Rediscovered Innovation? Bacteria Mutations and Evolutionary Thinking

[Originally published as Desperately Seeking Innovation]

One of the biggest problems facing evolutionists is the explanation of how brand new information can be added to a genome. After all, if flagellates eventually evolved into philosophers, an enormous amount of truly original information had to be added to the flagellates’ (and their descendants’) genomes. However, genomes are so well-designed and highly structured that it is difficult to imagine a naturalistic process that could add information to them. Nevertheless, evolutionists have tried their best.

One of the more popular notions is gene duplication followed by mutation. We know that genes can be duplicated. It happens quite frequently. The thought is that when a gene is duplicated, one of the copies can continue to produce the protein it is supposed to produce, while the other copy is free to mutate and find some completely new function.

While the thinking behind this idea is logical, experimental evidence to support it has been hard to find. As a result, evolutionists tend to jump on any experimental finding that might suggest the idea is accurate. This is well illustrated by a Science Daily article claiming that researchers have finally shown how a gene can pick up a brand new function, which can then be amplified and modified over time.

Unfortunately, the article’s claim is not accurate. I had already read the scientific paper on which the article was based¹, so when I read the popular level version, I understood how incorrect its claims are. However, I am sure many of their readers do not. As a result, I want to discuss the study’s actual findings. They are very interesting, and they tell us a lot about the genetics of bacterial adaptation. However, they don’t tell us anything about how genes acquire brand new functions or about how information can be added to a genome.

In the study, the authors examined populations of Salmonella enterica over many, many generations. Normal versions of these bacteria can produce (among other things) two amino acids, histidine and tryptophan, and they have many genes devoted to those processes.

As is the case with most chemical reactions that go on in living systems, many of the steps in the production of these two amino acids need to be sped up, and the bacteria produce specific enzymes to do that. In this case, the researchers studied two different enzymes, one for speeding up a step in the production of histidine, and another for speeding up a step in the production of tryptophan. The genes that produce these enzymes are called HisA and TrpF, respectively.

The researchers chose a strain of Salmonella enterica that did not have the TrpF gene. As a result, bacteria in this strain cannot produce tryptophan and must instead acquire it from their environment. They found that after many generations of stressing these bacteria with low levels of tryptophan, a new strain was produced that could make its own tryptophan! The amount it could make was very low, but it was enough for them to survive without getting any tryptophan from their environment. They found that if they studied this strain for 3,000 generations in a tryptophan-free environment, the bacteria got better and better at making tryptophan.

So how did the bacteria develop the ability to make tryptophan, even though they didn’t have the necessary gene? The HisA gene that they use to produce histidine experienced two mutations. The first mutation stopped its ability to make histidine, but it produced an ability to make tryptophan slowly. The second mutation then restored its ability to make histidine and had no effect on its ability to make tryptophan. So the gene went from making one amino acid to making two amino acids.

That sounds like the gene developed a brand new function, right? Actually, it didn’t, but more on that in a moment.

The main focus of the paper is what happened next.

When they started following the new strain of bacteria, they found that its tryptophan-making abilities got better and better. This happened because the gene was duplicated, and the duplicates experienced more mutations. They found that in the end, three specific kinds of genes were produced from the duplication and subsequent mutation of the original, multipurpose gene.

• Some lost their ability to make tryptophan and went back to making only histidine.
• Others lost their ability to make histidine and devoted themselves solely to making tryptophan.
• Still others kept making both amino acids, but they improved their ability to make tryptophan.

So in the end, gene duplication and subsequent mutation did, indeed, lead to an improved ability to make tryptophan.

But what of the original two mutations that took a gene which could only make histidine and turned it into a gene which could make both histidine and tryptophan?

What the Science Daily article leaves out, but the scientific paper includes, is the fact that the production methods for histidine and tryptophan are incredibly similar, at least when it comes to the steps in which these genes are involved. As a result, many bacteria (such as those from the genus Streptomyces and the genus Mycobacteria) do it with only one gene.

So in the end, there are “specialist” genes and “generalist” genes involved in the production of these two amino acids. Some bacteria (like normal Salmonella enterica) use specialist versions of the genes, and as a result, they require both genes. Other bacteria (such as those from the genus Streptomyces and the genus Mycobacteria) use a generalist gene, and as a result, they don’t need two genes. The generalist gene has all the information necessary to produce both amino acids.

So what does the experiment really show us?

It shows us how generalist genes become specialist genes. Most likely, the original bacterial genome had a generalist gene involved in the production of both amino acids. Over time, some species of bacteria experienced gene duplication and subsequent mutation that turned the generalist gene into two specialist genes, each devoted to making a separate amino acid.

However, when the Salmonella enterica used in the experiment were deprived of their tryptophan-making gene, mutations were able to “revert” the histidine-making gene to a poor version of its original, generalist form. Gene duplication and subsequent mutation could then develop either two specialist genes again or one really good generalist gene.

So the experiment tells us something very valuable. It tells us that bacteria probably started out as generalists when it came to making these two amino acids, but over time, gene duplication and subsequent mutation produced several species that became specialists. When those bacteria are deprived of one specialist gene, the right mutations can revert the other specialist gene back to its generalist form, and the process can then start over again. Thus, while this study tells us nothing about new information being added to a genome, it does tell us something about how bacteria have changed over time.

It also shows how desperate evolutionists are to find a method that will produce real innovation in a genome. In the end, they call it an “innovation” when a bacterium reverts to old information!

This reminds me of an event that happened a few years ago in Dr. Richard Lenski’s long-term bacterial evolution experiment. Even though that experiment confirms the creationist view of the genome, his team tried to spin it as an experiment that supports the evolutionary view of the genome. They said that bacteria which were unable to metabolize citrate in the presence of oxygen were eventually able to evolve the ability to do so.² This, they claimed, was an example of a brand new trait emerging as a result of evolution.

However, Dr. Michael Behe pointed out that the bacteria in question always had the ability to metabolize citrate, but the ability was restricted to environments where there was no oxygen. As a result, Dr. Behe suggested that the most likely way this “new ability” evolved was by the destruction of a regulatory sequence that restricted the process to situations without oxygen. When that regulatory sequence was destroyed, the bacteria could suddenly metabolize citrate in all environments. Thus, this “new trait” was really the result of a loss of information in the genome.³ Subsequent genetic analysis of the bacteria involved demonstrated that Behe was correct.

So in the end, we see that mutation, gene duplication, and natural selection can “tinker” with information that is already in the genome, but so far, there is no evidence that they can produce brand new information.

References

1. Joakim Näsvall, Lei Sun, John R. Roth, and Dan I. Andersson, “Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence,” Science 338:384-387, 2012.
2. Blount Z. D., Borland C. Z., and Lenski R., “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli,” Proceedings of the National Academy of Sciences USA 105:7899–7906, 2008.
3. Michael J. Behe, “Experimental Evolution, Loss-Of-Function Mutations, and The ‘First Rule of Adaptive Evolution’,” The Quarterly Review of Biology, 85(4):419-445, 2010.