Simulating the origin of life

An interesting beginning, though the conclusions thus far appear to be self-evident.

Avida operates by creating a virtual world in which programs compete for CPU time and memory access, just like organisms competing for resources in the real world. These virtual lifeforms can self-replicate, but crucially they have copy error programmed into them so that, just like in real life, mutations can be carried over to daughter programs to simulate evolution by natural selection.

In Avida the first replicator is purposefully written, but in real life the first biological replicator had to emerge spontaneously from nature, and this is where selectivity comes in. “It turns out that replicators, whether in nature or within Avida, are rare,” says Adami, “and the odds are that a random program – or assembly of molecules – will not replicate.”

The programs are written in a computer language that contains 26 instructions, analogous to individual monomers in chemistry, labelled as the letters of the alphabet from a to z. Adami uses this system to draw an analogy to the written word. If these polymers were meant to be ‘words,’ they would mostly be gibberish, containing a jumble of ‘q’s and ‘z’s and other letters without connoting meaning. Similarly, the molecules that were available on early Earth had many different ways to bind together to produce a variety of chemical reactions; the chance of nature generating the right molecular structure to enable self-replication is slim.

Adami points out though that language is loaded to favor certain letters that crop up more often than others. Seldom are ‘q’s or ‘z’s used, but ‘t’s and ‘e’s and ‘a’s are common letters in words. Adami suggests that the selection problem can be better understood as the ‘biased typewriter’ model, in which some molecules and chemical reactions are more likely to occur than others. If the letters in the bag were scrabble tiles, with more of the common letters and fewer of the rarely used letters, then even pulling them out at random would lead to some real words being produced, just by chance.

With his student Thomas LaBar, Adami tested the principle of the biased typewriter in Avida, loading the instructions with those monomers that are useful for self-replication. In a billion random programs made from chains of ‘letters’ that Avida subsequently produced, Adami found that 27 of them could self-replicate. He used those 27 to create a probability distribution and then kept running the program, finding that the number of self-replicators kept increasing dramatically. “In other words, what this tells you is that if you have a process that generates these monomers at the right frequency, then you’re going to be able to find the self-replicators much faster,” says Adami.

https://www.astrobio.net/news-exclusive/computing-the-origin-of-life/amp/