Free Living Bacteria

From here on in, it's a question of live fast, die young, leave a good looking cell.

Bacteria colonise everywhere on Earth, from the deepest ocean to the highest cloud forest, inside trees, outside trees, inside animals, on the skins of animals, everywhere.

Some get thicker outer walls, and become gram-positive, some thinner and become gram-positive.  Some become parasites that live on, or in, larger creatures.  Some become spiral shaped, and others learn to shape-shift dramatically as a means of locomotion.

They are arguably the most successful life form on the planet.

Chemical Eating Bacteria

You can afford to keep a lot of different genes around now, so you can survive pretty much wherever you go, on whatever you find.

However, you're one of the smallest, weakest life forms around, because at this time, the eukaryotes, with their big, multi-layered walls, have grown up.  They like eating you, like a little snack.

Wouldn't it be nice to be big and tough like them?  Well you might have the options: what if you get inside one in a failed snack attack, and stay in there, acting like a little chemistry factory, making food for them?  Better to feed than be food?  Or better to stay on the outside, maybe get faster, or hide away?

Join a gang?
Play your own game?

Photosythesising Prokaryote

Ah, that was clever.  By using the sun's rays to fix carbon from the atmosphere, you can grow and grow and reproduce and reproduce.  There's no competition for the sun's rays, so long as you stay in the light you are good to go.

But all this free food is making you a tasty target for various eukaryotes, which are swimming right up to you, engulfing you, and eating you whole! This is bad!  These guys are a lot tougher than you.  Well, if you can't beat 'em, join 'em, right?  With a bit of luck, one of these eukaryotic bad boys will engulf you, but then keep you around inside so that you can eat sunlight and make food and let them have some.  It's basically the evolutionary equivalent of the Mafia.

So, whaddya gonna tough, tough guy?  You got a nice little cell here, be a pity if something happened to it..

I'm toughing it out, on the outside.
Safer to become a made man.  I'm in.

Eukaryota

With your densely packed DNA, you can afford to express a lot more proteins.  There is some serious evolution (without splitting into species) in the next few million years.  In no particular order:

• your DNA stops being stored in a loop.  Instead, you develop end caps called telomeres which act like the bits on the end of shoelaces that stops them unravelling.
• You get bigger.  Much bigger.  
• Instead of 'stealing' genes in the process of eating other chaps similar to yourself, when a pair of you meet up, one 'gives up' some genetic material to the other.

If this last one sounds crazy, because the organism giving up material will lose out, you have to remember that genes are survival machines both in themselves, and in groups.  In this case, the gene may well get the chance to make many more copies of itself when it joins with a new set of partners.

To facilitate all of these things, one major change takes place: the cell wall becomes less thick, and eventually forms a cell membrane.

Additionally, you need to move around - your food demands are so high that you can't just wait around and hope.  To this end, any change which makes you able to move, no matter how small, will be copied around the community.  Eventually, those small changes add up to something called a flagellum.

However, this flagellum needs a lot of energy.  In order to make enough energy, you need to eat, which is done by engulfing smaller things, prokaryotes, until eventually something odd happens...  you eat one, and it survives.  Inside you.  Ewwwww.  The prokaryote inside you lives on, and, protected by you from most other threats, eventually loses the genes it isn't using.  What is left, is a pretty simple thing, no longer an organism, but an organelle.  It's called a mitochondrium.

After all this, finally there is a choice again:

Grow another flagellum?
No thanks, one is enough!

Life Starts Here

In the beginning was the word, and the word was...

No, only joking!  We're going to start a little later than that in the story.  We're not going to wonder at how on earth the universe started.  We're going to wonder about how, on Earth, life started.

The Earth coalesced out of a cloud of mostly iron based compounds, and formed a hot, rocky core.  Eventually, other elements and compounds rained down on it from the gravity well.

After about a billion years, comes the beginning.

In the beginning was the primordial soup.  A mixture of simple chemicals, some gaseous, some liquid, and quite possibly some lightning.  Nothing alive, in the sense that there was nothing that reproduced.  There were certainly some chemical reactions going on, but nothing that couldn't be described in a line or two on a school whiteboard.

Then some chance chemical interactions produced simple nucleobases (nitrogen containing compounds). This will have happened quite a lot.

Some more random chemical interactions caused several nucleobases to fuse together, creating a very short strand of ribonucleic acid.  This may have happened several times, until, at last, one very special molecule occurred.

Ribonucleic acid (RNA) is the simplest known class of self-replicating molecules.  Estimates of the minimum number of nucleobases needed for replication used to be over 200.  Then they were 50-60.  Finally it was demonstrated (in 1975) that under some conditions, a single RNA molecule can form of very, very few nucleobases, and still reproduce.

You may well be thinking that this is extremely unlikely.  You may well be right.  You may therefore prefer to think that some kind of direction must have been provided by a creator, whether terrestial, extra-terrestial or supernatural.  But it doesn't matter that it was unlikely.  What matters is that the conditions were there, and that they were there for millions of years.  If the spontaneous formation of RNA would only happen once in a million years on a planet in a given state, but that planet is in that state for hundreds of millions of years, then you don't need to conclude that.  Our planet was 400 million years in the Eoarchean era between the end of the Hadean (hell-like) eon and the start of the Paleoarchean era.  There was no life during the Hadean eon, and there were definitely bacteria in the Paleoarchean era. 400 million years is a lot of time to roll the chemical dice.

So, at some time in the Eoarchean era, the conditions were right, and the first RNA which could replicate was fused.

As it must have been near some more nucleobases, it immediately replicated.  Then each of the copies replicated. Each of those copies was a perfect replication of the first ever life.  Some of them will have been destroyed by simple chemical reactions such as meeting up with an alkali, but only some.

Soon it had replicated so many times that there was a shortage of the required nucleobases in the area.   Eventually, one could not replicate completely and an imperfect copy was formed.  Then another, and another, and another.  Many of these were not able to replicate, and simply stopped reacting, but instead of life ending just as soon as it had started, one or more of those imperfect copies was able to replicate itself despite the 'error' and use some other nucleobase, and that copy continued to replicate.

Eventually, a variety of replicating molecules was present.  Again, some will have been destroyed, but some will have remained.  Those which could replicate most quickly and withstand chemical attack will have been present in the highest numbers.

Later, perhaps a day, perhaps a million years, two very similar RNA strands found themselves in close proximity, and a new reaction occurred. They both lost oxygen atoms from down one side and fused alongside each other, forming deoxy-ribonucleic acid or DNA.  This molecule is slightly less able to replicate than RNA, but more stable and less likely to be damaged by other chemicals.  Only when the DNA is in the presence of the right chemicals for replication does it split into two RNA molecules and start reacting.

The benefits outweighed the costs, and after a while, more copies of the longer-lasting DNA existed than RNA.

When DNA encounters strands of RNA, it can cause it to partially reproduce, which results in the expression of amino acids.  If the right combination is present, it will result in a protein. A section of DNA which expresses a single protein is called a gene.

At some stage, random combinations of nucleobases occurred which caused proteins to be expressed that caused a bubble or membrane to form around the DNA.  Not that the membrane itself was created, but that the proteins present attracted lipids, and the lipids closed around the DNA, keeping it even safer and making it even longer lived.

Finally, each had to make the first genetic choice.  Not actively choosing - life never actively chooses - but simply that two successful variations lived when all other variations died.

Choices are mostly made by errors.  Copying isn't perfect, as we saw when the RNA ran out of nucleobases.  Eventually, small changes turn up in the DNA that change the proteins expressed in the presence of RNA.  Different proteins will have different effects.  Most of the errors make the DNA less likely to survive, but sometimes an 'error' will make survival more likely.

Because DNA is two sets of genes, an interesting effect occurs. If a cell has two copies of a given gene, it will express one protein.  If it has two different ones, it will express two proteins in half quantities.  Sometimes, having two proteins is best.  Sometimes, having twice as much of either of two proteins will better.

You are now the Last Universal Ancestor.  Time to start making choices...