Wednesday, February 1, 2017


Scientists have been successful in creating an extra base pair and synthesizing a whole new DNA and organism, according to this article that was shared by a great many readers here:
Beyond the usual thing that catches my attention with such articles, namely, the potential for all sorts of intentional "high mischief" and unintentional "nasty blowback" from such scientific tinkering, which is always accompanied by some moralizing rationalization about how wonderful science is and how helpful all this will be to human health and medicine &c &c blah blah blah (and by implication) what a "top drawer good lot of people these scientists are, wot?", there is something else that I couldn't help but wonder about, so today I'm going to forego my usual warnings about science run completely amok and the unintended consequences and blowback of the same, and concentrate on something that... well, is probably nothing more than a personal whimsy and eccentricity, because today I want to point out an oddly synchronous detail that adds a certain... well, the only words for it are ... a certain bizarre and quite frankly disquieting context to this story.
I'm referring to the producer of the celebrated 1990s science fiction television series, The X Files' Chris Carter.
Toward the end of the first season of that series, there was an episode that was a part of the "extraterrestrials-UFOs-we're being visited" story arc of the series called "The Erlenmeyer Flask", an episode written by Mr. Carter himself. The story of course centered on an Erlenmeyer flask which the ever-intrepid FBI agents Mulder and Scully found at the scene of a crime, a flask labeled "Purity Control." Mulder tasks the ever-skeptical scientific Scully to find out what's in the flask. Scully takes it to Georgetown University where a Dr. Ann Carpenter subjects the whole sample to a series of tests, including genetic sequencing and...
...lo and behold, the scientist discloses to an obviously disconcerted agent Scully that the sample contained an extra base pair in the genetic sample that existed nowhere in nature on planet Earth, and thus would have to be, "by definition," extraterrestrial.
Now, it takes no great mental leap of logic to understand that if there were to be any extra base pairs in DNA, that they would have to come in a group of two elements, for each element couples in the double helix to its conjugate element. One can't have just five elements, one can, however, have six, or eight, or... so on. But all known DNA on earth has but four base pairs of nucleotides: G-C and A-T (guanine-cytosine and adenine-thymine). So, just by simple reasoning Mr. Carter can easily figure out that one cannot have an unpaired fifth element, but in fact six elements with a new third base pair: (x,y). For the purposes of his episode, he does not have to explain organic chemistry or genetics, but merely leap to the conclusion that the extra base pairs in Scully's sample, since they exist in no known terrestrial DNA, must "be, by definition, extraterrestrial" if we may paraphrase Dr. Carpenter's report to Agent Scully once again.
But they could be synthetic. So, we now have three possibilities presented to us in the mix of science and science-fiction for the origin of an extra base pair to give the following list: G-C, A-T, and X-Y: (1) the extra pair is a synthetic artificial creation; or (2) it originates off planet but may not be artificial or synthetic, or (3) it is synthetic, artificial, and of off-planet origin. Given the genetic science of Mr. Carter's day, option 1 was theoretically possible but nowhere close, leaving options two and three are being more likely. Bear that in mind...
Now for the purposes of my high octane speculation of the day, what I found odd about this story, or rather, the reporting of this story, was that unlike the G-C and A-T base pairs, which are comprised of recognizable amino acids, the X-Y pair is left very unscientifically undefined and unspecified: are they meant to be understood as actual newly synthesized (or, perhaps, uhm... discovered?) base pairs, or are they simply inert genetic markers, perhaps even completely inorganic compounds inserted into the DNA helix of their synthetic organism and made to made via genetic moderators? (I know, it's a goofy idea, but in the absence of information...) We're not told. Now I don't know about you, but this seems to be at best a bit of sloppy reporting. I for one would like to know more. But this was, after all, the BBC, so in addition to the usual controlled media vapidity, we should expect a bit of non-reporting to occur here. So off I went to our friends at, to find this version of the story:
Unusually, this wasn't much help either, for that mysterious new base pair X-Y was still left hovering in mid-air with nothing to support it; new amino acids? Inert markers? what were they? Still undefined. It took finding the abstract of the actual scientific work linked at to find out:
Here we finally read that, yes, this is an entirely new base pair of nucleotides (Here I am citing the entire abstract):
All natural organisms store genetic information in a four-letter, two-base-pair genetic alphabet. The expansion of the genetic alphabet with two synthetic unnatural nucleotides that selectively pair to form an unnatural base pair (UBP) would increase the information storage potential of DNA, and semisynthetic organisms (SSOs) that stably harbor this expanded alphabet would thereby have the potential to store and retrieve increased information. Toward this goal, we previously reported that Escherichia coli grown in the presence of the unnatural nucleoside triphosphates dNaMTP and d5SICSTP, and provided with the means to import them via expression of a plasmid-borne nucleoside triphosphate transporter, replicates DNA containing a single dNaM-d5SICS UBP. Although this represented an important proof-of-concept, the nascent SSO grew poorly and, more problematically, required growth under controlled conditions and even then was unable to indefinitely store the unnatural information, which is clearly a prerequisite for true semisynthetic life. Here, to fortify and vivify the nascent SSO, we engineered the transporter, used a more chemically optimized UBP, and harnessed the power of the bacterial immune response by using Cas9 to eliminate DNA that had lost the UBP. The optimized SSO grows robustly, constitutively imports the unnatural triphosphates, and is able to indefinitely retain multiple UBPs in virtually any sequence context. This SSO is thus a form of life that can stably store genetic information using a six-letter, three-base-pair alphabet.(All emphases added)
So there we have it. Thus "option 1" of our previous list of three options appears to be the choice de jour for our high octane speculation: they're creating such expanded unnatural base pairs to increase the information storage capacity of DNA, and all sorts of possibilities pop up with that one, including bio-computers and data storage.
But I cannot escape the Chris Carter scenario, that such an unnatural base pair might also represent blacker, earlier projects, using clues provided "from off this world," say, for example, meteorites from Mars that land in places like, well, Antarctica?

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