Bacteria Take Up Dead DNA, Scrambling Evolution

It’s not just horizontal gene transfer that can obscure evolutionary history.  Scientists have found bacteria recycling fragmented DNA from long-dead organisms.   The impact on evolutionary theory could be substantial.

A paper in PNAS by an international team of researchers from multiple fields and institutions made a startling discovery: dead DNA can rise like zombies and invade the living.  The world is awash in fragmented DNA from dead organisms, gradually decaying the older it gets.  No one considered it a factor in genome evolution – till now. When lateral gene transfer was discovered in microbes a few years ago, evolutionists worried that the process could obscure phylogenetic studies, making it impossible to build Darwinian “trees of life” (2/01/07, 9/24/07).  This new finding compounds the problem enormously.

In “Bacterial natural transformation by highly fragmented and damaged DNA,” the authors described how they found bacteria taking up dead DNA with the recA recombinase enzyme.  It was a surprise, because “Fragmented DNA is recognized as nutrient source for microbes, but not as potential substrate for bacterial evolution.”  Then they tested the process, and found a bacterium able to uptake fragmented DNA from a mammoth bone thought to be 43,000 years old.  Here’s the upshot of what they found:

Our findings suggest that natural genetic exchange of DNA from dead and even extinct organisms to contemporary bacteria can take place over hundreds of thousands of years. Hence damaged and degraded DNA may be a previous unrecognized driver of bacterial evolution with implications for evolutionary theory….

Our findings reveal that short and damaged, including truly ancient, DNA molecules, which are present in large quantities in the environment, can be acquired by bacteria through natural transformation. Our findings open for the possibility that natural genetic exchange can occur with DNA up to several hundreds of thousands years old.

The finding, summarized on PhysOrg, has implications for more than evolution.  Hospitals cannot assume that sterilizing a room of live antibiotic-resistant bacteria confers protection, because new bacteria colonizing the room might find fragmented DNA containing resistance genes, take it up and become resistant themselves.

The authors could only speculate about the implications of this process to evolutionary theory.  On the one hand, it might be considered an additional source of genetic variation or mutation.  It might be a way for microbes to share beneficial mutations.  On the other hand, any hopes for establishing a phylogeny, or determining the history of microbes, are compromised by microbes’ ability to incorporate DNA fragments of widely varying ages from very different organisms, like those from the mammoth bone.  In their concluding discussion, the authors stated some potential implications for evolutionary theory:

The genetic process described here suggests that early horizontal genetic transfer could have occurred in primitive cells after uptake of short DNA segments, which would have augmented evolutionary change. In addition to its main function as an important nutrient source, short DNA fragments may have contributed to exchange of beneficial mutations in early cells and continue to do so in extant microbial populations.

The potential for bacteria to take up degraded DNA, leading to single or a few nucleotide changes, adds another perspective to our understanding of the factors that drive microbial genome evolution. Models of population genetics and molecular evolution often rely on “memoryless” Markov processes, which predict the future genetic state of a reproducing population solely from its current state. Such models may not fully represent dynamical feedback between the diversity of environmental DNA and the replicating microbial gene pool. We propose that rates of molecular evolution in naturally transformable species may be influenced by the diversity of free environmental DNA. Furthermore, our findings suggest that bacterial recombination occurs with DNA fragments of considerable age, even from extinct microbial species. This suggests an additional, previously unrecognized contributor to molecular evolution. Recombination with DNA from temporally separated populations or species will bypass generations of cellular division and result in the transfer of genetic information over evolutionary time. We call this phenomenon “anachronistic evolution.”

They also dub it “second-hand evolution.”   PhysOrg put a positive spin on the story, claiming the news is “great for our understanding of how microorganisms have exchanged genes through the history of life.”  The article compared the process to humans looking through a junk pile for “second-hand gold” they can use.  Such thoughts beg the questions of what constitutes a “beneficial mutation,” how the useful genes originated in the first place, and how bacteria obtained the machinery to recognize them as useful and incorporate them.   More ominously, the article recognizes this as a paradigm shift: “That DNA from dead organisms drives the evolution of living cells is in contradiction with common belief of what drives the evolution of life itself.”

This is why scientists should avoid the phrase “now we know.”  Here we see a factor completely ignored by evolutionists appearing out of nowhere, threatening to rewrite the textbooks on the evolution of microbial life.  Treat the spin doctoring with skepticism.  They want to turn this into a plus, saying it provides more ways for evolution to proceed.  On the contrary; how can they make any claims about how a microbe evolved when its genome has been potentially scrambled by significant chunks of DNA from who-knows-what, who-knows when?  This erases the phylogenetic history of single-celled organisms.  It casts serious doubt on the evolutionary significance of genome comparisons.

It’s too early to evaluate what this finding will mean.  Creationists might find a designed purpose in this ability of microbes to adapt to new environments, or to rescue their genomes from upsets by incorporating “junk” copies of essential genes from the soil.  How this potentially paradigm-shaking discovery plays out in evolutionary circles remains to be seen, but it could be the beginning of something big.