According to current
theory, there are three major domains of living organisms-- the
Prokaryotes (bacteria and cyanobacteria), the Archaea (thermophiles,
halophiles etc) and the Eukaryotes (protozoa, fungi, plants and
All three domains use DNA for coding genetic
material. In Prokaryotes and Archaeans it's usually in the
form of a single loop, while Eukaryotes usually have multiple chromosomes,
with the DNA bound into complex structures wrapped around polymers
of histone (an amino acid).
Evolutionary geneticists sometimes talk about
LUCA, the Last Universal Common Ancestor (sometimes also called a
progenote). This is the theoretical early organism that existed just
before the development of the three major life domains.
The search for LUCA is fraught with difficulties,
especially because modern organisms are very willing to swap genes
between different species (called 'horizontal transfer'),
and that process was probably even more common, back when organisms
were simpler. However, from our evolutionary viewpoint, this is about
where LUCA happens.
Many bacteria contain moderate quantities
of microsatellite DNA , so it seems likely that at least some Foxy
function developed before the separation of early life forms into
the three domains. But there are major divergences between the domains
in many important areas, so it seems likely that the schism occurred
before cells had specified important structures such as flagella.
Many microbiologists are examining small
chemical clues, to evaluate the relationship between the different
life domains, and their probable evolutionary paths. We won't
be able to add any new information to that search, but let's
at least take a brief look at the three life domains, and how they
probably were related to the introduction of Foxy.
The guiding philosophy for bacteria and cyanobacteria
(blue-green algae) is KISS-- Keep it Simple, Stupid. They are
small cells with a simple genome, and their cell interior doesn't
have very much structure. For example, the DNA in most bacterial
cells is not organized into a separate nucleus, and they lack most
of the organelles that are found in the cells of their more complex
It's a successful strategy, and bacteria are found in just
about every nook and cranny of Earth. In fact, the typical human
body contains ten times as many bacterial cells, as human ones!
Members of this domain tend to reproduce
quickly, and for the most part, they strive for the absolute minimum
of genetic content and the simplest of cell metabolisms. Anything
that can shave a few minutes off the cell generation time is a good
thing, from a bacterial point of view. And they've had trillions
of cell generations in which to perfect the process.
LUCA may have been similar to a bacterial
cell, or even simpler. But it's also possible that it was more
complexly structured than modern bacteria. In the latter case, bacteria
would have gradually substituted simpler systems with fewer parts.
You might think of a bacteria as a race car that started out as a
sedate family sedan, but gradually dispensed with amenities such
as doors, cup holders, turn signals and air conditioning. All that's
left is speed and fuel efficiency.
Many species of bacteria contain transposons,
but this domain includes relatively few self-splicing introns. That
suggests that bacteria may have dispensed with most helper chains
and scripts, and concentrated mainly on efficient proteins to manage
Once a protein is transcribed, it can fold
up into its final structure and start working immediately. So it
appears that many bacteria don't want to wait around for some
leisurely script to be run, and want to get right to business ASAP
The guiding philosophy for the Archaea is
BUSH-- Build Us Sturdy, Hercules. Many of the Archaea live in
extreme environments, where heat, cold, extreme
acidity or other hazards make it impossible
for bacteria to live.
The Archaea have some chemical modifications
that make them more tolerant of extreme conditions. For example,
the lipids in their cell membranes are connected by a ether bond
rather than a flimsier ester bond, and the lipids themselves are
tougher (they are built with the same chemical system that produces
The Archaea seem midway between the bacteria
and the eukaryotes, so it's possible that they are the closest
About 3.7 billion years ago, the Earth and
Moon suffered an extremely intense period of large meteor impacts
known as the Late Heavy Bombardment. It's possible that the
only organisms to survive the resulting chaos and climatic change
were deep-soil and extreme-condition cells such as the Archaea, which
would explain why they are now closest to the original roots of life.
On the other hand, it's also possible that the Archaea may
also have 'stripped down' over the past few billion years,
and they may actually be simpler than LUCA. As with the bacteria,
their selective pressure has been for simplicity and reliability,
and they may have evolved into efficient systems to replace the fancy-pants
scripts of their ancestors.
Perhaps the best analogy for the Archaea
would be the Demolition Derby car, that started out as a sedate family
sedan, but then lost its window glass and flammable interior details,
and traded comfort for extra reinforced welding, instead.
The guiding philosophy for the protozoa and
multi-cellular organisms is MICE-- Make It Complicated, Einstein.
We eukaryotes have complex cells, with a separate cell nucleus, and
many advanced cell structures. Members of this life domain take longer
to grow and reproduce, but they can also grow to larger sizes, and
have a much wider repertoire of metabolic tricks.
For example, one of the simplest of eukaryotes
is the common brewer's yeast, Saccharomyces cerevisiae. People
tend to think of it as just another microorganism, but it's
much bigger than the typical bacterial cell (3 to 5 microns vs .5
to 1 micron), and it contains much more DNA (12 million base pairs,
vs about 4 million base pairs in a typical bacteria). Yeast cells
are much more complex than bacteria-- they include a separate
nucleus, and many specialized cell structures. They also grow more
slowly than bacteria (under ideal conditions they take about 2.6
hours to split, while some bacteria can do the same in 15 to 20 minutes).
Eukaryotes are so closely tied to Foxy scripting
that in the remainder of this book, we'll only consider them.
They have definitely taken scripting and gene regulation to its highest
level (which is probably why the average Eukaryote gene contains
about 7 introns).
You might think of Eukaryotes as luxury cars
that started out as a sedate family sedan, but then let gadgetitis
take hold, complete with GPS navigation, an espresso machine on the
dash, and cupholders with napkin dispensers .
Foxy and the Domains
Eukaryotes are built from complex cells with
a nucleus, mitochondria and other organelles. If our 'scripting' theory
is correct, they would be organized with a relatively large number
of scripts, which in turn would mean a relatively high percentage
of repetitive DNA in introns and/or satellite DNA. In general, more
complex Eukaryotes do have more repetitive DNA, though the total
genome size varies enormously between different species (a problem
known as the C-value enigma, which we'll cover in Appendix
Prokaryote and Archaea cells also contain
some repetitive DNA , though in much smaller quantities than in eukaryotes.
A few genes in these simpler organisms contain introns (primarily 'self-splicing' type
II introns), but most repetitive DNA occurs as transposons instead.
There are two theories for the large difference
in intron counts between prokaryotes and eukaryotes-- that most
introns evolved after the split between the domains (called 'intron
early'), and that bacteria and other simple organisms lost
their introns (called 'intron late').
Since Prokaryotes in particular are small
organisms with rapid growth and high turnover, it may be that Prokaryote
and Archaeal cells started out with a Foxy system to specify cell
structures such as flagella, but then replaced most or all of the
scripts with protein-based controls, later on.
Modern bacteria live, reproduce and die very
quickly, and script-based structures may have simply taken too much
time or resources. So, even though it is more difficult for protein-based
control systems to evolve, they may have provided enough of a metabolic
advantage to out-compete the use of scripts.
If that is true, then Foxy may have still
provided a method for the first bacteria to evolve in prototype form,
and it might still be used in a few places where a more efficient
control system has never evolved, or as a secondary feature to allow
prokaryote species to evolve new features more easily.
It's also possible that Foxy (and the intron data that it uses)
only appeared in the Eukaryotes, after they had already diverged
from Prokaryotes and Archaea, or that it was used in some primitive
form before the first schism, and then reached its full maturity
only in eukaryotes.
Eukaryote cells tend to be longer-lived than
their bacterial cousins, with fewer, larger individuals. Because
of that, efficient evolutionary change is more important to them,
and Foxy would have been relatively more advantageous to them.
The short generation time and large population
sizes in the smaller, simpler Prokaryotes and Archaea may have allowed
them to accept a higher mutation rate so they could evolve via the
metabolically more simple protein-based controls, rather than Foxy
Any efforts to track down the early genetic
heritage among the different domains is complicated by 'horizontal
transfers' of genetic material between one cell and another.
This kind of genetic transfer still goes
on in modern bacteria, which frequently exchange genetic material
with other individuals and even other species.
It seems likely that this sort of horizontal
genetic transfer also occurred in early organisms (probably more
frequently, since the organisms themselves were simpler and more
able to use novel genes coming in from somewhere else).
Horizontal transfers of genetic information
would have made the schism between the different life domains much
more gradual, and it would have made evolution proceed more quickly
since a useful enzyme discovered by one species would have ended
up in many other species as well, without the need for them to discover