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The dawn of Life

Astronomers believe that Life’s building blocks winged in from Outer Space. But they would claim that wouldn’t they.

Enzymes When did life emerge? Phospholipids How did Life emerge?

The astronomers have detected many of the building blocks of life in the tenuous atmospheres of stars. But earth-bound scientists have found plenty of places here on Earth that could have given emerging life its first leg up just as easily. Many of Life’s building blocks do seem to be incredibly easy to make.

It’s noticeable, as we’ve hinted, that the astronomers are the main exponents of the theory that our planet’s life originated in outer space. And some would certainly argue that their motivation is plain old-fashioned empire building.

Whichever theory takes your fancy, the difficult bit remained to be done here on Earth. For other building blocks are much harder to make. As we’ll see later, scientists are still struggling to understand how emerging life managed to make the jump from the simple building blocks to something reasonably described as ‘life’.

All life the same

One of the things that originally got me following this story was a number of questions like the following. “How is it that we humans can eat, and obtain sustenance from, virtually every kind of living organism on the planet?” There are exceptions of course, mainly those organisms that have invested valuable resources in making poisons. They don’t do this for fun. They do it specifically to avoid being eaten.

And “why is it that biologists comb the tropical rainforests, looking for vaccines and other chemicals which might help cure humans?”

The answer turned out to be very simple. Down at the basic chemical level, all life is exactly the same.

Proteins and the genetic code

We’ve now reached the point where the scientists begin to be on firmer ground. The following is fact.

With rare exceptions: all life uses the same 5 so-called ‘bases’ to make its DNA and RNA with. (It’s 5 because RNA uses one that’s different from its DNA equivalent.) Life also uses the same 20 ‘amino acids’ to make its proteins from. And, again with rare exceptions, it uses the same genetic code to translate between the two.

The next couple of paragraphs are a bit turgid. I’ve put them in to lend an air of “artistic verisimilitude to an otherwise bald and unconvincinv narrative” (W.S. Gilbert, ‘The Mikado’). Please feel free to skip them.

This diagram of Life’s genetic code comes from New Scientist (13.8.05). The yellow column indicates a ‘word’, or codon in the jargon, made up of three of the 4 available ‘bases’. If you want to know more about bases, I’m afraid you will have to look them up on the Internet. The blue column shows which of the 20 amino acids the codon specifies. The second diagram indicates these. It comes from Scientific American (Oct. 85).

The first thing to notice is the large amount of redundancy in the code. A code of 3 letters, selected from 4 different possibilities, gives us 64 possible amino acids. And yet life has only found use for 20. In many of the codons, the third letter is ignored. And evolutionary biologists have found something queer about the way first letter is used too (which I don’t understand and won’t attempt to explain).

This has led them to speculate that the first code only used the middle letter of the three. The outside letters were simply used as ‘spacers’. This implies that the first organisms that used the code had to make do with 4 different amino acids. This was very limiting and, to get a wider choice, the outside letters were gradually brought into play. Presumably emerging life only found use for 20 amino acids. Or maybe there are only 20 that can be specified in this way.

This diagram shows the 20 amino acids that life chose. I won’t attempt to explain it, but it’s laid out to show how easily they link together. What may be less obvious is how similar the central portions are. The differences lie mainly in the bits that branch off.

Please start paying attention again now.

Quite quickly emerging life ended up with the code we find today. I say ‘quite quickly’ because the code must have become fixed before any of life’s surviving branches split off.

The amino acids do most of their work by linking together into long chains – to make proteins. Proteins are used to make structural components. For these the chains are straight. And many different chains have to link together, side by side, to provide stiffness. It’s a bit like dipping a piece of string into molten wax. It goes in flexible and comes out stiff.

Enzymes

The other main things that proteins make are enzymes. Enzymes do a different job. They are the cell’s chemical factories. Enzymes take in small chemical building blocks, and snap them together to make larger ones. For this, they have to clump together into a ball. And it’s the precise shape into which they clump that gives each individual enzyme its unique properties.

The clump has to include little niches, that are just the right size and shape to enable a particular molecular ‘building block’ to slip into it. It’s vital that only the right building block can fit in. Next door there’s a niche for another building block; also of course exactly the right one. The clump is continually vibrating. It forces the two building blocks together and pops them out before the next vibration can separate them again.

Other enzymes break down the large building blocks, so that the smaller blocks can be reused. In this case of course the single niche is the right size for the selected component to slip into. It is snapped apart and the individual blocks are ejected before they can be recombined.

Why have different enzymes for the two jobs? Presumably it’s because it provides better control of the two opposite activities.

It’s the bases (adenine, cytosine etc.) that are difficult to make. The amino acids are much easier, and it’s these that astronomers tend to find on their patch.

When it comes to plants and animals, even fungi, the similarities are very much greater still. We are all based on the same eukaryotic’ cells. Indeed you would be hard put to it to distinguish a plant cell from an animal or fungal cell, unless it was a green one. Then it would contain chlorophyll for converting light into energy.

Plant and animal genes, and probably those of fungi too, tend to be remarkably similar. The tropical rain forests are fundamentally some of the easiest places on the planet to live, with constant warmth and moisture. This makes them the most competitive and therefore paradoxically some of the toughest. Everything that lives there has to work extra hard to avoid being eaten and being infected by diseases. Since we are so similar, there’s every chance that the protective chemicals that they are forced to invent will be useful to us too.

When did Life emerge?

We will never know when Life first appeared on our planet. If you take the view that “extraordinary claims require extraordinary evidence” then you will want to put the date fairly late. Even 3½ thousand million years ago may be too early for you. But if you follow the “absence of evidence is not evidence of absence” way of thinking then you will want to put the dawn of life much earlier. You will, for example, be much more inclined to believe that the controversial evidence for life in the Isua deposits is real.

The legendary Stanley Miller was once asked how long it might have taken for life to originate. He said “a decade is probably too short, and so is a century. But ten- or a hundred-thousand years is probably O.K, and if you can’t do it in a million years then you probably can’t do it at all”.

The advent of life was originally thought to be a millions-to-one chance, and that we are probably unique in the Universe. But Miller is expressing very clearly the opposite view – that if the conditions are right, then the emergence of life is natural and probably inevitable. I think this is a widely held view these days.

There’s evidence from zircons that conditions could have been conducive to life as early as 4.4 thousand million years. This is less than 200 million years of our planet’s formation. There’s no evidence at all that life actually got going as incredibly as early as this. Nor will there ever be. But it’s perfectly possible. Unfortunately there were some terrible upheavals that happened after that. Some scientists believe that these would have wiped out any life that did emerge. However other scientists reckon that the evidence points to these late upheavals being a good deal less devastating than they have been painted. For my part, I’ve always felt that it would have been incredibly hard for an upheaval to completely wipe out every last vestige of life on the planet. And a single small colony, buried deep in the mud at the bottom of a deep ocean, would be enough to re-colonise the planet as soon as conditions eased.

This picture of an Achaean landscape is by Peter Sawyer of the Smithsonian Institute.

The Isua rocks that we mentioned above are something under 4 thousand million years old (3.8 kMy I think is the official figure). And they contain tantalising deposits of carbon. Now carbon deposits are normally the remains of long-dead life (think coal). But ‘extraordinary claims require extraordinary evidence’, and many scientists regard the idea that life could have got going so early as truly extraordinary. I can’t see what’s extraordinary about it myself, but there you go. Huge amounts of research have gone into trying to prove beyond any shadow of doubt that the Isua carbon is indeed the dead remains of early life. And the story has fluctuated wildly down the years.

I think we can safely say that life ‘may have’ been around as early as this. Or even that it ‘probably was’. But we may never be able to say that it ‘certainly was’. My guess is that, if there was life around at Isua time, then it was probably a primitive form of something not unlike today’s bacteria.

The first solid evidence of Life is ‘only’ 3½ thousand million years ago. And I’ve read that some scientists dispute even that.

The evidence takes the form of ‘micro’ fossils. As the link shows, they look remarkably like modern bacteria – so like in fact that the scientists that discovered them even gave them pseudo modern names. Bacteria may be one of the simplest life-forms on the planet. But they are very sophisticated little beasties just the same. I’ve put this diagram in just to show this. You will have to look on the Internet if you want to know what the various components are.

Some bacteria can move. In the jargon, they are ‘motile’ (what’s wrong with ‘mobile’ you may ask, and I have no answer). This is a motile one. The small lump on the end of the tail is called a proton motor, and it spins. The spinning tail propels the bacterium in a haphazard way, hopefully away from somewhere it doesn’t want to be to somewhere more desirable. This diagram only depicts one ‘flagellum’. But many pictures of bacteria, including the one in bacteria, show them sporting a forest of them.

By the time anything like this appears in the fossil record, life was already highly developed, and must have been going for a long time. More

How did Life emerge?

We’ll probably never know. It all happened a very long time ago, on an Earth substantially different from our modern one. Scientists are struggling to understand how emerging life could have made the jump from simple chemicals to even the simplest modern life-form. As the picture shows, even the humble bacterium is actually a very sophisticated organism. Viruses don’t count. They are pure parasites, and can’t exist without a more advanced host to prey on.

But there are some things that we can say to make it all seem a little less miraculous.

First the process will not have been simple (is it ever in this game?). There will have been many false starts and many side alleys travelled down.

An increasingly popular theory was originated by one Gunther Wächtershäuser. Wächtershäuser believes that the key ingredient that enabled life to get started was pyrite (iron pyrites, fool’s gold). You can see from the picture why it’s called fool’s gold. The yellow specks are very realistic. Pyrite is a mixture of crystals of hydrogen sulphide (H₂S, bad-eggs smell) and iron sulphide (FeS). And it grows spectacularly around the hydrothermal vents in the deep ocean.

We won’t go into it. It’s on the Internet (don’t forget the first ‘s’ if you look Wächtershäuser up). But it seems that various organic compounds are generated naturally, by processes that are entirely ‘inorganic’.

To get far, any emerging life-form would have to have some kind of enclosure, so that it doesn’t lose any building blocks. I’ve seen a number of ideas about what the very first enclosure might have been. But it seems that the ‘prebiotic soup’ will have contained a plentiful supply of detergent molecules. These detergent molecules form naturally into underwater bubbles, as this diagram from Scientific American (Oct. ’85) shows.

The blue-blob end loves water, but the the tail is waxy and hates it. If you pour some detergent into water then it will automatically form itself into bubbles, with the water-loving end facing out, and the other end protected.

But that’s not all. The bubble wall is automatically ‘semi-permeable’. It will allow the small molecules of simple chemicals through. But if these simple chemicals should combine together to form larger molecules – either by chance or because there’s some deliberate chemistry going on – then they cannot get out again. They are trapped. If the bubble should get too large and burst, the edges immediately close up again, to form two new offspring.

Emerging life took advantage of this natural feature of detergent bubbles. So the cells walls of bacteria are basically made of soap – as are the cells that you are made of. Our cells are much more sophisticated, as the second picture shows. But you can still see the soap molecules holding it all together.

The next thing that emerging life needs is some kind of ‘blueprint’ from which to make its chemical building blocks. Modern life uses DNA. DNA is ideal for the job, but it’s a sophisticated molecule and difficult to make. The RNA, that waits upon it like a servant and does its bidding, is less good as a permanent record. But it’s simpler, and there are hints that it may have done the job on its own at one time. Before that, who knows?

The third thing that life needs is energy. The ideal energy source for life, even today, is glucose (C₆H₁₂O₆). Amazingly, it seems that there was glucose around in the ‘pre-biotic soup’. Experiments to simulate the early-earth environment produce it, together with a wide range of other sugars. I got this fact from William Schopf’s book ‘Cradle of Life’, so how it fits in with Wächtershäuser’s work I can’t tell you.

And finally, life needs raw materials. The raw materials of life boil down to just four elements, what Schopf calls CHON – Carbon, Hydrogen, Oxygen and Nitrogen. The first three were already available in the sugar. Emerging life will have had plenty of ammonia available (NH₃), which which will have given it the nitrogen.

On this page we have been into speculation, and trying to establish what might have been possible.

The next chapter in the tale involves organisms very much like modern bacteria.