Here is an interesting story:

Researchers at the Albert Einstein College of Medicine (AEC) have found evidence that certain fungi possess another talent beyond their ability to decompose matter: the capacity to use radioactivity as an energy source for making food and spurring their growth.

the researchers measured the electron spin resonance signal after melanin was exposed to ionizing radiation and found that radiation interacts with melanin to alter its electron structure. This, they believe, is an essential step for capturing radiation and converting it into a different form of energy to make food. Until now, melanin’s biological role in fungi - if any - had been a mystery. Interestingly, the melanin in fungi is no different chemically from the melanin in our skin, leading Casadevall to speculate that melanin could be providing energy to skin cells.

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Let me remind you of two recent postings. First, the RNA world has played a crucial role in the evolution of the human brain. Second, as I have hinted, evolution by gene duplication echoes a teleological essence to evolution. Let me now unite these two themes with another phenomenon – functional pseudogenes.

Pseudogenes are sequences of DNA that are similar to functional genes, but have acquired defects that prevent the expression of functional products. Such sequences are generated by gene duplication, where one duplicate undergoes some lesion that is not selected against. As a result, the defective gene (now a pseudogene) may continue to undergo further mutational insult, effectively causing it to decay into oblivion over time.

Yet because the cellular architecture entails that an RNA world exists in parallel with a protein world, might many of these pseudogenes simply be genes escaping the constraints of the protein world in order for the opportunity to more fully participate in the RNA world?

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Arabidopsis thaliana is a plant that underwent a duplication of its entire genome about 20-40 million years ago. Researchers from the University of Texas recently tested the rate of expression divergence between these duplicated genes. [1] What they found was:

The proportion of duplicate genes upregulated under abiotic stress in roots or shoots is significantly greater than that of other genes in the genome.

Furthermore:

We obtained the same conclusion for duplicate genes in response to biotic stress induced by pathogen infections or pathogenic molecules.

And:

The data suggest that duplicate genes are preferentially involved in stress responses, probably through preferential retention or expression divergence of duplicate genes.

The researchers also looked at duplicated genes involved in development:

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From here:

Justin Gallivan, PhD, assistant professor of chemistry, and graduate student Shana Topp successfully reprogrammed E. coli’s chemo-navigational system to detect, follow and precisely localize to specific chemical signals. In doing so, the scientists exploited E. coli’s natural chemotaxis, a microbe’s ability to move toward specific chemicals in its environment.

“Equipping bacteria with a way to degrade pollutants, synthesize and release therapeutics, or transport chemicals with an ability to localize to a specific chemical signal would open new frontiers in environmental cleanup, drug delivery and synthetic biology,” says Dr. Gallivan.

[…]

Chemotactic bacteria navigate chemical environments by coupling their information-processing capabilities to powerful, tiny molecular motors that propel the cells forward.

Researchers have long envisioned reprogramming bacteria so that microbes capable of synthesizing an anti-cancer drug, for instance, can be used to target diseased cells while sparing healthy cells of side effects. Likewise, scientists are researching ways to use bacteria to clean up oil spills or remove other pollutants from soil, water and wastewater.

“This new ability to equip motile bacteria with a precise and tunable chemo-navigation system will greatly enhance the impressive arsenal of natural and engineered cell behaviors,” says Dr. Gallivan.

Such research teaches us two things.

1. Design and evolution can indeed co-exist. To sufficiently account for the existence of these bacteria, we must appeal to a) their evolutionary history and b) the researcher’s design. This may seem too obvious to have to point out, but given that so many think that design is somehow contradictory to evolution, it is important to establish this principle of co-existence.

2. It is intriguing that these bacteria can so easily be re-designed. The reprogramming of these bacteria involved minor tweaking that was facilitated by the inherent properties of the bacteria. Remember that natural selection itself cares only about one thing – turning out more survivable offspring than the next fellow. Whether such an approach to “design” is responsible for such a sophisticated, “reprogrammable” system is not clear.