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Am I missing some critical source, or is this simply pure conjecture on the part of the author?
The sources are named and quoted in the article, so I don't know why you think it's pure conjecture.
I wouldn't consider this a prank, but instead a whimsy. It's a prank only if he intentionally broke convention from using the first two letters with the sole purpose of fucking with everyone.
I remember discussing this when I was a kid doing Chemistry. We concluded it was probably to make the symbol more visually distinct from Pt and also to avoid confusion, since Pl could reasonably be expected to stand for either Plutonium or Platinum. In fact thinking about it, calling it Pl would have been an extraordinarily bad idea.
I'd probably be forever thinking Pl is Polonium.
If he named it Pl it could be mistaken with Plumbum, i.e. lead that itself has element abbreviation as Pb.
Or equally, Pl_3 (3 atoms of Plutonium) would be very hard to distinguish from PI_3 (Phosphorus Triiodide), especially in a sans-serif font. Pu seems like a good call to me. If it also amuses 4-year olds, then so much the better.
In French you would say 'ça pue' for 'that stinks'. Is there a link with this P-U business?
In the US saying "Peee Yooo" is often times combined with holding your nose. Sometimes each word is stretched for dramatic effect "Peeeeeuuueeee Yoooooooooo!"

It's somewhat of a children's expression for "that stinks", although adults use it to be funny.

In English, we have several similar words that are derived from this French meaning (putrid is an example). Both words are related to Latin "putere" meaning "to stink". The ultimate root of these words is the Proto-Indo-European root word *pu- "to rot, stink" [1].

It is not clear if the current meaning of the term pee-yoo is derived from this Indo-European root. The first Oxford English Dictionary entry is in 1604, where it shows up with several different spellings: pue, peuh, peugh, pyoo, and pew [2]. The "stretching" of the word into two syllables must have happened sometime later.

[1] http://www.etymonline.com/index.php?term=putrid

[2] http://www.grammarphobia.com/blog/2010/08/on-the-scent.html

The comments on the story mentioned it - but my wife immediately pointed out that since they wee calling it "copper" as a code name during the war, that Cu for cuprus is easily transformed ( ha ha ) into Pu. (I love my wife)
If the codename for Plutonium on the bomb project was 'Copper' then I wouldn't be surprised if 'Pu' as an homage to 'Cu' also factored into his decision.
Cu comes from the Latin word for copper, cuprum. So, that had nothing to do with it.
I think you must be honest to god person with no sense of humor. :)
Where Cu comes from is irrelevant. It may still have inspired the Pu naming.
Few of the other new ones follow the alledged standard, one other possible link, to go with the Cu one:

Np N e p tunium

Pu P l u tonium

Ne was already used for Neon. Plutonium is the only element that skipped the first available abbreviation.
Interesting that Robert Krulwich, from the Radiolab podcast, did the illustrations for this article. He even visited the comments section!
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The ultimate dad joke. 10/10.
So how should one take a prank like this to the next level? Use abbreviations like Bs and Fu, or even outright spelling out dirty words by discovering and naming a bunch of elements with consecutive element numbers?
Wow, that was incredibly unfunny.
In line with the scatological references in the periodic table, according to "The Disapearing Spoon" By Sam Kean, Berkelium was intended to have the initals Bm, but eventually Bk was decided upon.
Does anyone know what is being displayed in the background of the picture of Seaborg in the article?

See [1]. It looks like variations of the periodic table but arranged along something other than atomic weight. I suppose if they were still discovering/creating elements, they would align their table differently than one where there have been no changes in years.

[1] http://phenomena.nationalgeographic.com/files/2015/11/GettyI...