Links for May 2016

The New Mexico whiptail is like a mule in that it’s a hybrid of two species, but unlike the mule it can reproduce semi-cloning:

The New Mexico whiptail (Cnemidophorus neomexicanus) is a female species of lizard found in the southern United States in New Mexico and Arizona, and in northern Mexico in Chihuahua. It is the official state reptile of New Mexico. It is one of many lizard species known to be parthenogenic. Individuals of the species can be created either through the hybridization of the little striped whiptail (C. inornatus) and the western whiptail (C. tigris), or through the parthenogenic reproduction of an adult New Mexico whiptail.

The hybridization of these species prevents healthy males from forming whereas males do exist in both parent species (see Sexual differentiation). Parthenogenesis allows the resulting all-female population to reproduce and thus evolve into a unique species capable of reproduction. This combination of interspecific hybridization and parthenogenesis exists as a reproductive strategy in several species of whiptail lizard within the Cnemidophorus genus to which the New Mexico whiptail belongs.

And in the extremely unlikely event that you don’t already know what parthenogenesis is…

Parthenogenesis… is a natural form of asexual reproduction in which growth and development of embryos occur without fertilization. In animals, parthenogenesis means development of an embryo from an unfertilized egg cell and is a component process of apomixis.

One thing that has always annoyed me about popular accounts of string theory is that they often claim that known particles are just like vibrational modes of a physical string, bringing music into it, as an argument for the beauty of string theory. No one ever mentions that the analogs of physical string vibrational modes have nothing to do with observed particles. If they exist at all, they’re some sort of Planck-scale states. Known particles are modeled typically by zero modes, with the classical analog not playing your guitar strings, but picking up the guitar and carrying it around, a much less musical activity. I don’t remember ever bothering to make that argument publicly, because it seemed likely to lead nowhere but to silly arguments from string theorists. I’m now glad to see that 4gravitons has taken up the issue with a blog entry Particles Aren’t Vibrations And, yes, check the comments for the expected response.

Let me point a slightly sharper point on it: the popular-level claim that “different particles are vibrations of the same string” appears elegant because is sounds like multiple particles are being explained by a single string (or at least fewer number of them). That is, it sounds like string theory has increased explanatory power, compressing observable data into a strictly smaller number of bits. But in fact, all the particles we see are each the zero states of multiple different modes, and the ground-state properties of those modes is not explained from first principles; those bits of information are just mapped into the parameters describing the compactification.

Simple cells like bacteria generate all their energy in their outer membrane, which puts a physical limit on how big they can get and still make enough energy to support themselves. (In mathematical terms, their volume expands faster than their surface area, so their demand for energy eventually exceeds their ability to generate it.) Once cells had internalized the means of making energy—that is, once they had mitochondria—this constraint disappeared. Mitochondria also have specialized genomes focused on energy generation, but bacteria don’t. So cells with mitochondria could get much bigger, allowing for complex new arrangements

Of course, this prompts the question “Why does energy generation have to happen on the membrane wall?”. The first review article I could find, (popular introduction here) cites Lane and collaborator William Martin. However, they disagree with Lane and Martin, saying

It has previously been pointed out that the plasma membrane serves as the only region for ATP synthesis in bacteria, and since this surface area scales sublinearly with volume it will be outpaced by anything that is proportional to volume (Lane and Martin, 2010). Previous analyses have thus suggested that bacteria are becoming less efficient on a per-protein or per-gene level (Lane and Martin, 2010). However, the surprising superlinear scaling of metabolic rate and the sublinear scaling of both genome size and protein content lead to an increasing efficiency for both components. Figure 4a gives the power per gene as a function of cell size showing that it is increasing superlinearly across bacteria….Thus, it would seem that bacteria are not limited by an energetic efficiency challenge but rather by an energetic surplus that demands ever faster rates of biosynthesis and eventually leads to a space limitation via the packing of ribosomes as discussed earlier.

So I guess I’ve never heard of this stuff because it’s still disputed.

Tangentially related to the rest of Gates’ review, I’ve never heard a convincing order-of-magnitude argument against what seems to me to be the simplest theory: abiogenesis is stupendously rare. Folks who point to the relatively early development of life on Earth — that it “happened as soon as it was physically possible” — generally don’t understand the selection effects, and in particular the lock-picking paradox described by Robin Hanson. (That said, I think Robin himself is sympathetic to the hypothesis that single cell life is common, so maybe I don’t understand it…) This seems like the sort of case where the true experts have a short, convincing argument that just never filters out to the rest of the field, much less the public at large. Let me know if it’s written down somewhere.

There are a handful of commercial flights that travel over Antarctica:

Direct flights between South Africa and New Zealand would overfly Antarctica, but no airline has scheduled such flights. LAN Airlines flies nonstop between Auckland, Sydney and Santiago, Air New Zealand flies nonstop between Auckland and Buenos Aires starting December 1 2015, and Qantas flies nonstop between Sydney and Santiago, the most southerly polar route. Depending on winds, these reach 55 degrees south latitude, but other times 71 degrees, which is enough to cross the polar ice cap.

Depending on the winds, the Qantas flight QF 63 from Sydney to Johannesburg sometimes flies over the Antarctic Circle to latitude 71 degrees as well and allowing views of the icecap

Bonus: this (over saturated?) image of McMurdo Station from Wired.

Incidentally, the Google Maps coverage of Antarctica is terrible. Who’d have thought?

At 07:33, the cabin crew had begun to prepare for meal service. The plane had climbed to 17,400 feet (5,300 m) over Didcot, Oxfordshire. Suddenly, there was a loud bang, and the fuselage quickly filled with condensation. The left windscreen, on the captain’s side of the cockpit, had separated from the forward fuselage. Lancaster was jerked out of his seat by the rushing air and forced head first out of the cockpit, his knees snagging onto the flight controls. This left him with his whole upper torso out of the aircraft, and only his legs inside. The door to the flight deck was blown out onto the radio and navigation console, blocking the throttle control, causing the aircraft to continue gaining speed as it descended, while papers and other debris in the passenger cabin began blowing towards the cockpit. On the flight deck at the time, flight attendant Nigel Ogden quickly latched his hands onto the captain’s belt. Susan Price and another flight attendant began to reassure passengers, secure loose objects, and organise emergency positions. Meanwhile, Lancaster was being battered and frozen in the 345 mph wind, and was losing consciousness due to the thin air.

Atchison began an emergency descent, re-engaged the temporarily disabled autopilot, and broadcast a distress call. Due to rushing air on the flight deck, he was unable to hear the response from air traffic control….

Ogden, still latched onto Lancaster, had begun to suffer from frostbite, bruising and exhaustion. He was relieved by the remaining two flight attendants. By this time Lancaster had already shifted an additional six to eight inches out the window. From the flight deck, the flight and cabin crew were able to view his head and torso through the left direct vision window. Lancaster’s face was continuously hitting the direct vision window; when cabin crew saw this and noticed that Lancaster’s eyes were opened but not blinking despite the force against the window, they assumed that Lancaster was dead. Atchison ordered the cabin crew to not release Lancaster’s body despite the assumption of his death because he knew that releasing the body might cause it to fly into the left engine and cause an engine fire or failure which would cause further problems for Atchison in an already highly stressful environment.

Atchison eventually received clearance from air traffic control to land at Southampton, while the flight attendants managed in extreme conditions to free Lancaster’s ankles from the flight controls and hold on to him for the remainder of the flight. By 07:55 the aircraft had landed safely on Runway 02 at Southampton. Passengers immediately disembarked from the front and rear stairs, and emergency crews retrieved Lancaster.

Much to everyone’s surprise, Lancaster was found to be alive, and was taken to Southampton General Hospital, where he was found to be suffering from frostbite, bruising and shock, and fractures to his right arm, left thumb and right wrist. Flight attendant Nigel Ogden suffered a dislocated shoulder, frostbitten face and some frostbite damage to his left eye. Everyone else left the aircraft unhurt.

Less than five months after the accident Lancaster was working again. He later retired from British Airways when he reached the company’s mandatory retirement age of 55 at the time. In 2005 Lancaster was reported flying for easyJet.

Here is first-person testimony from the crew.

The London Crossrail project, which will eventually connect Reading and Heathrow in the west to Shenfield and Abbey Wood in the east, is Europe’s largest construction project, and one of the largest in the world. The centrepiece of the project is 13 miles of new twin-bore deep-tube tunnels that run through central London, at depths of up to 40 metres, from Royal Oak near Paddington in the west to Victoria Dock near Canary Wharf in the east.
Eight tunnel boring machines (TBMs), each about 100 metres long and weighing roughly 1,000 tonnes, worked around the clock for three years, with excavation completed at the end of 2015. Because the TBMs are so large and unwieldy, two of them—named Phyllis and Ada—were left buried in the ground near the new Farringdon tunnels.

I don’t really understand why they keep building the entrances further and further from the actual trains, though:

At 250 metres (820ft), the Elizabeth line platforms are more than twice the length of current Underground platforms, which range between 122 metres (400ft) and 107m (350ft). The first trains will be 200 metres (660ft) long, but they can be extended to 240m (790ft) in the future if passenger demand increases. Because the platforms are so long, and the capacity of the trains so great, most Elizabeth line stations will have two large ticket halls that are spaced far apart. The two ticket halls for the Bond Street station, for example, are on Davies Street and Hanover Square—about 500 metres (1,640ft) away from each other.

Why are the entrances so much further apart than the ends of the platform, adding multiple football fields of unavoidable walking to each commute?

Another good video showing the interior operation of tunnel borers.

Genome-wide association is unapologetic, high-tech p-hacking. In the modern era, when major social science journals discourage null-hypothesis significance tests and replication as opposed to significance has become an obsession, it is nothing short of odd that behavioral science at the bleeding edge of genomic technology has become an extended exercise in stringent but fundamentally old-fashioned significance testing. To assume that the current list of single nucleotide polymorphisms (SNPs) reaching significance for some behavioral trait will be significant again the next time someone collects DNA from 100,000 people is to make the most basic of errors about the relationship between statistical significance and replicable science. Some SNPs will replicate. Others will not. It will depend on context.

H/t Scott Alexander. Also from him: Researchers criticize the Mukherjee piece on epigenetics. It’s amazing that big name places can muck this stuff up so much. In my experience, the Economist does the best job of avoiding the Gell-Mann Amnesia effect.

In Sep 2013, it was announced that the property was purchased by Somerset Development Corp for $27 million. The redevelopment project will include a health and wellness center, skilled nursing facility and assisted living center, a hotel, restaurants and shopping, spa, office spaces and a 20,000-square-foot public library. Recreation space and luxury homes are planned for the surrounding land. Toll Brothers will be the residential developer the project, planning a total of 225 homes: 40 single-family properties and another 185 “active-adult” homes that will be available to residents aged 55 and older. Several office tenants have moved into the Bell Works building, and there is a cafe now open in the main lobby.

Ultra-deep sequencing to detect circulating tumor DNA has the potential to be the holy grail for early cancer detection in asymptomatic individuals. Most tumors shed nucleic acids into the blood. Circulating tumor DNA is a direct measurement of cancer DNA, rather than an indirect measure of the effects of cancer….The mission of Grail is to enable the early detection of cancer in asymptomatic individuals through a blood screen – with the goal of massively decreasing global cancer mortality by detection at a curable stage. Grail will leverage the power of “ultra-deep” sequencing technology, the best talent in the field and the passion of its leadership to deliver on that promise.

Pretty good press copy.

Detection of recent natural selection is a challenging problem in population genetics, as standard methods generally integrate over long timescales. Here we introduce the Singleton Density Score (SDS), a powerful measure to infer very recent changes in allele frequencies from contemporary genome sequences. When applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past 2,000 years. We see strong signals of selection at lactase and HLA, and in favor of blond hair and blue eyes. Turning to signals of polygenic adaptation we find, remarkably, that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we report suggestive new evidence for polygenic shifts affecting many other complex traits. Our results suggest that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.

(H/t Gwern.)

A study published in The American Journal of Political Science underscored how powerful political bias can be. In an experiment, Democrats and Republicans were asked to choose a scholarship winner from among (fictitious) finalists, with the experiment tweaked so that applicants sometimes included the president of the Democratic or Republican club, while varying the credentials and race of each. Four-fifths of Democrats and Republicans alike chose a student of their own party to win a scholarship, and discrimination against people of the other party was much greater than discrimination based on race.

(H/t Tyler Cowen.) The study is here [PDF].

This strongly confirms my priors so I’m very interested to hear criticisms of the methodology/statistics.

By the law of conservation of hate, the best solution is probably to invent fictitious countries and convince ourselves that they are the bad guys. Maybe aliens?

http://youtube.com/watch?v=WQEiYWGitKs

As [she] aged, the seizures, headaches, and suffering from her childhood head trauma continued to plague her. At some point in the late 1890s, she underwent brain surgery at Boston’s Massachusetts General Hospital. Unable to sleep because of pains and “buzzing” in her head, she asked a doctor if he could operate. He agreed and, in her words, “sawed open my skull, and raised it up, and now it feels more comfortable.” She had received no anesthesia for the procedure and reportedly chose instead to bite down on a bullet, as she had seen Civil War soldiers do when their limbs were amputated.

The bottom line is that you can’t use tachyons to send information faster than the speed of light from one place to another. Doing so would require creating a message encoded some way in a localized tachyon field, and sending it off at superluminal speed toward the intended receiver. But as we have seen you can’t have it both ways: localized tachyon disturbances are subluminal and superluminal disturbances are nonlocal.

(H/t Godfrey Miller.)

A common objection against starting a large-scale biomedical war on aging is the fear of catastrophic population consequences (overpopulation). This fear is only exacerbated by the fact that no detailed demographic projections for radical life extension scenario have been conducted so far. This study explores different demographic scenarios and population projections, in order to clarify what could be the demographic consequences of a successful biomedical war on aging. A general conclusion of this study is that population changes are surprisingly slow in their response to a dramatic life extension. For example, we applied the cohort-component method of population projections to 2005 Swedish population for several scenarios of life extension and a fertility schedule observed in 2005. Even for very long 100-year projection horizon, with the most radical life extension scenario (assuming no aging at all after age 60), the total population increases by 22% only (from 9.1 to 11.0 million). Moreover, if some members of society reject to use new anti-aging technologies for some religious or any other reasons (inconvenience, non-compliance, fear of side effects, costs, etc.), then the total population size may even decrease over time. Thus, even in the case of the most radical life extension scenario, population growth could be relatively slow and may not necessarily lead to overpopulation. Therefore, the real concerns should be placed not on the threat of catastrophic population consequences (overpopulation), but rather on such potential obstacles to a success of biomedical war on aging, as scientific, organizational, and financial limitations.

H/t Gwern. Also from Gwern: China is positioning itself as a world leader in primate research.

Three more camera angles here. If you’re sick of the Musk fanboyism here….well get off my lawn.

The new news is that SpaceX is launching a Dragon capsule to Mars as early as 2018. More here. This would be the heavy object landed on Mars by far. They key technical advance is supersonic retropropulsion Also:

If you read near the end of the article, they say that SpaceX is going to launch a Falcon Heavy in November as a test. But additionally they are going to try to land all three boosters. The two side boosters on land and the middle booster on the drone ship (because it will be going a lot faster)
Here is a simulation…. I have probably watch this video 20+ times just amazing.
https://www.youtube.com/watch?v=4Ca6x4QbpoM

Incidentally, the SpaceX subreddit has got to be the most exhaustive resource, and is a really impressive example of using reddit as a crowd-built website.

This makes it more clear than the standard picture what’s probably going on: most of our color-discriminating ability is focused on the red-green transition, where we have relatively fine discriminating ability.

Another of these little-known facts about the BBB: “We are not a consumer watchdog.” While the BBB offers consumers many services—lists of popular scams to watch out for and such—the organization’s mission isn’t to have your back. From top to bottom, the BBB is funded by the annual dues paid by businesses it anoints with “accreditation,” which allows the companies to put those iconic BBB stamps of approval on their storefronts and websites. This fact raises obvious questions about an inherent conflict of interest: The organization’s customers are businesses, not taxpayers or consumers. How can the BBB serve as an honest broker between businesses and consumers when it is fully funded by one of these parties? Many argue that it cannot — that there’s a natural incentive to paint its paying clients in the best possible light.

Whether or not a business is accredited, it can be graded by the BBB. The grading system, ranging from A+ to F, is confusing at best, useless at worst. Business grades are determined by 16 factors, including how many complaints have been filed with the BBB against the business, and if and how the business responded. Notably, however, a business’s grade won’t necessarily be hurt if nothing much comes of a complaint and the customer is left unsatisfied. Rather, all that matters, grading-wise, is that the business responded and made a “good faith effort to resolve complaints,” according to the BBB. This means that a business could have a good grade even if it is the subject of lots of complaints, as long as the business dutifully responds — even in a pro forma way.

On the flip side, a business that is committed to handling complaints directly with customers in a substantive way, but does so outside the purview of the BBB, will get a poor grade because the BBB is not involved. So a company can have a B or C rating, or even an F, simply because it doesn’t play by the BBB’s rules, which include looping in the organization with complaint responses and providing the BBB with background information about the company.

When I talk to people about what I do for a living, I often face blank stares (or, worse, rapidly retreating backs) when I describe problems like the Traveling Salesman Problem….I try to convince people the Traveling Salesman problem is hard by saying there are a lot of solutions to look through. And that is an extremely misleading argument that I am now convinced does more harm than good.

Imagine if I had said one of the following:

…“Sorting a bunch of numbers! Hoo-wee, that’s a hard one. If I had 1000 numbers, I would have to check all orderings of the numbers to find the sorted order. That is 1000*999*998*…*2*1 orders and that is more than the hairs on a Hobbit’s toes.”…

So why do we use this argument for the Traveling Salesman problem? We know from complexity theory that the problem is NP-Hard, so most of us believe that there is not now a known polynomial time algorithm (there are still some who believe they have such an algorithm, but they are in the very, very tiny minority), and many of us believe that no such algorithm exists.

But that does not mean complete enumeration is necessary: it is easy to come up with approaches that go through less than the full n! solutions to the Traveling Salesman problem (see the postscript for one example).

But the “complete enumeration” statement is even more harmful since it glosses over a much more important issue: many “hard” problems (in the complexity theory meaning) are not particularly hard (in the English sense), if you limit yourself to instances of practical interest. Due to the tremendous amount of work that has been done on the Traveling Salesman Problem, the TSP is one such problem. If you have an instance of the TSP of practical interest (i.e. it makes a difference to your life if you solve it or not, and it is really a TSP, not the result of some weird set of set of reductions from some other problem), then I bet you the Concorde program of Bill Cook and others will get you a provably optimal solution in a reasonable amount of time. In fact, I would be really interested in knowing the smallest “real” instance that Concorde cannot solve in, say, one day, on a normal laptop computer.

There is related ranting by Tricks.

Scott Aronson has complained about similar simplification of quantum computing by the media lead to the popular impression that “quantum computing = generic exponential speedups for optimization, machine learning, and Big Data problems, by trying all the possible answers at once.”

In January 1858, the first masonry building in Chicago to be thus raised—a four story, 70-foot (21 m) long, 750-ton brick structure situated at the north-east corner of Randolph Street and Dearborn Street—was lifted on two hundred jackscrews to its new grade, which was 6 feet 2 inches (1.88 m) higher than the old one, “without the slightest injury to the building.” It was the first of more than fifty comparably large masonry buildings to be raised that year.

(Ht Gwern.)

“On the Cult of Personality and Its Consequences”…was a report by Soviet leader Nikita Khrushchev made to the 20th Party Congress of the Communist Party of the Soviet Union on 25 February 1956. Khrushchev’s speech was sharply critical of the reign of deceased General Secretary and Premier Joseph Stalin, particularly with respect to the purges of the Communist Party of the Soviet Union which had especially marked the last years of the 1930s. Khrushchev charged Stalin with having fostered a leadership personality cult despite ostensibly maintaining support for the ideals of communism.

The speech was a milestone in the “Khrushchev Thaw.” Superficially, the speech was an attempt to draw the Soviet Communist Party closer to Leninism. Khrushchev’s ulterior motivation, however, was to legitimize and help consolidate his control of the Communist party and government, power obtained in a political struggle with Georgy Malenkov or firm Stalin loyalists such as Vyacheslav Molotov.

The Khrushchev report was known as the “Secret Speech” because it was delivered at an unpublicized closed session of Communist Party delegates, with guests and members of the press excluded. The text of the Khrushchev report was widely discussed in party cells already in early March, often with participation of non-party members; however the official Russian text was openly published only in 1989 during the glasnost campaign of Soviet leader Mikhail Gorbachev.

Ironically, then, the effort to automate driving may actually create a lot of jobs, especially in the early years as self-driving technology is being rolled out. As Google and its competitors expand their self-driving vehicle programs nationwide, they’re going to have to hire thousands of human analysts to produce the detailed maps that enable cars to drive safely.

And this won’t just be a one-off development, either. Landscapes are changing constantly, with changing speed limits, new construction, and trees growing and being cut down. So while maintaining maps may require less manpower than creating them initially, self-driving car technology is likely to employ a lot of people for the foreseeable future.

In their own words:

One might hope, given most scholars’ motivations for joining the academy, that Wikipedia would be a natural venue for scholarly communication. But Wikipedia has not succeeded in this regard. We believe the reasons this is the case are two-fold: (1) academics participate in a prestige-based economy, and in order to survive professionally we must devote our limited time to pursuits for which we can get professional credit. And (2), despite a lifetime spent in serious and critical study, the credibility and reputation academics have earned is worth nothing when contributing in non-scholarly forums.

This seems to miss the key point: The ultimate criterion on Wikipedia is verifiability, not truth. This is a very careful and purposefully made distinction. It constrains Wikipedia discussions to questions of (1) verification through secondary sources and (2) presentation. Without this constraint, the already sisyphean discussions on Wikipedia would be much worse. But ultimately, if you want to build Scientifica, you need to appeal to truth and so, ultimately, expert knowledge.