that he begins with a conclusion and starts trying to find evidence that supports that conclusion while omitting that which does not.

With that in mind, I wouldn't be too surprised that its thesis is contradicted by another book, though I admit I have not read Why Nations Fail yet. Hopefully a more comprehensive comparison will be posted soon, but in the meantime, I hope the linked FAQ noting the controversies with Guns, Germs and Steel helps you understand the failings in the book and why it was contradicted.

Enough has been said about how Guns, Germs and Steel is criticized by many historians in previous posts, but to talk more specifically about the differences of Why Nations Fail and how it considers geography, it does so not as an independent variable like Jared Diamond does (i.e. the idea that rivers and mountain ranges dictate a society) but instead as a means to facilitating or hindering the growth of institutions (which can be completely independent of geographic constraints, or dependent on them).

One example of this sort of difference might be for instance Tokugawa Japan, examined in the context of a particular part of the daimyo-shogun relationship called the sankin kotai. The sankin kotai was a shogunate policy whereby every daimyo had to spend at least some of the year living in the capital of Edo as well as his main estate. This also meant that the daimyo would need to leave what amounted to hostages in the Shogun's main power base at all times.

This particular governmental institution was very creative from a geographic perspective: because the most potentially disloyal daimyo were given domains as far as possible from Edo, the long distances that they were forced to travel exhausted their economic resources which may have been spent on, for instance, raising more troops for a possible rebellion. In addition, the long paths that they would need to take to get to Edo facilitate road and infrastructure development as well as inns, taverns, towns along the route, which in turn opened up opportunities for merchants to have easier trade routes as well as providing lenders with the opportunity to develop business opportunities with the daimyo to help them finance their expensive journeys and obligations. All of these new institutions were developed as a result of the constraints of the sankin kotai and the long distances that needed to be travelled to meet these obligations. And this is the sort of impact that Acemoglu would attribute to geography, rather than the nature of Japanese geography leading to their particular societal characteristics.

There are many criticisms of Acemoglu's work to be sure, and I'm not making any judgement here, but this hopefully illustrates his argument vs. that of Jared Diamond.

To add to the other comment:

As one of the sub's resident anthropologists, Guns Germs and Steel ain't particularly strong from an anthropologist's point of view either. There are two main reasons. The first is that Diamond doesn't use theory in the way that we consider best practice. The other reason is because Diamond's theories are obsolete.

Anthropologists broadly use something called middle-range theory in our work. That's a fancy way of saying that our understanding of a culture operates on two levels.

One is the broader structural level. We're talking big systematic patterns that limit individual autonomy. This limitation doesn't necessarily happen by force. It can just be that people are exposed to information through their specific culture, and so the culture tends to replicate itself. That doesn't even necessarily have to be a bad thing. What matters is that individuals are operating in a manner consistent with a broader system, and the system can be analyzed on the scale of the society as a whole. This level of culture is understood through the use of theory. Theory, however, is fundamentally a descriptive model which we use to organize systems of information about a culture. Not a prescriptive equation that automatically generates the culture.

The second level is the individual level. While people are limited by their society, they also have some level of autonomy, and often interpret the society in which they operate. Anthropologists will study this level of culture mainly through ethnography and participant observation. To simplify the importance of this part, it's basically about showing respect for the people under study, and humility on the behalf of the researcher. Ultimately, that's just good science, too. Having some level of humility helps to undercut bias. Of course, we don't use the word "humility" per se, and there's all sorts of technical terms in research design to articulate the particulars. But "humility" is still more or less what we're getting at. In order to understand a culture, you must see it's components in action, and you must understand the human element which plays an active role in interpreting those elements.

Middle-range theory essentially integrates these two levels into one whole. Theory helps to structure information, while ethnography helps to keep theory accountable. Cultivating knowledge becomes less about finding the equation for success and applying it again and again. Rather, it's about developing the attunement necessary as a researcher to balance these two elements. Why is this so important? Well, there's an unpleasant history of anthropology being used as a vehicle for people in power to dictate what the culture of marginalized groups is, and that has been accomplished through the interpretation of marginalized groups through theory. So lots of people in anthropology are somewhat turned off by the "grand theory" approach that Jared Diamond utilizes. Yes, there's also a general dispute in the field over the role of "grand theory", and some people will be more comfortable with it than others. But Diamond's way of doing things isn't really in play as part of the dispute. Like, even the people who support "grand theory" are liable to feel that Diamond takes it too far.

So that's why Diamond's way of applying theory has issues. But as I said, there's more to it than just that. There's also the added problem that Diamond tends to theorize about culture using patterns of theorizing which are simply obsolete. We have a mounting pile of evidence to suggest that societies do not operate in a fashion consistent with the assumptions that Diamond bases his theories on. This is because Diamond fundamentally struggles to understand a lot of the more recent (say, last fifty years) developments in social theory.

I'll delve into this from my particular area of expertise. My specialization, back when I was still involved in Anthropology, was in complex systems theory. Basically, systems tend to operate in a type of equilibrium called a basin of attraction. These equilibria are massive, and they internally exhibit a form of behavior called "nonperiodic complexity" or "chaos", which is a fancy way of saying that they tend not to repeat a pattern the exact same way twice, and it's very difficult to predict how a pattern will change within cycles.

Chaos theory is the study of nonperiodic complexity. It's a fascinating field, but fascinating in a boring mathematical way. Sadly, most of the pop culture image of chaos theory is entirely flawed. And, needless to say, Ian Malcom in Jurassic Park provides an explanation which is, um, lacking. The man is an ignoramus. A devilishly handsome ignoramus. See, a butterfly in Tokyo cannot, in fact, be linked to a hurricane in New York. That's kinda the whole point of 'the butterfly effect', which sadly is one of those principles which goes undermined by having too cool a name. See, it's impossible to predict the specific results of a butterfly flapping its wings, but that doesn't matter, because individual states of a complex system are irrelevant. All that matters is the basin of attraction. It is extremely predictable that the pattern will remain within the basin of attraction. I might not be able to calculate the effect of a butterfly's wingbeat, but I can predict the likelihood of a hurricane hitting New York, which is pretty small. A single perturbation to starting conditions, say by the wingbeat of a butterfly, cannot change the dynamics to the basin of attraction. It takes a much larger perturbation to do so. Say, the planet's climate warming by several degrees (ahem, not to editorialize).

So what happens when a large perturbation happens? Well, complex systems can be conceptualized as fields of adjacent basins of attraction, kinda like the honeycomb of a bee hive. Complex systems tend to remain relatively stable even under the pressure of changing conditions, until conditions change too much. As they approach the edge of the range in which the attractor can remain stable, the system begins to gravitate towards the extremes of the attractor. Chaos tends to increase closer to the extremes. The system wildly oscillates between periods of extreme minimal activity and periods of extreme maximum activity. Volatility between the two extremes increases, creating a new layer of chaos, where the system oscillates so rapidly that extremes can emerge with little to no signal that they're coming. Eventually, the attractor is incapable of retaining its stability, and the entire system shifts catastrophically into a new basin of attraction, stabilizing around a new attractor.

So what does this have to do with Jared Diamond? Well he tends to think in a very categorical fashion. He sees one pattern of a system, and assumes that all societies succeed on the ability to replicate that pattern. But societies are incredibly diverse, and even individual societies do not replicate the same pattern over very long periods of time. Anthropological research suggests that human societies can adapt and thrive to vastly different environments. This was true in the decades leading up to Jared Diamond's biggest books, but it's the research that's been cropping up more recently which bodes even worse for Diamond's legitimacy. See, Diamond wrote his biggest books at a time when Anthropology was entering a revolution in thinking. He retreated to a fixed theory of environmental determinism (already considered obsolete then) at around the same time that Anthropology started stumbling on lots of evidence to suggest that societies are even more adaptable than had been previously speculated.

Why? Because of a revolution in field tech. See, remote sensing tech has made it possible for anthropologists to gather data about environments which would otherwise difficult to access. Suddenly, we can trawl across data covering miles and miles of jungle and rainforest. Now, old timey historians and anthropologists used to speculate that civilizations are dependent on alluvial river plains to establish dense urban landscapes. That was already chipped away at, but remote sensing unveiled just how staggeringly wrong that assumption was. It turns out that dense urban landscapes could be found anywhere, even in places where it seemed almost certain that the environment itself couldn't support a dense population. Turns out there's a very simple explanation for why we mostly find ruins of cities on alluvial plains, and never in jungles. And it's not that jungles didn't have cities. No, it's just really really fucking hard to find things in jungles. The pattern we were observing wasn't a pattern created in the past, but rather a pattern in our ability to perceive the past.

CONTINUED IN REPLY

First, your observation is correct: the two books contradict one another. Or perhaps more accurately, Acemoglu disagrees comprehensively with Diamond (and similar, perhaps more sophisticated, environmental determinists).

Second, in some sense, comparative analyses in this genre are almost bound to contradict one another. In what genre? I don't think it has a recognized name, but I would basically call it "global scale comparative social science that argues that the current status quo has a single major underlying driver or direction". Maybe a simpler label would be "monocausal global history", only this kind of work is typically not written by historians.

Some examples of the genre in addition to Why Nations Fail and Guns, Germs and Steel might be Steven Pinker's Better Angels of Our Nature, Francis Fukuyama's End of History, Huntington's Clash of Civilizations.

There's an older style of this kind of work that is often referred to as "historical sociology" written by scholars like Charles Tilly or Eric Wolf, but that work was generally not "monocausal"--it wasn't trying to come up with a single driver that shapes most or all global outcomes. Even more Marxist work in this vein tended to leave a lot of room for different outcomes and multiple underlying drivers.

Any single "monocausal world history" is always going to be at least slightly contradictory to all other work in the genre because all other works are in some sense focused on the wrong thing. Sometimes that contradiction will be as sharp as it is in the case of Diamond v. Acemoglu.

More to the point, the link offered here by u/GrunkleCoffee to past dissections of Diamond in this subreddit is going to be the general response by historians to almost all work in this genre: that it oversimplifies both in its analyses of causality and in its omission of pertinent details in the cases it uses, that it is reductive, that it is teleological to the point of completely ignoring contingency (that things could have turned out differently than they did). Sometimes that reaction will be very sharply antagonistic, as it has been to Diamond and Pinker, who are very palpably trying to force all the contradictions and complexities of world history into a dramatically reductive argument and often are manipulating evidence in a way that almost no historian can tolerate. Sometimes less so: Acemoglu's argument is more sensitive to variations, is more historically constrained, is more attentive to the specificities of different cases. But in general this is just not how historians roll, even when they're writing comparative or global-scale work.

To follow up on what u/GrunkleCoffee shared about Guns, Germs, and Steel, here are some past answers from the sub regarding Why Nations Fail:

What do historians think of "Why Nations Fail" with response by u/Hey_Arnoldo

What do historians think of Acemoglu's "Why Nations Fail"? with response by u/tim_mcdaniel