The concept of irreducible complexity

Welcome to the Wikiversity learning project for exploration of the concept of irreducible complexity in living organisms.

Introduction
The idea of Irreducible complexity was made famous by Michael Behe. In his book, Darwin's Black Box, Behe described the multiple molecular components that are involved in biological processes such as translation. Within biology, "translation" is the term used to refer to the process by which cells convert genetic information into specific sequences of amino acids in proteins (see Figure 1). This process of translating a sequence of nucleotides in RNA into a corresponding sequence of amino acids in a newly produced protein is fundamental to all known living organisms on Earth and it involves the coordinated activity of many pre-existing specialized proteins. We must wonder, how did this biological process for producing new proteins arise? It seems paradoxical to say that new proteins are made by a complex process that uses many pre-existing proteins. Behe concluded that such "systems of horrendous irreducible complexity" force us to realize that, "life was designed by an intelligence".

This learning project explores in detail the specific example of the cellular process of translation as a test case for the concept of irreducible complexity.

Directed Panspermia
During the 1960s Francis Crick became concerned with the origins of the genetic code and the many cellular components involved in protein synthesis. In 1966 Crick took the place of Leslie Orgel at a meeting where Orgel was to talk about the origin of life. Crick speculated about possible stages by which an initially simple code with a few amino acid types might have evolved into the more complex code used by existing organisms.

At that time, all known cellular enzymes were known to be proteins and ribozymes had not yet been found. Many molecular biologists were worried about how to account for the origin of a protein synthesis system as complex as what exists in organisms currently living on Earth. How could a protein synthesis system that itself involves many protein enzymes arise spontaneously? In the early 1970s Crick and Orgel speculated about the possibility that maybe the production of life from collections of non-living molecules was a very rare event in the universe, but once it had developed it could then be spread by intelligent life forms using space travel technology, a process they called “Directed Panspermia”.

In a retrospective article, Crick and Orgel noted that they had been overly pessimistic about the chances of life evolving on Earth when they had assumed that some kind of self-replicating protein system was the molecular origin of life. Now it is easier to imagine an RNA World and the origin of life in the form of some self-replicating polymer besides protein.

Replication before translation
Even more fundamental to life than translation is replication of an organism's genetic molecule. All known existing cells use DNA as their genetic molecule, but some viruses use RNA as their genetic molecule. Cells and viruses must replicate their genetic molecules in order to pass their genetic information and identity on to additional cells or viruses. RNA is the one known type of biological polymer that functions efficiently as either a genetic molecule or as an enzyme. Might the first forms of life on Earth have had RNA before they had either DNA or translation?

If early organisms existed in an "RNA World", then ribozymes might have been responsible for producing early proteins. If so, this would remove the apparent paradox of pre-existing proteins seeming to be needed in order for a protein-producing translation system to arise.

Wolf and Koonin have recently addressed the idea that translation might be an irreducibly complex biological process. Wolf and Koonin described a series of steps by which a complex multi-protein translation system might have evolved from an earlier RNA-based protein synthesis system. Behe claimed that there are many complex multi-protein systems that could never have evolved by spontaneous steps of molecular evolution. Wolf and Koonin suggest that, "the translation system might appear to be the epitome of irreducible complexity because, although some elaborations of this machinery could be readily explainable by incremental evolution, the emergence of the basic principle of translation is not. Indeed, we are unaware of translation being possible without the involvement of ribosomes, the complete sets of tRNA and aminoacyl-tRNA synthetases (aaRS), and (at least, for translation to occur at a reasonable rate and accuracy) several translation factors. In other words, staggering complexity is inherent even in the minimally functional translation system."

Figure 1 (above) is intended to illustrate the complexity of eukaryotic protein synthesis. Modern protein biosynthesis requires pre-existing proteins that replicate and repair DNA, regulate the transcription of genes and the production and processing of RNA molecules. Proteins are used to coordinate the synthesis and availability of nucleotide and amino acid building blocks of DNA, RNA and protein as well as all the energy required for their assembly. The modern ribosome contains dozens of proteins in addition to the ribosomal RNA molecules. As shown in figure 1, in addition to messenger RNA and ribosomal RNA, protein synthesis involves the participation of transfer RNA molecules as the carriers of amino acids that embody the genetic code. Additional proteins, aminoacyl tRNA synthetases, are used to couple the amino acids to the transfer RNAs. Additional proteins and types of RNA molecules are required for the production of functional ribosomal RNA from ribosomal RNA gene transcripts, the splicing of intron-containing transcripts, maturation of the ribozymes that catalyze splicing and there are other RNAs that regulate the degradation of messenger RNAs. In addition, all existing life forms on Earth have lipid bilayer membranes and many proteins that function as integral components of those membranes. nuclear pore proteins control the movements of RNA and proteins into and out of the cell nucleus as well as the generation of most cellular energy and the transport of food and waste molecules across the cell surface membrane. The apparent complexity of cells and the biosynthesis of proteins can be greatly simplified by making a single assumption: that there was once a "RNA World" in which proteins were much less important than in existing organisms. This assumption is consistent with the fact that ribozymes exist and the many different types of RNA molecules that are still retained as elements of the protein biosynthetic system (orange colored components in Figure 1).

It might be useful to review this article: Self-Sustained Replication of an RNA Enzyme.

Wolf and Koonin model
The Wolf and Koonin model for molecular evolution of a first translation system includes a dozen steps.

Help make video clips corresponding to the figures in the Wolf and Koonin article: video workshop.

Step 0 - ribozymes
The model assumes that ribozymes existed within some type of RNA World before there was ever a translation system. In addition, Wolf and Koonin assume that there was a process in existence that allowed ribozymes to evolve under selective pressures. In particular, the model gives emphasis to the evolution of new enzymatic activities.

Step 1 - amino acid activators of ribozymes
The concept of an RNA World does not mean RNA-only. Amino acids are among the small molecules that have been found to form spontaneously. It should have been possible for amino acid binding sites to exist on early ribozymes. In some cases, the binding of amino acids to ribozymes should have resulted in activation of ribozyme activity, leading to to positive selection for ribozymes with structures allowing better of amino acids.