If Ewen Callaway at Nature can call it "alien" DNA, we will, too ("First life with ‘alien’ DNA"). If it’s not natural, it’s alien. Humans can be aliens if they tweak natural things by design. That’s what they did to bacterial DNA, changing out some of its natural letters for artificially constructed ones.
Callaway’s subtitle reads, "An engineered bacterium is able to copy DNA that contains unnatural genetic letters." (Emphasis added.)
For billions of years, the history of life has been written with just four letters — A, T, C and G, the labels given to the DNA subunits contained in all organisms. That alphabet has just grown longer, researchers announce, with the creation of a living cell that has two ‘foreign’ DNA building blocks in its genome.
You can’t add "letters" to something that isn’t an alphabet intended to share messages. Even if the letters are chemicals, or knots on a rope, they are designed to convey information. In this case, "What we have now is a living cell that literally stores increased genetic information." They can’t increase information unless there was information there to begin with. One doesn’t add pebbles to a rock pile to increase its information content.
The team at Scripps Research Institute even exercises "alien control" over the message, Callaway adds, to "prevent the survival of alien cells outside the lab, should they escape." There’s intelligent design all over this announcement. "If you’re given more letters, you can invent new words, you can find new ways to use those words and you can probably tell more interesting stories," one of the Scripps scientists says. Origin-of-life researcher Steven Benner sees no limit; scientists could create a "fully alien cell" someday with these techniques.
The concepts of control, alphabet and information also permeate a news release from Scripps where the research was conducted. Ditto for the write-up in New Scientist. Robert F. Service in Science adds the words design and engineering to the mix.
Incidentally, the new "letters" in the alien alphabet are abbreviated d5SICS and dNaM. These are engineered nucleosides that take the place of the A, T, C, and G bases in natural DNA. The normal cell machinery is able to transcribe these new letters into RNA, but making alien proteins with them will require further design.
Rational Design by Plagiarism
Scripps is not the only place that is engineering alien DNA. At Harvard’s Wyss Center for Biologically Inspired Engineering, with help from chemical engineers at Caltech, designers are exploring ways to engineer synthetic DNA. Their goal is "Evolving with purpose," an article in Nature says:
Genomes are great books of instructions on ‘how to’: how to extract materials and energy and convert them into self-repairing, self-reproducing machines; how to function in an extraordinary range of environments; even how to adapt over the long term. Evolution has accumulated a vast library of instructions. We argue that it is also a great tool for writing new ones. The results of directed evolution are rational and predictable, even if the underlying genetic changes follow an uncharted course.
This is an irrational paragraph. Nothing in nature accumulates a "vast library of instructions" by uncharted courses without assuming a priori that such a thing is possible. The point is underscored by the next paragraph that shows human intelligence is pitifully weak at this kind of design by comparison:
How good are synthetic biologists at writing useful biological instructions? We are getting better at synthesizing long stretches of DNA that can be inserted into a variety of organisms in which they will be read and — sometimes — acted on. But most of our writing merely rearranges passages lifted from the few genomes that we have read. We are plagiarists, poor crafters of original literature. We cannot yet create an enzyme or a biosynthetic pathway that compares favourably with nature’s engineering outputs. Nature’s writing is intricate (some say convoluted and opaque), but it is effective. We are just learning to hold the pencil.
No one plagiarizes a rock or a waterfall. If it’s writing — if it’s literature — it’s designed by a mind. Personifying that as "nature" is only a figure of speech. We all know that only intelligent agents create literature. It may appear convoluted or opaque to the uninitiated, just like Coleridge sounds to a freshman.
The authors of the article proceed to describe how they plan to use "evolution" for "rational design" of new products. The cacophony of incoherence is deafening:
Evolutionary engineering is not incompatible with ‘rational’ design; in fact, the two are highly complementary. Directed evolution requires a starting design, and the better the design, the easier the evolution. Evolution also requires a rational search strategy. Where should mutations be targeted, and how many of them? How do we measure success along the way? Directed evolution and rational design are even claiming common ground, for example in mutant libraries that have been designed with input from computational processes, accelerating the evolutionary process.
With a good starting point in hand, evolution is the most direct approach to engineering the biological world, and it is uniquely effective with biological substrates, the products of that same process. Biology is highly evolvable, and we should exploit that feature to the fullest, as we have for thousands of years with everything from rats to racehorses. The writer’s best friend is a good editor — the synthetic biologist’s should be directed evolution.
Talk about mixed metaphors. This is the real alien code: conflating rational design, including a starting design, a search strategy and a target, with the mindless, undirected process of evolution. It’s alien to everything in our experience about the causes of literature.
They seem to be assuming that natural evolution has a target: survival. Actually, a mindless process isn’t even aware of survival. It can’t be aware of anything. Extinction happens; who is there to care? If an organism dies, or stays static for billions of years, "evolution" couldn’t care less. Much less is it cognizant of intricate writing, libraries and literature.
The fact that human minds can take the cell’s literature and edit it by inserting new letters or seeking new outputs powerfully supports the inference that the original code was intelligently designed. From our uniform experience, only a mind can create literature — or plagiarize it.