It’s true that the term Prokaryote is going away. The problem is not that it is a bad word when contrasting Bacteria and Archae to Eukaryotes, but that it implies similarity between the two ‘Prokaryotic’ domains.
I see the rationale, but I need to read up a bit on this before I start changing my lectures. Thanks to Nucleoid for pushing this topic.
There are reasons to avoid using “prokaryote” in biology teaching. So, why are so many biologists resistant to the idea?
Why not use “prokaryote”? Norman Pace published a one-page piece in Nature, “Time for a change” that raised concern about use of “prokaryote” (in education), and the common biology textbook paradigm of splitting organisms up into prokaryotes vs. eukaryotes. Pace highlighted many of the differences between archaea and bacteria, discussed evolutionary relationships/history, and made a case for avoiding use of the term prokaryote with students. (Check out the 2005 article by Jan Sapp discussing the history behind the prokaryote-eukaryote dichotomy, too.) Pace expanded on this with a lengthier educational piece in 2008.
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DownHouseSoftware 
Ratabago
January 21, 2014 at 1:52 am
I think prokaryote is a perfectly good word, it’s just been subject to a lot of misuse and abuse. If we’re going to dump words just because they are misused we are also going to have to get rid of evolution, and gene, and mutation, and junk DNA, and non-coding DNA, and just about anything else that makes biology interesting.
As long as your students understand “prokaryote” is not a tightly defined phylogenetic grouping, and that Eubacteria and Archaea are separate Domains, and that Domains are useful organisational tools, I don’t see a problem.
Just my immediate thoughts on it, for what they’re worth.
downhousesoftware
January 21, 2014 at 3:11 pm
You’re right on. Lots of words break down when we try to challenge what they REALLY mean. The rationale for abandoning the word Prokaryote is sound, but that may be only one small part of the fight. I’m not ready to give it up myself until I feel that I can work in a better way to introduce the broad expanse of life in an intelligible way.