Watching Half Sigma and his commenters

talk about class is pretty much the same as watching Ta-Nehisi Coates and his sycophants learnedly discourse on genetics.

"I read the paper, understood most of it, but was basically lost trying to understand the graphs. (It's true that my math and science foundation is fairly weak.)"
-- Ta-Nehisi Coates

"Well when I was 17, I didn’t realize that my parents were poor and stupid."
-- Half Sigma

Background: Half Sigma was born to lower-middle-class Staten Island Jewish parents and blames the American class system for his failure at life. At some point he read Paul Fussell's 1983 book Class, decided this made him an expert on the subject, and started mixing up dated observations from Fussell with his own observations of the people he perceives to be his social superiors in present-day Manhattan.

Fussell could not have been any clearer on who he put in his "Top out-of-sight" category: "The top-out-of-sight class (Rockefellers, Pews, DuPonts, Mellons, Fords, Vanderbilts) lives on inherited capital entirely."

This class, as described by Fussell, barely exists today. The proportion of the richest Americans (or their children) with any particular connection to the mid-20th century or earlier American upper class is small and continually shrinking.

I just looked up the original Half Sigma "top out-of-sight" post, and his confusion is even deeper than I remembered:

The top out-of-sight upper class

A few days ago I threw out the idea that the country is run by WASPs, which I think is rather misleading and over-simplistic. It’s probably more accurate that there are several different power groups in the United States. The two most obvious power groups are the Republican Party and the Democratic Party.

(Please note that this was a post from June of 2012 -- not 1952.)

Searching for other power groups, one of the obvious power groups is the highest social class in the country. And to know what the highest class is, we turn to the late Paul Fussell’s book Class, and we find out that the highest class is what Fussell calls the “top out-of-sight upper class.” Fussell, unfortunately, doesn’t say much about this class, probably because he doesn’t know that much about them. The primary difference he talks about is that the regular upper class live in showy mansions and make their wealth known to the lower classes. The top out-of-sight upper class hides from public exposure.

In the movie Born Rich, directed by Jamie Johnson (which I previously blogged about), one of the important things he mentioned about his class of people is that they like their privacy and they were very opposed to him making a documentary about them. So Paul Fussell got the out-of-sight part right, although out-of-sight means that they are non-obvious rather than that you literally can never see them. The top out-of-sight is more often hiding in plain sight rather than on a private island off the coast of Maine. They might summer at such a place, although there are probably more of them summering on Nantucket.

I have personally met people from the top out-of-sight upper class, and maybe you have to. They are not rock stars, and because they are often hiding in plain sight, they are actually a lot easier to meet than upper class people who are more likely to have gatekeepers to restrict access to them. Imagine the unlikelihood of having a conversation with Donald Trump. But there are many top out-of-sight upper class people living in Manhattan who you can talk to easily enough, although they won’t be interested in being your friend for the same reason you (a middle to upper middle class person) wouldn’t want to be friends with a prole.

So now I will fill in some of the gaps of this class. Of course, I don’t have much personal knowledge, so I am mostly making educated guesses.

There's no ambiguity about who Fussell classes as "top out-of-sight". It's not any Manhattan yuppie/hipster/"bobo" who went to private schools and who Half Sigma could see himself crossing paths with. It is, in caricature, the stock mid-20th century estate-dwelling upper class of popular imagination (which, again, increasingly no longer exists).

And, yes, the "out-of-sight" part was meant literally -- referring to the houses, not the people. Half Sigma fails even at basic reading comprehension. Fussell:

No one whose money, no matter how copious, comes from his own work--film stars are an example--can be a member of the top-out-of-sight class, even if the size of his income and the extravagance of his expenditure permit him to simulate identity with it. Inheritance--"old money" in the vulgar phrase--is the indispensable principle defining the top three classes, and it's best if the money's been in the family for three or four generations. There are subtle local ways to ascertain how long the money's been there. Touring middle America, the British traveler Jonathan Raban came upon the girl Sally, who informed him that "New Money says Missouri; Old Money says Missoura."

"When I think of a really rich man," says a Boston blue-collar, "I think of one of those estates where you can't see the house from the road." Hence the name of the top class, which could just as well be called "the class in hiding." Their houses are never seen from the street or road. They like to hide away deep in the hills or way off on Greek or Caribbean islands (which they tend to own), safe, for the moment, from envy and its ultimate attendants, confiscatory taxation and finally expropriation. It was the Great Depression, Vance Packard speculates, that badly frightened the very rich, teaching them to be "discreet, almost reticent, in exhibiting their wealth." From the 1930s dates the flight of money from such exhibitionistic venues as the mansions of upper Fifth Avenue to hideaways in Virginia, upper New York State, Connecticut, Long Island, and New Jersey. [. . .]

The next class down, the upper class, differs from the top-out-of-sight class in two main ways. First, although it inherits a lot of its money, it earns quite a bit too, usually from some attractive, if slight, work, without which it would feel bored and even ashamed. It's likely to make its money by controlling banks and the more historic corporations, think tanks, and foundations, and to busy itself with things like the older universities, the Council on Foreign Relations, the Foreign Policy Association, the Committee for Economic Development, and the like, together with the executive branch of the federal government, and often the Senate.

HGP10 Symposium - The Genomics Landscape a Decade after the Human Genome Project

April 25, 2013: A commemorative all-day symposium, in Kirschstein Auditorium, Natcher Conference Center, featured a group of speakers. The event, The Genomics Landscape a Decade after the Human Genome Project,looked at the accomplishments of the decade with an eye to what is on the horizon. The date of the symposium was significant, occurring in the month that the HGP was announced 10 years ago, and coinciding with the date 60 years ago when James Watson and Francis Crick's article describing DNA's double-helical structure was published. The symposium is timed with both historic achievements in mind.

The $1,000 Genome, the $1,000,000 Interpretation - Kevin Davies

African Integrative Genomics: Implications for Human Origins - Sarah Tishkoff

Progress Since the Human Genome Project

Whole Genome Sequencing in Newborn Screening - Jeff Botkin

Annotating and Understanding Genomes - Ewan Birney

The complete list of talks is available here (with slides).

Another dent in the Rosalind Franklin myth

A comment on a recent editorial discussing Raymond Gosling:
In this article, I (the author) followed multiple sources in referring to 'Photo 51' as the work of Rosalind Franklin. However, medical geneticist Jim Lupski raised a query about the accuracy of the attribution, having received correspondence from Jim Watson which mentioned in passing that Ray Gosling had taken the photo.

I put the query to Gosling, who confirms that he was indeed 'Photo 51' photographer:

'It was part of the program that Rosalind and I were carrying out to check the effect of the humidity on the crystallization of DNA. This was the 51st of that program, and I was the one who took that particular diffraction pattern.'

Thanks to Jim Lupski for bringing the inaccuracy to my attention, to Ray Gosling for providing further information, and to Jim Watson for confirming that this was his understanding of events.

Note that Gosling was originally Wilkins' graduate student. The two were taking X-ray photographs of DNA before Franklin ever became involved. Additional background:

Wilkins began using optical spectroscopy to study DNA in the late 1940s. In 1950 he and Gosling obtained the first clearly crystalline X-ray diffraction patterns from DNA fibres, and Alec Stokes suggested that the patterns indicated that DNA was helical (spiral) in structure. [source]

Franklin's fellowship proposal called for her to work on x-ray diffraction studies of proteins in solution. However, there was a shift in research priorities after Maurice Wilkins, the assistant director of Randall's lab, began working with an unusually pure sample of DNA obtained from Rudolf Signer. Excited about the possibilities, Wilkins suggested to Randall that Franklin's expertise might be better applied to this promising DNA research. Randall agreed; he wrote to Franklin in November 1950, explaining the change of plan, and stated that she and graduate student Raymond Gosling would be the only staff doing crystallographic studies of DNA. Randall did not mention Wilkins' serious interest in DNA, nor did he tell Wilkins the details of the letter. These omissions soon generated misunderstandings between Wilkins and Franklin--Franklin assumed that the x-ray diffraction studies of DNA would be her project alone; Wilkins assumed that she was joining the loosely organized research team ("Randall's Circus") at the biophysics lab, as the expert on crystallography. When Wilkins continued working on DNA and suggested that he and Franklin collaborate, she resented what she regarded as interference. [source]

Rosalind Franklin has become such a symbolic figure that it is now hard to separate facts from myths. However, in the rush to see Franklin as wronged, it needs to be recalled that Wilkins was a senior independent scientist, had laid a lot of groundwork for the DNA work, and had obtained the actual DNA samples Franklin went on to take x-ray pictures of. All this was then essentially taken off him by the unit head (Randall) and given to Franklin. So it could be argued with a good deal of justification that the DNA project at King's was very much Wilkins' baby, and would not have existed for Franklin to take forward without years of Wilkins' groundwork. [source]

“To think that Rosy had all the 3D data for 9 months & wouldn’t fit a helix to it and there was I taking her word for it that the data was anti-helical. Christ,” Dr. Wilkins wrote, musing on how close he might have come to making the discovery himself. [source]

Population genetics notes and lectures

Genome 562 - Population Genetics - Joe Felsenstein

Theoretical Evolutionary Genetics - a draft text - Joe Felsenstein

Population Genetics notes - Graham Coop

Population genetics teaching resources - Graham Coop

Lecture notes in population genetics - Kent Holsinger

The Progress of Genetics From the 1930s to Today - James Crow (2010)

Introduction to Population Genetics - Lynn Jorde (2012)

"More Genomes From Denisova Cave Show Mixing of Early Human Groups"

More Genomes From Denisova Cave Show Mixing of Early Human Groups
From the detailed genomes of both Neandertals and Denisovans, Pääbo and Montgomery Slatkin of the University of California, Berkeley, estimated that 17% of the Denisovan DNA was from the local Neandertals. And the comparison revealed another surprise: Four percent of the Denisovan genome comes from yet another, more ancient, human—"something unknown," Pääbo reported. "Getting better coverage and more genomes, you can start to see the networks of interactions in a world long ago," says David Kingsley, an evolutionary biologist at Stanford University in Palo Alto, California.

With all the interbreeding, "it's more a network than a tree," points out Carles Lalueza-Fox, a paleogeneticist from the Institute of Evolutionary Biology in Barcelona, Spain. Pääbo hesitates to call Denisovans a distinct species, and the picture is getting more complicated with each new genome.

John Hawks: New Denisova and Neandertal DNA results reported
Now, we may be learning that the Denisovan genome itself represents different ancestral groups -- not only a more ancient "something unknown" population, but substantially the local Neandertals. That kind of mixture is not the population history described by papers on the Denisova genome so far. And a third Denisovan mtDNA from one of the third molars at the site is substantially different from the other two, pointing to greater mtDNA diversity within the Denisovan population than now known from either Neandertals or living people.

What does it mean? I don't think there's a contradiction here in the data. What this shows is that the methods applied to the data have been too simplistic. The methods will come to a result, but that result may not fit the data as well as a population model with more complexity. Looking only at one kind of comparison -- as the Li and Durbin model applied to the Denisova genome by Meyer and colleagues last year [1] -- will probably not give a result that describes the true population history. We need to keep our minds open to more complex population histories that may be more consistent with other sources of data, including archaeological and fossil information.

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