Sunday, August 5, 2007

Information, please- Part 3

In this installment, let’s actually look at the genetic basis for showing that new information in organisms has appeared many, many times.

First of all, let’s discuss some principles of population genetics that relate to the definitions of information we discussed last post.

Evolution does not act upon individuals, it acts upon populations. As a population evolves, new alleles (types of a single gene) will appear due to mutation and other events. Some of these alleles will increase fitness, some will decrease it, and some will have no effect at all. As natural selection acts upon the population over time, the frequency of these alleles will change. And that, in a nutshell, is evolution.

Mutations, gene duplications and other events that change the genome can be seen as adding Shannon information. The added information may or may not “make sense,” but it increases the randomness of the genome while decreasing compressibility- the definition of Shannon information. Then, as natural selection acts upon the variation produced by such events, randomness and compressibility is decreased- an increase in complexity information. But this is a dynamic process; as complexity increases in one area of the genome, mutation may cause randomness to increase in another. There is plenty of information here, and it is ever-changing.

A common misconception is that the information content (either in terms of Shannon information or complexity) of a genome is directly related to how “simple” or “advanced” we perceive that organism to be. There is no such relation. Some very interesting data on animal genome size measured in picograms shows this easily.

The organism with the largest genome isn’t us humans. It isn’t even a primate or a mammal. It’s an amoeba, Chaos chaos, with a whopping 1400 pg genome (the average mammal has a wimpy 3.47 pgs)! Among vertebrates, the award goes to the marbled lungfish (talk about primitive animals!) with 132.83 pg. Among mammals, the winner is the red viscacha rat with 8.40 pg. How about the primates? The winner is the tarsier, a bushbaby-like critter with a genome of 5.26 pg.

So how do we stack up with the apes?

Human- 3.50 pg
Chimpanzee- 3.46 to 3.85 pg
Gorilla- 3.52 to 4.16 pg
Orangutan- 3.6 to 4. 1 pg.

So, as this shows, size isn’t everything.

It is also a common misconception that the “purpose” or “trend” in evolution is to produce increasingly-complex organisms. There is no trend in evolution towards ever-increasing complexity, nor is there a reason to be one. Evolution favors what works, not what is most complex. If what works in a population is simple, then simple will be favored, and evolution will show increasing simplicity. This explains, for example, the loss of some features in parasitic organisms. Evolution also has no “purpose” or “direction.” It isn’t headed anywhere in particular.

All right then. The information in genomes changes over time as information is added or subtracted then acted upon by natural selection. So how about some examples of how this happens?

One of the commonest scenarios for the evolution of completely novel information is gene duplication, where part or all of a gene is doubled. When this happens, the organism can often keep functioning normally, as no genetic material is lost. However, as there are now extra copies of some genetic material, that material is free to mutate, as the original copies retain the original function. This is the most common method by which totally new genes are created. These genes are definitely “new information” in any meaningful sense of the word; they often code for proteins never before observed. As we discussed last installment, as long as one accepts that writing sentences in the English language can lead to new information, one has to accept that writing new sentences in DNA leads to new information.

I decided to query the Medline database, which indexes most journals having to do with genetics, for “gene duplication”, and turned up thousands of studies. Here are just a handful of them- all published in the last four months from April 2007 onwards! In each case, I’ve given a very brief synopsis of the research, along with what the authors had to say about the role of gene duplication in evolution, if stated.

Venom and coagulation factor in Australian snakes
(also here and here)
“Proteins with new function originate through gene duplication followed by divergence.”
In several Australian elapid snakes, two similar proteins exist. One codes for a clotting factor very similar to that found in many vertebrates, the other is a venom. The venom arose from a duplication and subsequent mutation of the clotting factor.

Butterfly color
At least four separate duplications of the L-opsin gene and subsequent changes are responsible for blue colors in two families of butterflies. Each duplication has resulted in a different color.

Cichlid potassium channel genes
Thus, the evolution of kir7.1 genes in cichlids provides a typical example of gene duplication-one gene is conserved while the other becomes specialized for a novel function.
Many families of cichlid fishes have an extra copy of the inward rectifier potassium channel gene, kir7.1. This copy arose in a cichlid ancestor through duplication. It has evolved to perform different functions and ins found in different tissues than the original gene.

Fish colors
Fish have more types of pigment synthesis genes than any other vertebrate. This is due to duplications and subsequent modifications of various genes in the different pigment production systems in fish.

SKP in angiosperms
Gene duplication plays important roles in organismal evolution, because duplicate genes provide raw materials for the evolution of mechanisms controlling physiological and/or morphological novelties.
SKP-1, an enzyme that mediates protein degradation, has undergone multiple duplication events, resulting in at least 47 different genes. It is one of the most rapidly-evolving plant genes known.

Shrimp antimicrobials
Penaeid shrimps (the group including most commercially-harvested shrimp) produce several different peptides that fight microbes and funguses. Each of these peptides arose from a novel gene duplication.

Chordate evolution
Internal duplication can enhance the function of a gene or provide raw material for the emergence of a new function in a gene.
The number of duplications present in the genome increases with increasing complexity of the organism. Chordates have more duplication than worms, which have more than fungi.

Corn borer sex pheromones
Female corn borers, a species of moth, attract mates with pheromones. One genus of corn borer, Ostrinia, has an “entirely novel class” of genes producing the pheromones, derived from duplication of one gene that then fused with a retroposon.

Yeast enzymes
Gene duplication in one species of yeast led to “a 'novel' transaminase enzyme” which has a wider range of function than the original.

MHC genes in bank voles
Our findings suggest a snapshot in an evolutionary process of ongoing birth-and-death evolution.
Bank voles are in the process of evolving better parasite resistance. They have at least 26 different alleles of one of the most important genes in the parasite-fighting process, with up to 4 duplications of the gene involved. One group of genes has lost function, one group is being lost due to parasite resistance, and one group functions well.

Mosquito pesticide resistance
Gene duplication is thought to be the main potential source of material for the evolution of new gene functions.
The common house mosquito has, at least three times in the past 40 years, developed pesticide resistance through gene duplication events.

Fish eggs
Ray-finned fishes are the most successful group of vertebrates in terms of species diversity. They evolved with great speed. Originally a freshwater group, hey were able to colonize the oceans when they began to lay eggs adapted to seawater. This adaptation arose when gene duplication and modification produced a modified protein that allowed eggs to survive in seawater.

And, if that’s not enough for you, here are a few more examples from other sources that I found interesting and compelling:

Fish antifreeze
A duplicated gene for a protease (digestive enzyme) mutated into a gene that produces an antifreeze that allows Arctic cod to live in freezing waters.

Leaf-eating monkeys
As scientists piece together the genomes of more and more life forms---from fruit flies to humans---they're finding ample evidence that new genes have often been created through the duplication of existing genes. Of the more than 40,000 genes in the human genome, for example, about 15,000 appear to have been produced by gene duplication.
A duplicated an mutated RNAase gene produces a new enzyme that helps leaf-eating monkeys digest their food.

Bicoid gene in flies
The bicoid gene, which affects egg development, arose from gene duplication.

Looking at all of these examples- which are just a tiny fraction of the articles available on one tiny facet of the possible ways that information arises in evolution- the fact that evolution can and does create new information is blindingly obvious. The only way to deny it is for the creationists to come up with yet more warped definitions of "new" and "information" that will be simply verbal games that ignore what is obvious scientific fact. But those new sophistries, by the creationists' own definitions, cannot be "new," as they will create them from the same tired alphabet of 26 letters which gave rise to the ancestral deceptions.


Nancy Blog said...

This is quite an interesting, and lengthly argument. I think the fact that all those scientists involved in the Steve Project are all named Steve and believe in evolution is proof of God's sense of humor, if not Her wisdom. Here's the thing - one person's creation(ist) story is another person's myth. There are many creation stories from many religions, each one claiming to be the truth, as revealed by God. The Theory of Evolution is the only theory that is consistent across all history, and is flexible enough to be updated when new discoveries are made. But you will never convince a creationist of this. It is possible to believe in God, and not discount science and the theory of evolution. In my opinion, the theory of evolution proves just how magnificent and awesome God is.

Cris Waller said...

Thanks, Nancy.

You bring up a very important point. Once does not have to be an atheist in order to accept the reality of evolution. Only a very narrow view of deity demands such a restriction.