Chocolate really shouldn't exist. Well, that might be a little exaggerated but its existence does seem to be highly improbable and not just in a how-did-someone-eat-roasted-fermented-cacao-beans-and-think-yummy-in-the-first-place way.
Since I am a plant-insect ecologist that focuses on pollination, let's start with the pollination biology of Theobroma cacao (the very accurate Latin name of the species, meaning "food of the gods", aka cacao). In order to produce those delicious seeds, a cacao tree needs to produce a flower which will be pollinated and produce fruit. Most trees excel at this step. In fact, cultivated varieties of cacao usually produce flowers all year round and each tree can produce up to 100 new flowers every day. Sadly, past this point, things start to go down hill.
The first problem is that most varieties of cacao are self-incompatible. This means that their flowers need pollen from another tree that has a different genetic composition than them in order to be successfully fertilized. In many fields, most of the trees are clones of each other, meaning that they all have the same genetic composition and so can not fertilize each others flowers. By mixing different clones in the same field, farmers can improve the chance of pollination and so the chance of fruit. Farmers could also plant one of the very few varieties of cacao that are self-compatible, such as CCN-51, but as the flavor of CCN-51and other self-compatible varieties has been called "weak", "astringent" and "lead-based" by various chocolatiers, these beans can only be sold at the lowest of prices. So if you are a farmer that would like to produce high-quality beans for a premium (perhaps through a fair-trade cooperative or organic growing system), you have to use self-incompatible trees that rely on insects to transfer pollen from one clone to another.
The next problem is that the flowers of cacao are tiny, complicated and do not produce rewards for pollinators. They are about dime-sized in diameter and the pollen is not readily available to floral visitors. In fact, the pollen is deftly hidden inside modified petals that cap the tops of the anthers (the pollen-producing parts of the flower) so that there is about 2mm of space between the petal and the pollen. This space can only be accessed by a tiny insect (<2mm) or a very dexterous insect leg (think pollen-robbing bee). While some sweat bees do visit cacao flowers, albeit infrequently (I have seen 3 in my >60 days of watching flowers in the field), these bees tend to harvest pollen without interacting with any other parts of the flower. This is important because getting pollen is only half of the equation, depositing that pollen in the right place on the flower of a different tree is the other, sometimes harder, half. See the crown of red spikes in the center of that flower? Those surround the stigma or the pollen-receiving organ of the flower which is a delicate, semi-transparent white tower.
While this crown is not made of metal and could be easily broken by a careless human hand, it does prevent accidental interaction with the stigma, meaning that a pollinating insect needs to crawl down the center of the crown to deposit pollen in the right place for fertilization. Now, this complicated flower form might not impede pollination if this flower was incredibly attractive to pollinators and produced rewards (nectar, nutrient-rich pollen, perfumed wax, etc.) to keep them coming back. However, as far as scientists know, there is nothing attractive or rewarding about visiting this flower. The pollen is slightly more nutrient rich when compared to other plant tissue (hence the pollen-robbing bees) but the flower does not produce nectar, wax or even scents to attract would-be pollinators to the flower. Some scientists have hypothesized that the deep red colors of the inside of the petals and on the crown could be a sign of nutrient rich tissue that would attract insects that feed on plant juices. In other cases, scientists have suggested that the very heavy volatile compounds that this flower produces in trace amounts could be its attractive scent. However, without incredibly attractive rewards, cacao flowers are not well visited. On top of that, flowers are only able to be successfully pollinated in the first 24 hours after opening meaning the window for an insect to visit and deposit pollen on a flower's stigma is pretty short.
Viable (aka genetically different) pollen reaching the stigma does not always guarantee a fruit. The full explanation dives into how self-incompatibility functions in Theobroma cacao at a cellular and biochemical level in great detail. Suffice to say, if there is too much self-pollen (pollen from the same tree) on the stigma, even if there is enough viable pollen, the flower will still fall off the tree (be aborted) without producing a fruit. So the requisite amount of viable pollen (about 40 grains) must be deposited on a flower before there is too much interference from self pollen. Since these flowers are commonly explored by ants, thrips or aphids (all crawling insects that generally do not visit multiple trees), most pollen transfer occurs within the same flower or the same tree rather than between trees of different varieties.
So far, these trees produce lots of flowers (+1) but need pollen from trees with different genetics in order to produce fruit (-1). They also have a complicated flower form which means insects need to truly explore the flower to find pollen or the pollen-receptor (-2). These flowers do not produce any scientifically confirmed rewards or attractants (-1) and so are not visited frequently (-1) or by specialized pollinators (-1) but are only viable for 24 hours after opening (-1). Finally, if the flowers receive too much self pollen before other pollen, the flower will abort (-1). Could it get worse? The short answer is yes. The long answer covers all the possible things that can befall a small cacao fruit while it is growing from a grain of rice to the size of a football. Systematic abortion of all small fruits (i.e. cherrelle wilt), insect herbivory, and fungal diseases all play their role in stopping a successfully pollinated flower from growing into a harvestable fruit.
Even though there are many other problems on the path of a cacao flower to becoming a large ripe fruit, I decided to study the pollination biology because it seemed the most intriguing and the most understudied. While there are some studies from Brazil published in the 50s and 60s, some from Costa Rica in the late 80s and early 90s and a few recent studies from Indonesia and Ghana, none of these studies were performed with in the native range of T. cacao. Since plants co-evolve their pollination syndromes with local pollinators, I decided to study cacao within its native range, which is composed of the Upper Amazonian Basin and small pockets of rainforest on the Western side of the Andes mountains in Ecuador and Columbia. While I dreamed of doing side by side comparisons of wild T. cacao with cultivated trees, I have trained my sights on a few projects that are a bit more feasible for a dissertation. Instead of building scaffolding around cacao trees on steep mountain slopes in order to look at flowers 6m off the ground, I am studying flowers no more than head high in order to quantify how the pollination and the pollinator communities of T. cacao are affected by the management and the surrounding landscapes of the cacao fields.