I would argue this not an example of intelligence, but of instinct. Penguins already migrate long distances each year for mating, as many birds do. This penguin developed a familial bond with the gentleman due to the extended period of time he was being cared for, thus his innate migration shifted to his new "home". This is actually observable in zoology, as birds caught in the wild and brought long distances into captivity, after remaining in captivity long enough to integrate the new place as a home, will not migrate back to the original home in the wild.
This story, while interesting and sweet, does not demonstrate an intelligence previously unknown to penguins.
The example with birds is probably not the best one as it demonstrates domestication. This penguin went back into the wild and swims back to this man every year. You can argue that it is instinct, but we don't know if the penguin did not find another family among the penguins down at the tip of South America. For all we know, this penguin breeds every year and most likely has a "real" penguin family. Yet it still comes back, every year, to hang out with a creature it undoubtedly knows is NOT his kin. It does not look like him, does not smell like him, does not move like him, feed like him, his companions do not look like penguins, etc.
Unless they GPS tag this penguin and it turns out he is a loner rejected by his penguin peers (and thus without penguin family) travelling solely because the man is his only family, then I would not jump to conclusions. Just think about it, if the penguin was indeed without family and the man is his only family why would it go back to Patagonia every year? Clearly something is drawing him to other penguins too. Just because something is likely/logical, does not mean it is the case. The evidence so far is that the penguin has found other penguins and hangs out with them for 7 months of the year and swims back to meet this man and spend 4 months with him.
Now, find me a human that has ever done a similar feat for his/her (non-human) friend
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