The synthetic biology controversy continues. The latest salvo was in the December 2012 Scientific American article entitled “World Changing Ideas: 10 innovations that are radical enough to alter our lives”. The lead idea is “New Life-Forms, No DNA Required” written by Ferris Jabr. This optimistic article again raises issues first identified on this blog seven months ago in a posting entitled, “Troubling Progress for Synthetic Biology”. The Scientific American article largely ignores synthetic biology dangers and offers only modest possible future benefits.
Citing Philipp Holliger of the Medical Research Council’s Laboratory of Molecular Biology in Cambridge, the article states that when compared to DNA and RNA “Related polymers – at least six more – can do the same function.” That the earth’s flora and fauna rely only on DNA and RNA, Holliger says, is an “accident from the origin of life.” In another article he elaborates this thought by saying “There is nothing ‘Goldilocks’ about DNA and RNA – there is no overwhelming functional imperative for genetic systems or biology to be based on these two nucleic acids.”
The problem with these thoughts is that they ignore DNA and RNA have functioned successfully through fully 3+ billion years and have served as the flexible infrastructure allowing the development of the wide variety of life forms on the planet. In addition, they survived all of the changes and dangers in Earth’s environment somehow helping the evolutionary process produce all the various and sundry species. The reality is that “related polymers” and XNAs have not done this and have not naturally occurred anywhere to our knowledge. It is as if with a sweep of the hand we negate the importance of DNA and RNA and their role in the history of life. At the same time we fail to acknowledge the uniqueness of the life phenomenon and how it integrates with the incredibly complex universe of which it is a part.
The Scientific American article credits Holliger with creating XNA or xeno nucleic acid, his replacement for DNA and RNA by “substituting entirely different molecules, such as cyclohexane and threose. Just as important, they created enzymes that work with the XNAs to form a complete genetic system. The enzymes enable XNAs to do something no other artificial nucleic acids can do: they evolve…Holliger reprogrammed natural polymerase enzymes to translate DNA into XNA and back again, establishing a novel system for storing and transmitting genetic information, which is the foundation of evolution.”
In another article written by Holliger entitled “XNA is synthetic DNA that’s stronger than the real thing” he uses an analogy to explain translation of DNA into XNA and back again. He states “You can think of a DNA strand like a classmate’s lecture notes. DNA polymerase is the pen that lets you copy these notes directly to a new sheet of paper. But let’s say your friend’s notes are written in the ‘language’ of XNA. Ideally, your XNA-based genetic system would have a pen that could copy these notes directly to a new sheet of paper. What Pinheiro’s team did was create two distinct classes of writing utensil – one pen that copies your friend’s XNA-notes into DNA-notes, and a second pen that converts those DNA notes back into XNA-notes. Is it the most efficient method of replication? No. But it gets the job done.”
These descriptions contain a contradiction. In order to produce copies of the XNA, the research team uses the flexibility of DNA in the middle of the copying process. Its reliance on the flexibility of traditional DNA means they have not formed a complete genetic system. Instead they were forced to rely on DNA. They go on to claim their enzymes evolve. Absent DNA they do not replicate themselves or store their information. Hence they do not evolve. Again we see an under-appreciated DNA dismissed as completely incidental to the evolution of their XNAs as opposed to the absolutely necessary role it performs.
Anticipating criticism from antagonists of synthetic biology, the article further states, “Holliger emphasizes that XNA-based life-forms are a long way off, but he already recognizes a distinct advantage. If such a creature escaped into the wild, it would die without a steady supply of XNA-specific enzymes. And XNA could not weave itself into the genomes of natural organisms, because their native enzymes would not recognize it. XNA-based bacteria designed to devour oil spills or turn wastewater into electricity, for example, could not interfere with native organisms.” The Scientific American article further asserts, “Alternatively, scientists could enclose XNA within protocells – the origin of a new life-form that could evolve in ways no one can predict.”
When thinking about a creature of his creation escaping “into the wild” Holliger uses the word ‘wild’ as a substitute for the word ‘world’. People do not live in the wild. They do live in the world within which these organisms would escape. When contemplating an escape he observes his creature would die without a steady supply of XNA-specific enzymes. There are several problems with this statement. If he was able to modify enzymes to work with DNA in copying his XNAs, is it not possible for the same enzymes to mutate to the new form or become truly self-replicating? Is it also not possible for existing DNA to produce a mutation that allows it to recognize, accept and incorporate these XNAs into the DNA of our normal life forms? In other words, are our researchers not ignoring the most powerful life processes, mutation and evolution?
Against the obvious risks of what Holliger and others are doing is an array of unimpressive and limited applications they offer to justify the risks they are taking. They suggest XNAs could be injected into the human body to detect early, subtle signs of viruses or other infections. They indicate that XNA-based bacteria could be designed to devour oil spills or turn wastewater into electricity. So what happens if these bacteria get underground in oil fields or get loose in the world’s water supplies? Does anyone really know what will happen with the release of Holliger’s creatures? No one knows, but are these the types of “earth shaking” developments that would justify the risks?
We know that life forms are incredibly tenacious always seeking survival and replication. Holliger claims his creature will evolve. The author of the article mentions “The origin of a new life-form that could evolve in ways that no one can predict.” This last sentence describes simply the threat Holliger’s creatures represent.
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