Once upon a time,
on a planet right here in our own
galaxy, there was a puddle on the
shoreline of a primitive sea. It filled a depression in a rugged
and rocky place, up above the high
tide line. For centuries, sea water
splashed into it at each high
tide, and then centuries
of evaporation filled it with
salt crystals, along with a few tarry
blobs, films, crystals and membranes of condensed organic
matter. You might think of it as
primordial soup that had evaporated
into primordial slime, or primordial jerky, at least during dry
spells (for more about the soup,
In fact, the whole neighborhood was that
way, with every crack, cranny and crevasse filled with pools and
puddles of salt water or evaporated salt, and various sorts of condensed
organic goo. The tides rolled in three times a day , and splashed
sea water into the puddle and its neighbors. Then the tides rolled
out, and left it all to bake and dry in the sun (for more about the
puddles and the concentration process, see Appendix
It was not unlike, say, the coast of California
or Maine. Except that it was four billion years ago, give or take
a couple of hundred million, and none of that organic stuff was alive.
Instead, it was just a mix of random organic chemicals that had flown
in by comet over the past billion years, or that had synthesized
on Earth via various natural processes.
Meet the Neighborhood
This particular neighborhood was a wee bit
unusual, since it had experienced some interesting chemistry history
that produced a high concentration of a few small, organic compounds.
That concentration may have resulted from
simple crystallization of a few organic chemicals. Once a 'seed
crystal' formed, it would have grown, bit by bit, as new soup
washed into the local puddle and then evaporated .
There may have been a few organic crystals
in the neighborhood, right from the beginning, formed in interstellar
space and then brought in as part of some cometary debris, or washed
in after forming in some other location on Earth.
Or the concentrations may have happened because
some of the condensed bits of organic material were catalysts-- which
means they could speed up the formation of specific chemicals, when
presented with the right raw materials. In fact, in this particular
neighborhood, there may have been several supercatalysts-- clusters
of catalysts that were positioned just right so they produced a series
of chemical reactions, much like a 'chemical factory'.
Each of those catalytic clusters would have taken common raw materials,
and created high concentrations of a specific organic chemical (for
more about early catalysis, see Appendix
For whatever reason, in this particular puddle
there happened to be large quantities of two different amino acids.
An amino acid is a fairly small molecule that is chemically stable,
and that has a very interesting property. Each amino acid has both
a positive (amino) end and a negative (acid) end. Two amino acids
will attract each other, positive to negative. With the right catalyst
or in a very concentrated solution, the two molecules will then merge
into a larger bipeptide, with the loss of one water molecule.
More amino acids can join at the two ends
of the bipeptide, eventually creating a much
longer chain-- called a polypeptide, or a
protein, depending on its size.
In our special neighborhood, it's likely
that one of those amino acid molecules had
a bit of an electrical charge in its side
chain, which gave it an affinity for water.
We'll call it the polar one. The other
was probably an oily character that avoided
water like it was, well, water. We'll
call it the hydrophobic one. Their interactions
were pretty much like salad dressing made
from oil and vinegar, only on a much teensier
During wet spells and very high tides, some
of these two local amino acids dissolved,
and washed out into neighboring puddles and
pools that were within splashing distance
of the source. During dry spells, they linked
up into polymers, eventually creating many
random protein chains that were dozens of
The Aromatic Chains
This special neighborhood also included a
high concentration of two other organic chemicals.
These molecules had flat 'aromatic' rings
built from carbon and nitrogen, and surrounded
by a whirling cloud of free-floating pi electrons.
They may have been purines or pyrimidines
(shown below), or they may have been some
The ring portion of these molecules were
hydrophobic, while the edges were polar.
In a water solution, that means that the
hydrophobic rings would attract each other,
then link up into moderately rigid chains,
stacked up with the rings parallel, much
like a pile of coins. The chains may have
had some sort of chemical 'backbone' to
connect each molecule, or they may have relied
on simple hydrophobic repulsion to stay together.
Thanks to the natural clumpability of the
two molecules, there were many short, aromatic
chains in the neighborhood, each with a random
sequence that might have been dozens of molecules
The earliest part of our story takes place
in some tiny puddle on a rocky shoreline,
slightly above the high tide line. The teensy
bit of water between two sand grains would
be sufficient space for all this molecular
drama to occur (we'll call it a micro-puddle).
At each high tide, splashing waves sent gobs
and droplets of dilute primordial soup flying
into the air. They'd land on the rocks,
and then flow from puddle to puddle, bringing
in new raw materials, dissolving portions
of the organic materials that had previously
condensed in the area, and rearranging the
contents of each small pocket and pool.
Any local catalysts or supercatalysts might
create a few new molecules from the incoming
raw materials, then plain old gravity flow
and wave splash would send them off to nearby
pools and puddles.
At each low tide, everything baked, concentrated,
polymerized and crystallized in the sun and
wind. Then the tides rolled in again, and
brought further change.
The whole system was not unlike a demented
chemical factory, with assembly lines set
up completely at random, acting at the whim
of whichever way the waves splashed each
day. All that blobular 'machinery' might
have continued for many millennia, producing
a local concentration of 'interesting' molecules
that had absolutely nothing to do with life.
However, during one dark and stormy night,
a rugged and handsome polypeptide, and a
perky and vivacious aromatic chain, both
happened to wash into one very special micropuddle.
The stage is set for our first molecular
drama, and it's time to meet the actors
The Cast of Characters
It all began with two short polymers. One
was a polypeptide that we'll call Fred (our First REplicating Device), and the other
was an aromatic chain that we'll call
Sofia (Sequence Of Fred InformAtion).
A Closer Look at Fred
Fred was a dapper and relatively short polypeptide
(possibly 20 or 30 amino acids in length).
It was shaped just exactly right so it had
two functional groups, which we'll
call its elbow and its knee. In this illustration,
we represent each amino acid as a circle,
and we include the side chains for a few
of the amino acids that are located at the
elbow and knee.
Fred's elbow is at the top. It happens
to have just the right chemical shape so
it fits very closely around a single molecule
of an aromatic chain. It probably wrapped
around the chain, partly or completely, but
to make the drawings clearer we'll
just have it ride along the bottom of the
Fred's knee is at the bottom. It is
a catalytically active group that is able
to attract two amino acids, and merge them
together via a dehydration reaction. Fred
has no source of outside energy, so it can
only do that in a salty, concentrated solution,
where the energy equation is in favor of
polymers. But fortunately for us all, that
is exactly where it happens to be.
Fred also contains a moveable linkage between
the two groups (the shaded section in the
illustration below). When there is one type
of aromatic molecule at the elbow, it shifts
the Fred molecule into one position, which
puts the knee into an orientation where it
will attract only a hydrophobic, oily amino
When there is a different molecule at the
elbow, it shifts the position of the chain,
which in turn 'snaps' Fred's
knee into a slightly different position.
In this new conformation, Fred only attracts
a polar, water-loving amino acid.
Small polypeptides are easily capable of
this kind of conformational shifting and
enzymatic activity, so we can't say
that Fred was particularly uncommon. It was
just very, very lucky, once it met the chain
of its dreams.
A Closer Look at Sofia
Sofia, the aromatic chain, is our other starring
It is a relatively short chain (possibly
20 or 30 molecules in length) assembled from
two different aromatic molecules. Each oval
in the illustration below represents one
chain molecule. Some of the aromatic chain
molecules are a bit bigger than the others,
so we draw them with an extra circle beneath
the main part of the molecule.
Sofia was originally condensed randomly from
the two aromatic chain molecules that were
common in the local puddle. Nothing special,
just a random sequence of two different molecules,
assembled into a linear chain by simple hydrophobic
The two molecules may have been a purine
and a pyrimidine (similar to modern RNA and
DNA), or they could also have been just about
anything else. Right now we don't need
to be too fussy about the chemical composition
of our starring molecules. They just need
to be different enough from each other, and
capable of forming long polymers.
Sofia has the potential to be a very tough
and resourceful molecule, and later on we'll
see some of the chemical tricks it can do.
But right now, none of those skills are important,
and we will just let it be a passive participant
in the drama to follow.
Fred and Sofia were nothing special on their
own. But once they splashed into the same
puddle and diffused close together, they
did something that would literally change
Fred's elbow bonded to one of the chain
molecules in Sofia, and then Fred gradually
moved along Sofia's sequence of molecules,
and 'read' it. Meanwhile, Fred's
catalytic end used that information to build
an exact duplicate of itself. We'll
call it Fred Junior.
It was the very first step in the very long
process of forming life. The first protein
transcription had begun.
Fred and Sofia in Pictures
Let's take a closer look at Fred and
Sofia's first meeting, step by step,
since what we just described is extremely
important. It's the very first courtship
For raw materials, we are using two 'modern' amino
acids-- leucine (hydrophobic, L) and
glutamate (polar, E). Of course, Fred may
have been built from entirely different amino
acids, perhaps ones that are not even found
in current living organisms.
Here is the very first protein transcription,
step by step:
1. At the beginning, Fred's elbow (at
the top) attaches to the first element of
the Sofia aromatic chain.
2. A hydrophobic group in the knee (bottom)
attracts a hydrophobic amino acid.
3. That jiggles Fred, which slides over to
the next molecule in the aromatic chain.
Fred's elbow attracts another hydrophobic
amino acid. Because it's in a very
concentrated solution, the two amino acids
bind together, with the loss of one water
4. Another day, another amino acid.
5. Fred jiggles onto the fourth chain molecule,
which is different from the first three.
It forces Fred's elbow into a slightly
different position, which pushes on the knee
and forces that into a slightly different
position. The result is that Fred now has
a polar group sticking out at the knee. That
attracts a different type of amino acid,
which binds to the new chain.
6. A few more jiggles, and we're further
along the chain, with a growing polypeptide
at the knee end.
7. Fred continues, reading each molecule
in Sofia, and using it to determine the structure
of the embryonic polypeptide:
8. After a few more of the same, Fred reaches
the end of the chain, and detaches. It also
detaches from the new polypeptide it has
9. Amino acid chains are very flexible, and
they usually like to fold up into compact
blobs. So each of those amino acids responds
to attractions and repulsions from the surrounding
water and the other molecules in the chain,
and the entire polypeptide folds up into
a specific globular structure…
which just happens to be another Fred. Welcome
to Baby Fred Junior! Awww, ain't it
Of course, Fred and Fred Junior were still
sitting very close to Sofia, and sooner or
later one of them probably succumbed to temptation,
diffused back to the beginning of the chain,
and transcribed another copy. Then there
were even more Freds, and even higher odds
that a Fred would manage to transcribe still
By the end of the tidal cycle, the result
would have been a puddle o' Freds,
with many of the local amino acids assembled
into tiny but potent Fred-making machines.
Survival of the Fittest
So then better and better Freds evolved,
Well, no. Not yet. There is only one
Sofia, and whenever a Fred hooks up with
it, the result will always be a plain old
There may be mutant Freds produced by
erroneous transcriptions, that do a better
job of transcribing Sofia. But whenever
a more efficient new Fred happens to roll
off the Sofia assembly line, it has absolutely
no way to pass along the improvement. When
that better Fred connects to Sofia, all
it will do is reel off a bunch of same
old original Freds (though in an improved
and more efficient way).
There is still more that needs to happen,
before we can have any real evolution of
our first life-like chemicals.
It's important to keep in mind
that life really hasn't begun yet.
All we have is the most primitive of self-replications,
and there is no such thing as 'natural
selection' yet. That means that Fred
and Sofia have absolutely no instinct or
skills for survival and reproduction.
Fred would be just as happy to attach
to a different aromatic chain, and use
it to create a different enzyme that would
slice Freds or Sofias into small pieces
For the sake of story telling we won't
have this Fred do that , but it's
important to remember that for quite a
while yet, any 'selective pressure' on
Fred or its progeny must happen strictly
in the random, chemical sense. It will
take several more chapters before we start
seeing any real natural selection and evolution.
In fact, you might say that this very
early form of self replication was totally
hanging onto to life by a thread. It wasn't
very good at doing much of anything that
would help it to survive.
If the local puddle dried up too much,
Fred would polymerize into a FredFredFred,
which would just be an amorphous blob that
wouldn't do anything interesting.
If the puddle got too dilute, Freds would
tend to gain a water molecule and break
up into Frs and eds that would also be
Introduce a new amino acid to the local
molecular mix, and Fred was doomed-- it
would produce Frzd and Fzed and Frzz, and
collapse into chaos. Zap Sofia with an
energetic photon, and it's end of
story. And let's not even think about
comet impacts, volcanic events, or massive
There were many, many ways for Fred and
Sofia to simply return to random
soup, and it's quite likely that
is what happened in many puddles, with
Freds and Sofias. This couple went
a little further, but it took some luck!
The Diffusion of Fred
Back in the 'home
right now we have a single Sofia
in a puddle with a local concentration
of Freds, created
by other Freds whenever they happened
to hook up with Sofia.
At each high
tide or storm there might be a few
Freds diffusing out
into the outside world, but those
be totally unable to do anything
interesting, when they got there.
the moment, we have a very fragile,
barely self-replicating system that
survive the loss of Sofia, or even
a drastic change in the local chemical
Some of the traveling
Freds might meet up with other aromatic
and form other polypeptide chains
(perhaps made from completely different
They would be interesting new polypeptides,
but they wouldn't be Freds, and they
wouldn't contribute anything to our
story of life.
More things need to
happen before Fred can be anything
more than a
temporary, chemical curiosity. And
to look at the next of those steps, now.
More About Fred
Fred & Sofia Q&A