Gymrek M, McGuire AL, Golan D, Halperin E, & Erlich Y (2013). Identifying personal genomes by surname inference. Science (New York, N.Y.), 339 (6117), 321-4 PMID: 23329047
For most of us, David Golann became a household name when CNN caught him heroically saving the life of a terrified rat stuck in New York City traffic. (“I just sort of know what it’s like to be pretty scared.”) So it was not surprising this week when several thousand fans wrote in to ask if this was the same David Golan who appears as third author on this crotch-kickin’ Pape which burst forth onto the earth-realm last week. To which we reply: thank you for writing, but, no, these two men spell their names differently.
But on the topic of last names, there are now manyservices that allow folks to try to identify the last name of their biological father via DNA testing. For these sites, you send in some DNA, and they examine sequences on the Y-chromosome (which are inherited only from your father), and then they look for the closest match in their big ol’ sequence databases. While they probably don’t have your father himself in their database, they are likely to have several distant patrilinear relatives, and by analyzing those names, they can hypothesize the likely last name of your father, and apparently with pretty good success.
What the Foot Clan-esque authors of this pape realized is that these publically available databases allow hackers to identify the names of the “anonymous” genomic databases that are increasingly available on the internet. The basic algorithm is: submit the Y-chromosome data from these supposedly anonymous genomes to the paternity websites, which gives you the most likely last names. At this point, you’ve narrowed it down to ~40,000 individuals. Then, parse through these candidates using two other publically available pieces of information (D.O.B. and State of residence), which typically narrows it down to about 12 males. At which point, you are fucked.
Basically, these dudes are like Robert Redford’s gang in Sneakers: they hacked the system not to do harm, but to show us the system’s weakness. I mean, it only works on males and it doesn’t work all the time, but it’s still NASTY!!!
Sick Papes Special on Central Pattern Generators, Part 2
Finan DS, & Barlow SM (1998). Intrinsic dynamics and mechanosensory modulation of non-nutritive sucking in human infants. Early human development, 52 (2), 181-97 PMID: 9783819
There is a rumor in the scientific community that, by entering the right combination of keywords and Boolean expressions into PubMed, one can unlock a clandestine trove of high-quality, peer-reviewed, NIH-funded pornography. Although the cipher has not yet been cracked (it’s definitely not “intrinsic+sucking+dynamics-nutritive”), this exercise recently led us to a fetching little pape of disarming sickness.
In 1998, Donald Finan and Steven Barlow embarked on the exploration of the central pattern generator that regulates baby feeding, referred to in this pape as the “suck CPG”. Since Aristotle, and perhaps even before, it has been known that babies will happily slurp on a gorgeous nipple. However, it was not known whether this behavior requires mechanical feedback from the mouth, or if it is controlled exclusively by feedforward signals from the brain. To solve this inscrutable question, Finan and Barlow endeavored to control the mechanical stimulation that babies experienced as they sucked.
The sword in the stone that enabled these experiments was a home-made device called “the actifier” (described in a separate technical report). The actifier was to pacifiers what the 1998 Arctic Cat Jag 440 Deluxe was to snowmobiles: that is, voluptuous. The actifier came fully loaded with 4 pairs of EMG electrodes (to record jaw muscle signals), a pressure transducer (to track the sucking amplitude of the baby), and a strain gauge (to measure jaw displacement). Unlike the ’98 Jag, she did not have a Big Slam sized cup-holder with built-in koozie, but made up for it with a pneumatic cylinder coupled to a breast-like “baglet”. My impression is that, in terms of blowing the mind of stoned high school kids who have just discovered the unfettered liberty of complimentary snowmobile test drives, the actifier would have given the Arctic Cat a run for its proverbial money.
That needlessly complex description should not dissuade you from fully appreciating this instrument. Let’s start over. Basically, what these guys built is a fake boob that measures baby sucking. It’s non-nutritive cause the babies don’t get fed. The experimenters pump the baglet in various ways, and observed that baby sucking activity depends on the baglet’s movements.
According to my lovely girlfriend, who is not herself a mother as far as I know, but an avid eavesdropper of breastfeeding street-women, it can actually be kind of hard to get your baby “to latch on” to the nipple. Indeed, the authors argue that “non-nutritive sucking is a deceptively complex behavior”, because it is not purely controlled by a central pattern generator, but also involves some sensory feedback. We should all be thankful that babies don’t go around needlessly sucking all over town, but only feel compelled to do so when they encounter a nipple or sinusoidally inflating baglet.
The thing is, although this pape is kind of ridiculous in its discussion of the “suck CPG” and the “cortical sucking area”, it’s got some deeply embedded sickness. If President Sarah Palin were to cut all funding for pure basic research, this is exactly the type of shit we would all love to work on. These Hoosiers got to spend months, or, more likely, years, building a nifty little virtual reality nip consisting of a bunch of sensors and actuators. I feel that this is something that the Burning Man community could really get behind, and probably ruin for everybody.
In this age of inflatable pillows and personal seltzer machines, it is easy to forget that we are engaged in a constant and horrific war against nature. This is a war that we will not win. The overwhelming chaos of entropy will inevitably smother each of us in turn, leaving behind only a fleetingly stinky husk and whatever genetic code we manage to propagate in the form of pathetic progeny.
In this hopeless battle against thermodynamics, man’s only defense is the 3 billion base pairs that constitute his meager genome (as well as whatever epigenetic mumbo-jumbo he might be harboring). An even more sobering thought is that the human genome contains the code for only ~20,000 proteins, a mere 1.5% of our DNA. The rest is either bullshit or (more likely) regulatory, “non-coding” DNA. The genome represents the zenith of violence and despair. It is the scroll upon which is written the curse of our miserable existence.
Given the stakes of the battle, and the precarious nature of existence, you might guess that even a small loss of genetic armor would be catastrophic. However, disrupting expression of a single protein produces measurable consequences in only a very small minority of cases. For the most part, knocking out a random gene in a worm or a fly has no detectable phenotype. This finding is at odds with the high levels of genetic conservation across species, which suggests that each and every gene is essential for survival. To resolve this, it has been proposed that many genes are functionally redundant, or required under only highly specific environmental conditions.
However, the problem with these type of genetic loss-of-function experiments is that humans are hopelessly shitty at measuring functional consequences. Although we can easily notice if a genetic manipulation leads to underdeveloped genitalia, we would never notice if it resulted in a slight propensity to produce inside-out sperm. To overcome our observational inadequacies, the Canadian authors of a recent sick pape used a more ambiguous but perhaps more sensitive measure of phenotypic consequence: the ability of an animal to pass on its genes. This is also known as fitness.
Ramani et al studied how fucking with expression of individual genes affected the fitness of nematode worms. They disrupted the expression of 300 random genes using RNA interference, and measured (1) how many worms survived after 2-3 reproductive generations, and (2) the rate at which a surviving population consumed a meal of bacteria. They found that mucking with a single gene resulted in decreased fitness in most cases (~70%). So it turns out that the majority of genes are relatively necessary for the development and function of an animal, if measured under the correct circumstances.
Although this approach might not provide specific insight into the function of individual genes, it serves as a firm reminder that real animals live in a world of hellish and ceaseless competition. Every one of our genes, as well as those belonging to our brother worm, has been struggling for billions of years to overcome the hulking abyss of nonexistence. The point of animals is to kill each other and fuck and transmit genetic code on to some hapless ungrateful child beasts. Let us not forget that survival and propagation is the ultimate arbiter of biological function.
This Valentine’s Day, Sick Papes brings you an exclusive heart-wrenching interview with one of the world’s most lovable biologists: Peter Weir of the California Institute of Technology. In last month’s issue of Current Biology, Peter brought readers to their knees with his seductive demonstration of how flies use polarized light to guide their flight patterns. He then kindly sat down with Sick Papes to answer a few questions.
SP:Your pape demonstrates that flies orient to the polarization pattern of the sky. If we could see polarized light, what song would the sky sound like? Also, what would it look like?
PW: I like to think it would sound like “Lucy in the Sky with Diamonds” or “Purple Haze”, but I’m wondering if “Every Breath you Take” by the Police is more descriptive of what it sings to flies, in its almost ever-present availability and scope. It might look something like concentric rings of different shades of color emanating from the sun that shifted hue as you turned your head. Short answer: Pretty Trippy.
SP:From a hungry fly’s perspective, you argue that orientation to polarization cues might be a good way to avoid wandering around in circles. But do you think that polarization orientation is actually beneficial to the average fruit fly, or might it just be a vestigial behavior? Did any of Drosophila’s ancestors possess sophisticated navigation skills like bees or desert ants?
PW: Polarization orientation might be beneficial in environments that require extensive dispersal, such as deserts or places with dramatic seasonal variation in habitability. I hope that our observation of flies viewing a natural sky at least argues that it is not totally irrelevant, even if it is not the most important sensory modality available to flies. I think the evidence supports the existence of a navigating ancestor, since locusts, which are more distantly related to flies than ants and bees, appear to have all the neural requirements for polarization-based navigation.
SP:Something that Sick Papes found very admirable in your pape was the rigorous treatment of the variability in your data. A lesser scientist might have shown a statistically significant mean and retired to the bar for the afternoon. Was there a particularly formative event in your childhood that instilled you with such solid character?
PW: Haha, Michael (Dickinson) should get at least part of the credit for including that part. Also, throughout the course of grad school I’ve participated in enough journal clubs to realize that readers will scrutinize your data, and it’s best to give an honest report of what you see. Scientists, I think, are very sensitive to people over-selling a result (for good reason), so trying to dodge skepticism rather than embrace it isn’t a good idea.
SP:A related question: it seems like not every fly was super-amped about orienting to polarization cues. What do you think was going on with the 40% of flies that ignored polarization? Was the distribution of flies bimodal, or relatively uniform?
PW: Well, I’m not sure I can infer the underlying distribution from our sample size, but it was relatively unimodal – there was not a clear threshold between flies that completely relied on the polarization cue and those that did not. Out of all the cues available to the flies in our experiments, for some reason polarization was given a higher priority of by some individuals than others. Internal state (hunger, time since mating, etc.), genotype, and variability in the cues themselves could all contribute. It would be interesting to look for a possible trigger that releases polarization orientation, but for now I’m just speculating.
SP:Some of your experiments were conducted outside, so that the fly could see the natural polarization pattern of the sky overhead. Where did you conduct these experiments, and how did you control for birds, airplanes, and local juvenile delinquents?
PW: Yeah, for most of last year I knew exactly when the sun would set each day, and an hour beforehand I could be found on the north end of a building at Caltech. Birds and airplanes were not too much of a problem – they were almost always too small to be resolvable by the fly visual system. Contrails and clouds were potential issues, but luckily the Southern California sky has few of either. Usually my only companions besides the flies were occasional Europeans who smoke on the roof. Once I did get locked out of the spot, and had to clamber along a ledge past the fourth floor offices for the length of the building.
SP:Let’s say we just invented a drug that would allow you to perceive polarized light. How much would you pay for a dose, and what would you spend your time (~3 hrs) looking at?
PW: Well, I hope that would be covered by the lab budget, so I’d pay market rate… Beyond marveling at the sky, a snorkeling trip would be my first choice – light bouncing and bending around in water and at its interfaces with air and solids results in some cool polarization effects, not to mention the patterns of polarized reflections off various sea creatures that are truly amazing.
SP:Many of your experiments make use of an optoelectronic liquid crystal polarization rotator. What is the real world application of this device and where the hell did you get it?
PW: They are used for making 3D projection systems – when you watched Avatar you were basically watching two movies shot from slightly different locations in space. The glasses filtered one movie to one eye, and the other movie to other eye. They accomplished this by blocking one type of polarized light. In order to display each movie with the correct type of polarization, they are projected through the type of device I used, which can alternate the polarization state synchronously with the frames of the two movies. So the device ensures that alternating frames are viewed by alternating eyes. I ordered it from a company in Sweden that I found on the internet, where else?!
This week, Sick Papes brings you an exclusive interview with Dr. Heather M. King, the celebrity author of a dangerously feverish pape that rejiggers how we think about the the evolution of tetrapod locomotion (i.e., how four-legged animals walk).
SP: Your pape describes a hybrid walking/swimming gait in lungfish which looks curiously like that of four-legged critters that walk on land. Do lungfish need to trundle along on the bottom of the lake, or can they also swim throughout the water column like normal self-respecting fish? What do you think is the advantage of the lungfish style?
HK: They certainly can use their body/tail to swim as typical fish do, but they tend to do this only when frightened or startled. However, they seem to nearly always use their fins for walking instead. We don’t know why exactly they do this, but we have some hypotheses: using the fins to walk instead of the whole body would use less energy, since the muscles in the fins are so much smaller than the muscles in the body. Lungfish live a long time and don’t seem to move much (in my experience) so their metabolism might be lower than that of other fish, and it would likely be to their advantage to use the fins for slow movements. In addition, aquatic animals can sense each other by tracking the vibrations in the water made by other animals, and it’s possible that lungfish use these smaller movements to be more ‘quiet’ underwater, which would help them both avoid predators and ambush potential prey.
SP: Lungfish defy classification: they possess traits of both fish and land-dwelling critters. Some describe them as unlikely monsters. Do you identify personally with these misfits of the animal kingdom? If so, what childhood experience led you to realize that you were somehow “different”?
I knew I was different the first time I saw the lungfish. It was like looking in a mirror.
SP: I read on Wikipedia that lungfish can survive the seasonal drying out of lakes by just chilling in the mud for many months. Is it possible that the walking-like propulsion you described is also useful during mud season?
HK: Yes, that’s true. They make a cocoon of mud and their own mucus and survive in a state of hibernation for up to 4 years. This behavior has been studied fairly well, and it turns out that they actually use their axial muscle and head to burrow into the mud. The fins are not strong or large enough to contribute.
SP: Imagine that you had a time machine and high-speed video camera. Given your obsession with the “water-to-land transition”, what historical epoch would you travel to, and what would you film? Who would you bring with you as your ideal assistant?
HK: I would like to travel to the Mid or Late Devonian with my camera, and film any creature I saw. I would probably take my husband as my assistant because he’s the only one that would still help me/like me as I traversed the near-alien landscape in search of large fishapods, all while muttering about the insane amounts of Nature papes I would author upon returning to the present day. I can be a little obnoxious sometimes.
SP: Figure 3 clearly shows a lungfish doing a push-up, yet your paper describes this behavior as “lifting the body and appendages clear of the substrate”. Is there some reason that you chose to use this jargony description instead of the more familiar colloquialism? Isn’t this what’s wrong with science, that scientists refuse to describe anything in plain-spoken English that my dad, Newt Gingrich, or your average hairdresser could understand? Why not just call the pape: “Lungfish walk like horses and do push-ups”?
HK: I didn’t realize that you were the son of Newt - tell him to rein it in a bit on TV or he’s gonna blow this nomination thing. You will have to take this one up with the powers that be - such jargon is necessary for publication, since so many journals demand short, succinct, articles. Taking the time to explain exactly how I define ‘walk like horses’ and ‘push-ups’ would have taken at least half a page. Plus, I doubt your dad, Newt Gingrich, and I have the same idea of what ‘walking like a horse’ means.
SP: You show that lungfish not only walk- they also bound. Do they move faster when they bound, like cats?
HK: Based on studies on other animals, gait transitions are indeed associated with changes in speed. However, we did not find evidence for transitions to the bounding gait being associated with an increased speed. Perhaps the lungfish know that they are outsiders, and like many outsiders, decide not to conform to the norm.
SP: Your pape is being covered extensively by the press (National Geographic, Discover, Scientific American, NY Times). Why do you think your pape has received so much attention compared to other PNAS papes from 2011, like, for example, that one about flies perceiving a really fascinating visual illusion?
HK: I am sure that said fly vision pape is of equal or greater value than my pape - all I can say is that some of my co-authors are very good at promoting their research and know the value of a well-written press release. I merely benefit from their experience and notoriety.
SP: My sources report that you were once so exhausted from working on this project that you fainted in a bank, throwing thousands of dollars of cash into the air as you collapsed to the floor. Any comment?