The Origin of Life, Part IV: Genetic Code

Ok. We’ve shown that it is possible for cell-like structures to spontaneously generate in certain conditions. How do we get from protobionts to all the enormously complicated and diverse stuff that we see today? We don’t know the answer to that question and we probably never will. We do know, however, part of the answer. Part of the answer has to do with reproduction.

How does a living system reproduce? What minimally do we need to get reproduction? How reproduction arose is an especially tricky problem. It is the problem that is most debated today in the area of the origin of life.

To understand what is needed for reproduction, let’s imagine we’re back in time. Let’s imagine we have some proto-cells that are functioning. Let’s say that by chance, one of these protobionts just happens to come up with some unique new trait. This trait could be anything. For example, it could be a new kind of molecule that makes this cell more durable. It could be a new kind of molecule that increases its ability to take up material from the outside.

This protobiont is different from the rest. It is somehow more efficient, better at doing its job. The problem is that we have only one of them. That individual won’t last forever. Even if it does, there will only be one of them. This issue leads us to reproduction. This problem would be solved if our protobiont could reproduce itself in a way that would pass that useful trait on to its progeny. How does it do that? Well, cells split into two. We have one cell, it grows a little larger and splits into two. In essence, that’s reproduction. This is not enough, however.

The Genetic Code and the Problem of Replication

If the trait we are talking about is a molecule, which of the daughter cells gets the molecule? Even if there is a lot of these molecules and each daughter cell gets a half of it, and the daughters of these cells get the half again, eventually this property will fade away. What we need instead is for these primitive cells to somehow be able to make completely new and accurate copies of themselves. They have to be able to store information about the structure of the molecule and transfer that information to its offspring.

How such a mechanism for storing and transmitting this kind of information came about is one of the unresolved questions about the origin of life. We know, however, that there is such a molecule in modern cells. This is a cell that accesses a blueprint for making more molecules. This molecule is called Deoxyribonucleic acid, or DNA.

DNA passes its information onto another kind of nucleic acid, RNA, and then the information goes from RNA into proteins. This is the way information works in modern cells. In this system, DNA acts as some kind of blueprint, RNA as the translator and proteins are the product of that blueprint. Proteins do much of the real work in modern cells.

Here we encounter a really serious problem, however. DNA could not have been the storage molecule that first arose in early life. Why not? The reason is that DNA can’t replicate itself. DNA requires a huge number of other proteins acting as enzymes to replicate. DNA in modern cells can be replicated but only if there are proteins to do the replication job. Proteins that could do that replication job might have arisen sometime in the early history of life on Earth, but they couldn’t have arisen before there was DNA to store their code. We need to postulate simultaneously the appearance of DNA that could store information about proteins and proteins that could replicate that DNA. Which came first, the chicken or the egg?

Neither could have come first because DNA and proteins can’t exist without each other in modern cells. Also, it is unbelievably improbable to think that just the right kind of proteins and just the right kind of DNA happened to arise spontaneously sometime in the early history of life.

What was need, instead, is for some kind of molecule that could do both of these things. A molecule that could replicate itself and it could do other useful things in the cell. Today we’re beginning to think that when life arose the molecule that did that was the nucleic acid RNA, or some early form of what we know today as RNA. Why we think that?

The RNA World

At the beginning of the 1960’s researchers have begun to suspect that RNA might have acted as the first blueprint or genetic material. In the laboratory, it is possible to put in some kind of RNA and then some building blocks, and under the right conditions the RNA replicates itself. RNA in the solution somehow acts as a template that helps the monomers come together in the right way and also polymerize.

A second breakthrough that led people to think that RNA might be the first information processing molecule came in 1983, when Thomas Cech actually discovered that, in modern cells, there are some kinds of RNA that do act as catalysts the way protein enzymes do. That is, they perform some important biochemical tasks in the cell. They are generally called ribozymes.

The important point is that these rybozymes are functioning as catalytic molecules just like protein enzymes. We’ve got two things now. We’ve got evidence that RNA can replicate itself and also evidence that RNA can have some sort of catalytic function. Taken together, these two sets of results suggest that in the very early stages of life, that magical point where a non-living protobiont somehow slipped over the edge into the state that we might want to call a living cell, happened in what we now call an RNA world. RNA actually dominated as the key biological molecule.

At some point after the RNA world, things changed. RNA had gotten the system rolling, but eventually DNA and proteins took over. DNA took over the job of being the information-bearing molecule. Proteins took over the job of doing all of the catalytic and other kinds of work in the cell. RNA became relegated to just an intermediate in the process.

Why this would happen is fairly obvious. Proteins are extraordinarily versatile molecules. They do an enormous number of tasks. Their versatility comes from the fact that they can assume all sorts of complicated shapes in a way that RNA can’t. Proteins clearly took over doing the real work in the cell because they were really good at it. DNA assumes a particular kind of chemical configuration that makes it really good at storing information in a way that RNA is not particularly good. Once we have DNA, it is much better than RNA at making more copies of itself and storing that information. So, it took over that job. RNA became just an intermediate.

I think that with this we have what is basically needed to the appearance of life. We’ve explained the origin of life, at least in part. Quite an accomplishment, eh? How do we get from these simple cells to platypuses and other things is another subject, and don’t worry, I’ll try to tackle it.

Return from Genetic Code to The Origin of Life

1 Comment:

Sam Imnot said...

Has anyone ever calculated the probability of a self-encoding, self-replicating, robust piece of RNA spontaneously forming is? It seems impossible that something like that could form in large enough quantities to allow for any significant evolution of the molecule. With that probability in mind, how did a piece of RNA evolve from a primordial soup that produced racemic amino acids and basic polypeptides, in an environment that required considerable water for a cell membrane to form in? How would the polypeptides not undergo hydrolysis while the cell membrane was forming? None of this seems realistic to me, whatever the biological community may say. I didn't use to give much credence to Michael B.'s irreducible complexity argument before, but now after reading your entire section on origins, I'm beginning to think he could be right- too many things have to happen simultaneously where the process of creating one would likely destroy another, or where two or more processes must evolve simultaneously in order to work at all. While some processes seem plausible in vitro in some conditions, like polypeptide polymerization, those same polypeptides would likely degrade in the highly aqueous environment necessary for cell membrane formation.
Seriously, what are the odds!? I sincerely want to know the statistical if you know them, because they seem too improbable for me to believe this explanation at this point.

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