Journalistic Phylogeny of the Silicon Valley Apocalypse

For some reason, doomsday mania is totally in this season.

In 2014 I talked about the tendency of internet writers to regurgitate the press release for trendy science news. The direct lineage from press release to press coverage makes it easy for writers to phone it in: university press offices essentially hand out pre-written sensationalist versions of recent publications. It’s not surprising that with so much of the resulting material in circulation taking text verbatim from the same origin, it is possible to visualize the similarities as genetic sequences in a phylogenetic tree.

Recently the same sort of journalistic laziness reared its head as stories about the luxury doomsday prepper market. Evan Osnos at The New Yorker wrote an article describing the trend in Silicon Valley to buy up bunkers, bullets, and body armor-they think we’ll all soon rise up against them following the advent of A.I. Without a press release to serve as a ready-made template, other outlets turned to reporting on the New Yorker story itself as if it were a primary source. This is a bit different than copying down the press release as your own, and the inheritance is not as direct. If anything, this practice is even more hackneyed. At least a press office puts out their releases with the intention that the text serves as material for coverage so that the topic gets as much circulation as possible. Covering another story as a primary source, rather than writing an original commentary or rebuttal, is just a way to skim traffic off a trend.

In any case, I decided to subject this batch of articles to my previous workflow: converting the text to a DNA sequence with DNA writer by Lensyl Urbano, aligning the sequences with MAFFT and/or T-Coffee Expresso, and using the distances from the alignment to make a tree in Phyl.io. Here’s the result:

Heredity isn’t as clear-cut as it was when I looked at science articles: there’s more remixing in this case and we see that in increased branch distances from the New Yorker article to most of the others. Interestingly, there are a few articles that are quite close to each other, much more so than they are to the New Yorker article. Perhaps this rabbit hole of quasi-plagiarism is even deeper than it first appears, with one article covering another article about an article about an article. . .

In any case, now that I’ve gone through this workflow twice, the next time I’ll be obligated to automate the whole thing in Python.

You can tinker with the MAFFT alignment, at least for a while, here:
http://mafft.cbrc.jp/alignment/server/spool/_out1701310631s24824093CAxLP69W2ZebokqEy0TuG.html

My tree:

Sources:

New Year’s Eve 2015

A particular pair of protein structures, Protein Database designations 1afz and 3coS. Depending on your genotype you may be strongly cursing or thanking these enzymes later.

X-Ray diffraction solution data from:

Kavanagh, K.L., Shafqat, N., Yue, W., von Delft, F., Bishop, S., Roos, A., Murray, J., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Oppermann, U. Crystal structure of human class II alcohol dehydrogenase (ADH4) in complex with NAD and Zn. To Be Published

Steinmetz, C.G., Xie, P., Weiner, H., Hurley, T.D. Structure of mitochondrial aldehyde dehydrogenase: the genetic component of ethanol aversion (1997) Structure 5: 701-711. PubMed: 9195888

When life gives you lemons, go exploring

xkcd is celebrating Randall Munroes new book with a browser game. It doesn’t take long to guess that there’s a lot more than the small coin-gathering area the player starts out in.

After escaping the small coin maze and vaulting a barrier wall on the left. . .

Eventually the first foray of our brave protagonist came to an end when I got stuck in a statue of George Washington.

aSOC: Speculative Fiction

SF vs. SF: what’s the best way out of the werewolves and wizards section and onto the serious shelves?

Friendship and mentorship doesn’t need to be limited to those one has the chance to meet in a given lifetime. Thoughts recorded in the written word and other forms make it possible to take on teachers, fellows, and adversaries across vast swathes of space and time. A friend in a book, they don’t even have to listen, only speak. These can provide a welcome refuge when alone despite the crowd, adrift in a sea of humanity with an unrelenting feeling of solitude. A special case of being surrounded by an intellectual version of water, water everywhere, but not a drop of it to drink.

The back sections of bookstores have long been a strong attractor for the lonely imaginative ones, the awkward and detached (not quite that far back, you don’t need to know a password or ask the clerk to be let in). For those bookstores still standing, this section will be tucked away in a corner somewhere, maybe hidden on the top floor next to the owner’s apartment or sandwiched between the WC and the fire escape. This is the science fiction section.

Typically sci-fi is, ironically in some ways, lumped in with fantasy. One genre describes what might be possible while the other describes what is definitely impossible. It’s true that much of the so called SF genre (particularly the “indistinguishable from magic” variety) carries little to differentiate itself from your run-of-the-mill swords and sorcery. Despite this, the gold standard hallmark of the genre is an  element of science that, if removed, would diminish the story. That doesn’t mean the plot won’t be character driven or relatable, but it does give the writer the chance to experiment with people in an enhanced diversity of contexts. Within a single genre,  science fiction is tops for the sheer breadth of different stories, societal structures, and characters that are possible.

The stereotypical sci-fi enthusiast I describe above are perhaps a bit lonely and awkward, distracted from the normal world as it is and even a bit antisocial. The negative connotation of the sci-fi nerd as a misanthropic outcast is a convenient stereotype and oversimpification. The mindset and nuance that cause one to seek a realm apart is not so much a type of person but an aspect of human experience that we all dip into from time to time, with often creative and fulfilling results.

So unlike the societal myth of the unwashed legions of basement dwelling fandom, we probably all contain some antisocial nerd deep down inside. It’s a part of life with some valuable rewards in terms of introspection and preparing for an uncertain future. So why do some authors, typically literary types with degrees $\geq$ Masters, try so hard to distance themselves from the genre by insisting their work is “speculative fiction,” mutually exclusive to science fiction. Even not considering the continued migration of sci-fi fandom to the mainstream, claiming the spec-fic label distances your work from its obvious target audience while denigrating a useful and enjoyable mindset. It’s a bit pompous, a bit pretentious, and ultimately meaningless? The books may not qualify as hard sci-fi, but I promise not to be offended that they end up in the same section, with or without the accompanying speculative fiction proselytizing. Remember that speculation comes from the Latin specere, to observe, and is based on coming to conclusions about the world through thought. Science, beginning with observation, continues to rending untruth from plausibility based on experiment and exploration. Both begin with observation, where do your dreams stop?

A mimic without a model

Macroglossum stellatarum looks and behaves remarkably like a hummingbird, albeit without the “swordfighting” and high-pitched battle cries of their avian lookalikes. Selective advantage of mimicry is obvious in situations where the imitated organism is less palatable or more dangerous, or when said mimicry furthers the mimic’s own life cycle, but what if the apparent object of imitation is no longer found in the mimic’s range? Such is the case with the European hummingbird hawk-moth, which confuses birders in northern Europe in late summer. Hummingbirds are a purely New World group of birds, so what exactly are the European hummingbird moths gaining from mimicking a non-existent group of birds or, on the other hand, when is a mimic not a mimic?

If you ask your hipster friends you are sure to receive an explanation for why partaking in a trend can be a truly novel act, owing to some small esoteric twist or another. Macroglossum in the Old World may have undergone a mutual convergent co-evolution, rather than outright mimicry as the common name for these insects might suggest. Fossils of largely modern hummingbirds in Europe have been described dating to the Oligocene (about 30 million years ago). Add to that the apparent evolutionary footprint of significant pollination by hummingbirds seen in a number of Old World flowers, and it begins to look plausible that Macroglossum and other Old World humming-moths settled into a niche of pollinating long-stemmed, nectar-heavy and perch-free flowers, alongside but not dependent on hummingbirds. If your mouth-part is longer than the rest of your body combined you might as well use it, whether or not a hummingbirds are currently trending in your area. A 30 cm proboscis never goes out of style*.

This digression was kindled by a few sunny afternoons spent in the company of beautiful hawk-moths in the Tuscan hills.

*I’m not an expert in long-tongued pollinators, and it’s not clear to me how much of a role mimicry and convergent evolution both may have played in European hummingbird moths. The extremely long proboscis of Xanthophan morgani and the correspondingly deep nectar placement of Angraecum sesquipedale is a famous example of co-evolution that had a strong impact on Darwin’s thinking. To my knowledge, there has never been a hummingbird with a 35 cm tongue, and in many ways hawk-moths may have pioneered the lifestyle of deep-seated nectarivory, before it was cool. The fossil records for hummingbirds and hawk-moths alike are rather spotty.

Xanthophan morgani with extended proboscis from the London Museum of Natural History, by Wikipedia user Esculapio

Equally remarkable is the visual system. Behold those pseudopupils!

aSOC: Plant physiology (on Mars?)

Hubble Space Telescope image of Mars

Several months ago Andy Weir’s The Martian showed up on the feed of personalised advertisements for Kindle books on my account. No surprise, I read tons of sci-fi. Preferably no magic or dragons, as I can only tolerate so much “any sufficiently advanced technology is indistinguishable from magic.” So-called “hard” sci-fi tends to be the what I like most, and I gravitate to authors that have a propensity for characters on “the spectrum” or that are artificial intelligences (::ahem::). In any case, I read the sample from Amazon for the ebook, and I didn’t get into it.

Then last Wednesday Randall Munroe mentioned it was a cool story on xkcd. So I read it, and it was awesome. It’s a story about a guy fixing things in space. The flippant personality of the protoganist (Mark Watney, aka Matt Damon) is actually a tried-and-true literary device used to explain technical concepts to readers without being patronising. There’s a specific name for it that my exocortex is failing to bring me right now, but in any case, Andy Weir goes a long way to make sure his story is technically legit.

But this is aSOC, and I have to mention at least one thing I think was a mistake. And that thing is: space potatoes. Watney’s official job description entailed two roles on the mission to Mars: botanist and mechanical engineer. These are bascially the two skill sets most likely to enable someone to survive after being abandoned on another planet, which is a convenient coincidence for our buddy Mr. Damon. He grows potatoes and (oh sorry, spoiler alert starting a few sentences ago) at one point he worries about “suffocating” the potatoes by leaving the space house for a few days, thus not providing the plants with the CO2 they need to “breathe.” One problem: plants don’t breath CO2.

Don’t get me wrong, plants definitely need CO2 to make triose phosphates, sugars, starches and cellulose, etc., but this isn’t what they “breathe” on a cellular level. Plants need to respire just like we do to power aerobic metabolism. Plants need CO2 for photosynthesis, not respiration. A metabolically active plant doesn’t photosynthesize at night, but in general it will still need a low level of oxygen to survive. And I sure would have liked to see an energy balance for his indoor Mars farm. Photosynthetically active radiation on old Terra is about 300 Watts per square meter, and I’d be surprised if the reading lights in his space house are up to the task of meeting that level of output.

In any case, I can recommend that you go ahead and read the book, maybe watch the movie later, and think about space some more.