Things to Think About From 2016

thescinder2016wordle

A word cloud of theScinder’s output for 2016, made with wordle.net

CRISPR/Cas9

This subject includes throwbacks to 2015, when I did most of my writing about CRISPR/Cas9. That’s not to say 2016 didn’t contain any major genetic engineering news. In particular scientists are continue to move ahead with the genetic modification of human embryos.

If you feel like I did before I engaged in some deeper background reading, you can catch up with my notes on the basics. I used the protein structures for existing gene-editing techniques to highlight the differences between the old-school gene editing techniques and editing with cas9. I also compared the effort it takes to modify a genome with cas9 to how difficult it was using zinc-finger nucleases, the previous state-of-the-art (spoiler: it amounts to days of difference).

TLDR: The advantage of genetic engineering with Cas9 over previous methods is the difference between writing out a sequence of letters and solving complex molecular binding problems.

aLIGO and the detection of gravitational waves

Among the most impressive scientific breakthroughs of the previous hundred years or so, a bunch of clever people with very sensitive machines announced they’ve detected the squidge-squodging of space. A lot of the LIGO data is available from the LIGO Open Science Center, and this is a great way to learn signal processing techniques in Python. I synchronized the sound of gravitational wave chirp GW150914 to a simulated visualization (from SXS) of a corresponding black hole inspiral and the result is the following video. You can read my notes about the process here. I also modified the chirp to play the first few notes of the “Super Mario Brothers” theme.

Machine Learning

I’ve just started an intensive study of the subject, but machine learning continues to dip its toes into everything to do with modern human life. We have a lot of experience with meat-based learning programs, which should give us some insight into how to avoid common pitfalls. The related renewed interest in artificial intelligence should make the next few years interesting. If we do end up with a “hard” general artificial intelligence sometime soon, it might make competition a bit tough, if you could call it competition at all.

Devote a few seconds of thought to the twin issues of privacy and data ownership.

Mars

2016 also marked a renewed interest in manned space exploration, largely because of the announcement from space enthusiast Elon Musk that he’s really stoked to send a few people to Mars. NASA is still interested in Mars as well, and might be a good partner to temper Musk’s enthusiasm. In the Q&A at about 1:21 in the video below, Musk seems to suggest a willingness to die as the primary prerequisite for his first batch of settlers. There’s some known unavoidable and unknown unknowable dangers in the venture, but de-prioritizing survivability as a mission constraint runs a better chance of delaying manned exploration as long as it remains as expensive as Musk optimistically expects.

Here’s some stuff that’s a little a lot less serious about living on Mars.

It doesn’t grab the headlines with such vigor, but Jeff Bezo’s Blue Origins had an impressive year: retiring their first rocket after five flights and exceeding the mission design in a final test of a launch escape system.
Blue Origin is also working on an orbital launch system called New Glenn, in honor of the first astronaut from the USA to orbit the earth.

In that case, where are we headed?

The previous year provided some exciting moments to really trip the synapses, but we had some worrying turns as well. The biggest challenges of the next few decades will all have technical components, and understanding them doesn’t come for free. Humanity is learning more about biology at more fundamental levels, and medicine won’t look the same in ten years. A lot of people seem unconcerned that we probably won’t make the 2 degrees Celsius threshold for limiting climate change, although not worrying about something doesn’t mean it won’t kill anyone. Scientists and engineers have been clever enough to develop machine learners to assist our curiosity, and it’s exciting to think that resurgent interest in AI might give us someone to talk to soon. Hopefully they’ll be better conversationalists than the currently available chatbots, and a second opinion on the nature of the universe could be useful. It’s not going to be easy to keep up with improving automation, and humans will have to think about what working means to them.

Take some time to really dig into these subjects. You probably already have some thoughts and opinions on some of them, so try to read a contrary take. If you can’t think of evidence that might change your mind, you don’t deserve your conclusions.

Remember that science, technological development, and innovation have a much larger long-term effect on humans and our place in the universe than the petty machinations of human fractionation. So keep learning, figure out something new, and remember that if you possess general intelligence you can approach any subject. On the other hand, autogenous annihilation is one of the most plausible solutions to the Fermi Paradox. This is no time to get Kehoed

A month on Mars

The year is 2035, and the new space race is well underway.

Jeffrey Aussat straightened his back under the Martian sun. He stretched as he leaned onto the handle of his space-shovel, raising his hand to wipe the sweat from his tired brow. Of course this made him feel stupid, as it had every time since they landed. His clumsy hand, gloved up and looking for all the world just like the hand of Gozer the Destructor, stops short as it meets the clear glass of his visor. Jeff curses himself at the unavoidable fact that, despite nearly a (Mars) month since they arrived on the spaceship Clever Reference, he still couldn’t get used to the simplest things. Like the need to have this damn fish-bowl on every time he goes outside.

Jeff curses himself again as his shovel snaps in half. Losing focus during retrospection and self-pity, he somehow must have applied an off-axis load onto the carbon fiber handle. A few moments respite for his weary, microgravity-weakened bones, had turned into disaster. On Mars, the gravity may be slight but the days sure are long, but they don’t tell you that in the brochure.

Jeff now found himself up a recurring slope lineae without a planetary-protection cleared drill bit. Jeff and his partner had started out their ‘stead with 32 shovels, and in just a few weeks every single on had fallen prey to some combination of user error and catastrophic failure. Every building in their inflatable homestead creation kit was designed to be placed underground, damping temperature swings and blocking some of the deadly radiation pouring down on Mars surface. Specifically, the buildings needed to have a huge amount of ground piled on top of them to keep the humans alive, and without a working shovel they couldn’t move regolith quickly enough to make their new home habitable. Due to some shady logistics, they wouldn’t receive their “mule”- a heavy lifting robot- until the next colonization flotilla arrived, roughly two years on.

Jeff holds the transmit button on his radio as he slumps down in the shade of his space-wheelbarrow, half-piled high with regolith and also made from carbon fiber. “Becky, I think we have a problem,” he said.

After a short intermission of static, Becky replied with a sigh, “You’ve got a leak in your suit again, don’t you?” Getting used to the strange Martian gravity after playing zero-G ping pong for three months, Jeff had often ended up tumbling down to hands and knees during the first weeks of their stay, a stress the suits were well-designed to withstand. Repeated joint flexion of the suit fabric with embedded Martian dust, however, rapidly opened up a community of near-microscopic pinholes that were almost impossible to find and patch.

“No, not this time. It’s the shovel.”

“The last shovel?”

Jeff paused. “… Yeah.” This was bad. They would have to resort to much less efficient regolith maneuvering techniques, working only at night and sleeping under the raw materials in the shed to limit radiation exposure. After the recurring problem with clumsiness-induced suit leaks, Becky’s patience was sure to be running out on him. The trip over had already placed enough stress on their relationship. “Is the 3D printer working yet? Maybe we can print a new one, or print a repair splint for one of the frayed shovel shafts.”

Silence followed for nearly a minute. She was either checking the printer status or seriously considering filing flight plans to leave. “I’m afraid the printer’s still down. The print nozzle was damaged during the last maintenance test.”

“Oh.” Jeff replied. He didn’t finish converting the thought running through his head to speech: so we’re screwed then.

“No problem. I’ll order a fresh crate from Amazon.”

“What?” This was either a joke, a hoax, or lifesaving news.

“Check your email. They’ve opened up a new distribution center on Phobos. Bezos built it up and staffed it without telling anybody.”

“You’ve got to be kidding me.”

“No joke. I need a few extra items to qualify for free shipping, do you need anything?”

“I’m sure we can think of something. I’ll return to the compound with the regolith I’ve collected and we can run an inventory.” Jeff tossed the broken shovel on top of the regolith in the enormous wheelbarrow. The designers had figured that, if everything on Mars would weigh so much less than on Earth, all the tools should be designed to be that much larger. The result was a suite of construction and farming tools that were cartoonishly two and a half times too large when fully assembled. As Jeff wheeled the barrow around to face the glint from the compound’s solar panels, he felt his mood pick up. They were going to be OK after all.

“There’s something else going on that’s a bit weird.” Becky said.

Jeff skipped a step, catching himself on the wheelbarrow handles to prevent impregnating the knees on his suit with more abrasive dust. “What is it?” he asked.

“You remember that huge rover from 2020?”

Jeff made a vague confirmatory noise “Uh . . . the Scrutiny, was it?”

“Yeah, that’s the one. It’s attacking the water scavenging plant.”

“What? Why? I thought that thing was supposed to be retired by now, parked somewhere near Jezero delta?”

“Well it’s here, and it’s pushing the water plant over. The LEDs are putting out some sort of morse code, I’m still trying to figure it out.” Becky explained.

“How long until it damages the water plant?” Jeff inquired.

“At this rate, probably a couple of weeks. They didn’t move very fast back then.”

Jeff felt the spring return to his step. Two weeks was enough time to contact the mission controllers to get some help debugging the rovers strange behavior. As he realized the problem was tractable, the physical sensation of a weight lifted from his shoulders. Also, the motility assist systems on his suit had finally finished calibrating.

“Too bad they didn’t set up the distro center in time for Mars One.” Jeff joked

“Too soon, Jeff, that’s not funny.” Becky said coldly.

The Mars One mission had ended in a tragicomic maelstrom of cannibalism and incidental lyophilization. The cameras, intended to live-broadcast the travails of the crew around the clock, were among the last systems still running on the capsule. Although the sponsors had long disavowed any relationship to the mission, anyone with a standard transceiver and a darkly morbid curiosity could ping the ship and tune in to the dismal situation. A series of planned challenges/mission planning fiascos ultimately meant they never got onto the correct Mars rendezvous trajectory. In their current orbit, apoapsis would never quite reach Mars orbit, nor would periapsis ever bring them close enough for an earthly recapture. Ironically, what remained of the crew and craft would probably outlast them all. The perfectly preserved astronauts would remained unchanged for millennia in their wayward but stable orbit, like confused Pharaohs circling the portal to the netherworld.

aSOC: Plant physiology (on Mars?)

Mars_23_aug_2003_hubble

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.

Last week’s links: does running water on Mars matter all that much if the universe is a hologram?

Gaining much publicity after a Nature write-up of pre-publication articles, science has (un)officially justified the existential crisis you had last week by demonstrating that the universe is indistinguishable from a much simpler holographic universe with only one dimension and no gravity.

But the simulated universe is not our universe, and apparently does not resemble our own either (also, who minds potentially being holographic? Not me). So we can still get excited about what looks a bit like flowing water in equatorial regions of Mars (well, flowing something anyway). The link is paywalled, but read the news report here. The article makes a case for a rover ban for all but the most sterile of robots, which I guess means no humans either (bummer).
The recurring slope lineae, aka repetitious incline lines, were also described in Science a few years ago (mirrored at seti.org). A strange occurence without an explanation, think of the Martian streaks as an enigmatic, saltier version of the suspected plumes of water vapour picked up by the Hubble telescope around Europa.

In other happenings, the Jade Rabbit is on Luna.

Mars orbiter MAVEN will make its launch window

MAVEN is back on line

The federal government shutdown this week has a lot of scientists scratching their heads and packing their bags. All “non-essential” elements of the federal government, i.e. things without guns attached and people with high IQs, get the axe. It is a bit like congress holding the nation hostage while whining about themselves. Oh, and congress still gets paid while the CDC isn’t allowed to keep track of the coming flu season.

In somewhat of a surprise move, the NASA Mars orbiter mission, MAVEN, has been deemed “essential” and will actually get to make its launch window. But its not just a case of the grinch’s heart growing three sizes, spurred on by the magic of xmas. The status of the MAVEN project was switched to essential due to an exception in a law from 1884 called the Antideficiency Act.

The act’s main provisions are actually in place to prevent government institutions or employees from spending money that has not been appropriated to them through legislation. Federal institutions and workers aren’t allowed to accept voluntary services or spend any non-appropriated money. . .

. . .except in cases of emergency involving the safety of human life or the protection of property. 31 U.S.C. § 1342.

The Mars Oddyssey and Mars Reconaissance Orbiter are currently serving as necessary communication relays for Curiosity and Opportunity rovers on the planet surface. Launching MAVEN on time (a three week window from November 18 to December 7) ensures that communication with the rovers will continue unabated. Bruce Jakosky, principal investigator for MAVEN at the University of Colorado Boulder, points out that the decision was made for non-science reasons, but the reactivation should allow for MAVEN to meet all of its scientific objectives as well as act as a rover relay.

MAVEN, for Mars Atmostphere and Volatile EvolutioN, has primary scientific objectives are to sample and measure the Martian atmosphere, uncovering clues as to the current and past rates of atmosphere loss and what this has meant and will mean for the planet. The orbiter will use a highly elliptical orbit to make measurements ranging from direct sampling of the Mars atmosphere when MAVEN dips into the upper atmosphere as close as 125 km (77 mi) to the red plant, to global ultraviolet imaging from 6000 km (3278 mi) at apogee. The three sensor suites will include the Particles and Fields package, measuring particles and electromagnetic fields mostly associated with solar wind, the Remote Sensing Package for imaging the upper atmosphere, and the Neutral Gas and Ion Mass Spectrometer for spectroscopy of atmospheric samples (it is not clear from the mission facts sheet whether the spectrometer package might provide any insight into the ongoing methane measurement discrepancies discrepancies reported by Chris Webster et al). These instruments should gather data that will point to the role of solar radiation in atmosphere loss on Mars, how fast it is happening today and what this might have meant for ancient Mars.

I hate to think that the state of U.S. Congress will become the new norm, but does this point to a mission operations strategy that could lessen vulnerability to government shutdowns? Incorporating some sort of reliance on future missions into probes like the Mars rovers prevents those future missions from being postponed and ultimately cancelled might be tempting, but I’d hate to see mission design robustness sacrificed to account for the decidedly un-robust nature of U.S. lawmakers.