Pesticides, RNA⇒DNA and wilderness

Enjoying beautiful June weather–and its been the best this year–is destroyed by a spray plane flying over.  But after this week we will have fewer. The Governor has signed a regulation outlawing the pesticide dicamba.  Last year I lost several trees to drift of dicamba.  No telling what it did to my health.

Pigweed is a weed most crop farmers will have to fight at some point. Pigweed has developed immunity to chemical pesticides.  Conventional farmers try every new chemical they can find to rid their fields of this pest. Organic farmers know that no weed is resistant to a sharp steel blade and use tillage to eradicate the weed.wildnessIn 2016 and 2017 farmers in the Delta have resorted to a very volatile chemical, dicamba, because nothing else works on pigweed.  The problem with dicamba is that it drifts to neighboring farms and kills the neighbors’ crops.  Unless your crops have been genetically modified to resist dicamba, they will be destroyed along with the pigweed.

Pigweed is a fascinating species in the genus Amaranthus.  This genus is also known for grain amaranth–which is high in lysine, an amino acid found in low quantities in other grains. Amaranth grain is free of gluten, which makes it a viable grain for people with gluten intolerance.  The many wild species of amaranth provide a pool for disease and pest resistance which can be used by plant breeders to improve grain amaranth.

Unfortunately for conventional farmers, the diversity and adaptability of the pigweed amaranth has overcome the best chemicals modern science can produce.

One research group has shifted the tolerance of pigweed to dicamba about three-fold in only three generations.  So dicamba will soon have to be replaced with other pest control techniques.  The co-evolution of herbicides and weeds makes some farmers get on the pesticide treadmill. Farmers who rely on pesticides are forced to use more and more and increasingly toxic chemicals to control insects and weeds that develop resistance to pesticides.

Pigweed’s ability to adapt makes it a resilient species in conventional farming systems.  No matter what chemical disturbance is thrown at it, it adapts and overcomes the disruption.

In ecological resilience circles, pigweed’s ability to adapt is known as conservative innovation. Pigweed innovates to meet the new disturbance, but its innovations conservatively maintain the other characteristics which make it adapted to farmers’ fields: short life-span, extremely high growth rate and seed production and ability to withstand overly dry or wet conditions. These qualities reflect the redundancy and ecological integration that resilient systems are also known for.

Resilience research not only explains the co-evolution of crops and weeds it also provides explanations for the changes in species which traditional Darwinian theory cannot explain.

Traditional evolution theory explains change in species as occurring by gradual accumulation of random mutations.  The fossil record does not bear this out.  Instead species appear to make radical sudden changes after staying the same for long periods. From trilobites to dinosaurs to worms, nearly all species have been shown to remain the same for eons only to abruptly change into a new species. These sudden changes after eons of stasis is known as punctuated equilibrium.

Resilience theory explains punctuated equilibrium with the quality of all resilient systems called self-organization. Self-organization turns a collection of interacting elements into an individual, coherent whole. This whole has properties that arise out of its organization, and that cannot be reduced to the properties of its elements. Such properties are called emergent.

We see this routinely in human systems.  Communities which bounce back most quickly after disaster are ones which are self-organized and do not wait for outside assistance. The creative destruction which characterizes economic change is based on emergent self-organization.  All the elements for production of automobiles were known long before cars were invented. When they were organized into a new system, the horse and buggy were consigned to the dustbin of history.

Many times in human history the same invention has been made in many different parts of the world at about the same time. Though certainly an inventor was involved in each case, the invention occurs by self-organization of the different components in the inventor’s mind.

Punctuated equilibrium at the species level is self-organization of an existing species into something better adapted. To better adapt to its environment, a member of a species reorganizes itself to create a new species. If the change results in more surviving offspring, the new species supplants the old species.

Possible mechanisms for this self-organization are being revealed. The most likely mechanism relies on a paradigmatic shift in our understanding of genetics. For many years, genetic researchers accepted a simple dogma: DNA was a string of genes which were copied onto messenger RNA.  These are know to travel to the ribosome where proteins were made. Then it became clear that when DNA was copied into RNA, many sections were not translated into the protein. These sections, called introns, had to be edited out. The remaining sections, exons, are spliced to become the RNA from which proteins are made.

Later, the genome project showed that there are only 20,000 genes but at least 100,000 different types of proteins in the human body, and probably many more. Also many of the proteins in humans have subtle differences from other creatures. How could so few genes make so many different proteins?RNA splicing

Researchers finally realized that DNA was just a library. A form of RNA selects from DNA whatever exons it needs to form the desired messenger RNA which is then turned into proteins by the ribosomes.

The very same sequence of DNA can be considered an exon or an intron, creating a tremendous variation in the construction of proteins between different cells. Also, the points at which the cut is made is not as fixed as it seemed at first. Specific types of cells, such as those from organs like the brain, the kidney, etc., have multiple alternative splicing patterns.

Each type of cell is a self-organized system which recreates itself.  RNA changes the proteins produced depending on the cellular environment. RNA selects from the available DNA to create RNA which is adapted to the each cellular environment in the body.  If a new RNA is more successful than others, it can be incorporated into its DNA library.

When this new conservative innovation is created, it can be inserted and saved in the DNA library by an enzyme known as reserve transcriptase (RT). Reverse transcriptase was discovered independently by two researchers in 1970.  It is most famous as the mechanism by which the HIV virus infects humans.

A role for reverse transcriptase in evolution was made by many researchers–most influentially when Cairns reported his observations on ‘directed mutations’ in bacteria in 1988. James Shapiro had shown in 1984 that the appearance of mutations corresponding to an araB-LacZ cistron fusion could not be accounted for by models of random hereditary mutations. Through a precise statistical analysis of the formation of mutants, Cairns and his collaborators demonstrated that in the case of a nonlethal selective procedure, the time of appearance and the distribution of mutations are different from the random ones observed by Salvador Luria and Max Delbrück in their famous 1943 paper and they suggested that bacteria were able to choose the mutations that they should produce. The mechanism that Cairns favored was the reverse transcription of mRNAs permitting bacteria to adapt to new nutrients. The way in which the variant favorable forms of mRNAs were selectively recognized was not precisely described.

Cairns’s article initiated a flood of publications and a huge debate in which many eminent molecular biologists participated. Not only did Cairns’s observations show the limits of one of the iconic experiments of molecular biology, but they were shaking one of the pillars of Darwinism – the randomness of mutations. The debate lasted for seven years, and a consensus was reached that the mutations were not directed, but resulted from an increase in the rate of mutation of specific genes, and a rapid diffusion of the favorable mutations by conjugation.

Cairns himself afforded the strongest experimental arguments against an involvement of reverse transcriptase by showing that some of the adaptive mutations were due to suppressor mutations, unlinked to the gene (LacZ) under selective pressure.  Still to be discovered is why specific genes are stimulated to increase mutation rate.

Regardless of the mechanism, the many new mutations produce proteins which then self organize into new pathways which enable bacteria to adapt to almost any change. Directed evolution tools have been used to improve synthesis yields of desired products, limit or expand substrate specificity, alter cofactor specificity, and improve stability over a wider range of temperature and pH. Reverse transcriptase is not needed to explain rapid evolution in bacteria.  However, in organisms with a nucleus (eukaryotes such as pigweed and humans), RT may be involved as a mechanism of increasing mutation rate.

Reverse transcriptase is being discovered more and more widely in animals and plants. Self-replicating stretches of eukaryotic genomes known as retrotransposons utilize reverse transcriptase to move from one position in the genome to another via an RNA intermediate. They are found abundantly in the genomes of plants and animals. Also in many eukaryotes, including humans, another reverse transcriptase is telomerase. It carries its own RNA template which is used as a template for DNA replication.

Remaining to be discovered is whether newly organized RNA can be incorporated by RT in germ line DNA in eukaryotes so that it is passed to the next generation.  We do know that the genomes of many eukaryotes, particularly complex multicellular forms such as mammals or flowering plants, consist mostly of sequences derived from mobile genetic elements (transposons) which are inserted into the germ line. Also well established is that transposons have been a recurrent source of coding sequences for the emergence of new genes. Increasing the activity of transposons coupled with selection, has enabled “directed evolution” in the eukaryote yeast.

We don’t yet know if this is the way pigweed evolves to be resistant to pesticides. More broadly, we don’t know how the vast changes occur that create new species. What does seem likely is that stressors stimulate production of multiple DNA changes, probably through transposons.  Then the protein products of these DNA changes self-organize providing fodder for selection of a better adapted species.

Some are not sure we really want to know the answers to all this because that opens the door to controlling evolution.  But this research can’t be stopped.  The good news is that only resilient organisms and species survive. Resilience requires fitting into existing systems. Any new species will only survive if it fits.  As long as new species must survive in the natural world, non-complementary innovations will not survive.

The problem is that humans are creating conditions where non-resilient innovations survive.  Infectious organisms thrive in hospitals when they would die in the natural world.  Pigweed thrives in cultivated fields, but dies out in more natural conditions. So we must set aside wild areas.  Thoreau said it best long before we even knew what DNA was: “In Wildness is the preservation of the world.”



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