The false eukaryote/prokaryote dichotomy

OLD Audio recording
Video recording (.mov format, 0.8Gbytes)
Video recording (480p .mp4 format, 0.1Gbytes)
Video recording (1080p .mp4 format, 0.7Gbytes
 

What is the point?

  1. To be able to describe why the term "prokaryote" is not a valid label for a group of organisms
  2. To be able to describe why Eukarotes/Prokaryote tables are misguided and incorrect

The classic major division of living things is between “eukaryotes” and “prokaryotes”. Most textbooks have a chart something like this indicating how different these kinds of living things are:

Eukaryotes

“Prokaryotes” 

large - 20 to 100 microns
small - 1 to 5 microns
contain a nucleus
no nucleus
contain many large linear chromosomes
one small circular DNA chromosome
contain organelles
no organelles
diploid
haploid
cell cycle includes mitosis
no mitosis
reproduce sexually or by budding
reproduce by binary fission
cells contain a cytoskeleton
no internal skeleton
ingestive or photosynthetic
absorptive
multicellular
unicellular
complex life cycles & cellular differentiation
simple divison cycle, no differentiation
mRNAs are polyadenylated
no polyadenylation
genes are transcribed separately
genes are transcribed together in operons
genes contain introns
no introns
DNA packaged with histones
DNA not packaged

The problem with the prokaryote/eukaryote dichotomy is that it is exclusionary; it’s a lot like the vertebrate/invertebrate dichotomy of animals. The terms "prokaryote" and "invertebrate" describes what an organism is not, but it doesn't describe what it is. All "prokaryote" means is "not a eukaryote"! Therefore, the term "prokaryote" as a label for a group of organisms is scientifically invalid. The notions of “prokaryotes” arose over the years for no real reason other than default; it became an assumption that all non-eukaryotes were of a single kind, because the existing tools could not distinguish them, but as we know now this is not the case - any more than it is the case that all “invertebrates” are of a kind. There are in fact two fundamentally different kinds of "prokaryotes", Bacteria and Archaea, that are as different or more from each other as either are from eukaryotes.

Banish the term “prokaryote” from your vocabulary, along with “evolutionary ladder” and “higher eukaryote”, except to use (in quotation marks) in reference to a quaint, outdated anachronism. File them in your mind alongside the terms “phlogiston” and the notion of a flat Earth.

In addition, many of the stark contrasts between Bacteria (“prokaryotes” in the case of this table) and eukaryotes come from falsely assuming that plants and animals are typical eukaryotes, and E. coli and Bacillus subtilis are typical prokaryotes, and from an active striving to identify differences, no matter how trivial, in order to make eukaryotes “higher” and prokaryotes “lower”. But what's true in E. coli and B. subtilis is not necessarily true in other Bacteria, and what's true in plants and animals is not necessarily true in other eukaryotes. Bacteria are not primitive - they are modern organisms, the result of over 3.6 billion years of evolution, just like eukaryotes. As a matter of fact, eukaryotes, Bacteria, and Archaea aren't at all as different as these tables suggest. All of the apparent differences listed above are bogus in one way or another; at best over-generalizations, and at worse just plain false.