👓 What really happened when two mathematicians tried to publish a paper on gender differences? The tale of the emails | Retraction Watch

Read What really happened when two mathematicians tried to publish a paper on gender differences? The tale of the emails (Retraction Watch)
Retraction Watch readers may be familiar with the story of a paper about gender differences by two mathematicians. Last month, in Weekend Reads, we highlighted an account of that story, which appea…

This article and the related links cover a lot of the questions I had when I read the original in Quillette the other day and only wish I’d had the time to follow up on as a result. Now to go on and read all the associated links and emails….

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👓 Using Medieval DNA to track the barbarian spread into Italy | Ars Technica

Read Using Medieval DNA to track the barbarian spread into Italy (Ars Technica)
Cemeteries from the Longobard spread into Italy tell tales of migration and mixing.
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👓 Statement by Amie Wilkinson addressing unfounded allegations. | Amie Wilkinson

Read Statement by Amie Wilkinson addressing unfounded allegations. by Amie Wilkinson (math.uchicago.edu)
This statement addresses some unfounded allegations about my personal involvement with the publishing of Ted Hill's preprint "An evolutionary theory for the variability hypothesis" (and the earlier version of this paper co-authored with Sergei Tabachnikov). As a number of erroneous statements have been made, I think it's important to state formally what transpired and my beliefs overall about academic freedom and integrity. I first saw the publicly-available paper of Hill and Tabachnikov on 9/6/17, listed to appear in The Mathematical Intelligencer. While the original link has been taken down, the version of the paper that was publicly available on the arxiv at that time is here. I sent an email, on 9/7/17, to the Editor-in-Chief of The Mathematical Intelligencer, about the paper of Hill and Tabachnikov. In it, I criticized the scientific merits of the paper and the decision to accept it for publication, but I never made the suggestion that the decision to publish it be reversed. Instead, I suggested that the journal publish a response rebuttal article by experts in the field to accompany the article. One day later, on 9/8/17, the editor wrote to me that she had decided not to publish the paper. I had no involvement in any editorial decisions concerning Hill's revised version of this paper in The New York Journal of Mathematics. Any indications or commentary otherwise are completely unfounded. I would like to make clear my own views on academic freedom and the integrity of the editorial process. I believe that discussion of scientific merits of research should never be stifled. This is consistent with my original suggestion to bring in outside experts to rebut the Hill-Tabachnikov paper. Invoking purely mathematical arguments to explain scientific phenomena without serious engagement with science and data is an offense against both mathematics and science.

A response to an article I read the other day in Quillette.

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👓 Adaptable lizards illustrate key evolutionary process proposed a century ago | Science Daily

Read Adaptable lizards illustrate key evolutionary process proposed a century ago (ScienceDaily)
The 'Baldwin effect' has now been demonstrated at the genetic level in a population of dark-colored lizards adapted to live on a lava flow in the desert.

Highlights, Quotes, Annotations, & Marginalia

One explanation has been that many of an animal’s traits are not fixed, but can change during its lifetime. This “phenotypic plasticity” enables individual animals to alter their appearance or behavior enough to survive in a new environment. Eventually, new adaptations promoting survival arise in the population through genetic changes and natural selection, which acts on the population over generations. This is known as the “Baldwin effect” after the psychologist James Mark Baldwin, who presented the idea in a landmark paper published in 1896.  

September 11, 2018 at 08:57AM

Journal article available at: https://www.cell.com/current-biology/pdfExtended/S0960-9822(18)30899-6

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👓 Academic Activists Send a Published Paper Down the Memory Hole | Quillette

Read Academic Activists Send a Published Paper Down the Memory Hole by Theodore P. Hill (Quillette)
In the highly controversial area of human intelligence, the ‘Greater Male Variability Hypothesis’ (GMVH) asserts that there are more idiots and more geniuses among men than among women. Darwin’s research on evolution in the nineteenth century found that, although there are many exceptions for ...

I understand the potential political implications of such research, but blocking publication like this seems a tad underhanded. I’ve not yet read the paper, but want to take a look at it at least from an evolutionary theoretic standpoint. Admittedly on its face it sounds a bit more like pure theory rather than anything supported by actual evidence and underlying research in reality, but there’s no reason to stop the idea if it could potentially be a fruitful area.

If a formally refereed and published paper can later be erased from the scientific record and replaced by a completely different article, without any discussion with the author or any announcement in the journal, what will this mean for the future of electronic journals?

This is a very concerning issue and a good reason why people should also practice samizdat and place multiple copies online in various repositories.

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👓 Disconnected, fragmented, or united? a trans-disciplinary review of network science | Applied Network Science | César A. Hidalgo

Read Disconnected, fragmented, or united? a trans-disciplinary review of network science by César A. HidalgoCésar A. Hidalgo (Applied Network Science | SpringerLink)
During decades the study of networks has been divided between the efforts of social scientists and natural scientists, two groups of scholars who often do not see eye to eye. In this review I present an effort to mutually translate the work conducted by scholars from both of these academic fronts hoping to continue to unify what has become a diverging body of literature. I argue that social and natural scientists fail to see eye to eye because they have diverging academic goals. Social scientists focus on explaining how context specific social and economic mechanisms drive the structure of networks and on how networks shape social and economic outcomes. By contrast, natural scientists focus primarily on modeling network characteristics that are independent of context, since their focus is to identify universal characteristics of systems instead of context specific mechanisms. In the following pages I discuss the differences between both of these literatures by summarizing the parallel theories advanced to explain link formation and the applications used by scholars in each field to justify their approach to network science. I conclude by providing an outlook on how these literatures can be further unified.

Highlights, Quotes, Annotations, & Marginalia

Social scientists focus on explaining how context specific social and economic mechanisms drive the structure of networks and on how networks shape social and economic outcomes. By contrast, natural scientists focus primarily on modeling network characteristics that are independent of context, since their focus is to identify universal characteristics of systems instead of context specific mechanisms.  

August 25, 2018 at 10:18PM

Science and Complexity (Weaver 1948); explained the three eras that according to him defined the history of science. These were the era of simplicity, disorganized complexity, and organized complexity. In the eyes of Weaver what separated these three eras was the development of mathematical tools allowing scholars to describe systems of increasing complexity.  

August 25, 2018 at 10:19PM

Problems of disorganized complexity are problems that can be described using averages and distributions, and that do not depend on the identity of the elements involved in a system, or their precise patterns of interactions. A classic example of a problem of disorganized complexity is the statistical mechanics of Ludwig Boltzmann, James-Clerk Maxwell, and Willard Gibbs, which focuses on the properties of gases.  

August 25, 2018 at 10:20PM

Soon after Weaver’s paper, biologists like Francois Jacob (Jacob and Monod 1961), (Jacob et al. 1963) and Stuart Kaufmann (Kauffman 1969), developed the idea of regulatory networks. Mathematicians like Paul Erdos and Alfred Renyi, advanced graph theory (Erdős and Rényi 1960) while Benoit Mandelbrot worked on Fractals (Mandelbrot and Van Ness 1968), (Mandelbrot 1982). Economists like Thomas Schelling (Schelling 1960) and Wasily Leontief (Leontief 1936), (Leontief 1936), respectively explored self-organization and input-output networks. Sociologists, like Harrison White (Lorrain and White 1971) and Mark Granovetter (Granovetter 1985), explored social networks, while psychologists like Stanley Milgram (Travers and Milgram 1969) explored the now famous small world problem.   

Some excellent references
August 25, 2018 at 10:24PM

First, I will focus in these larger groups because reviews that transcend the boundary between the social and natural sciences are rare, but I believe them to be valuable. One such review is Borgatti et al. (2009), which compares the network science of natural and social sciences arriving at a similar conclusion to the one I arrived.  

August 25, 2018 at 10:27PM

Links are the essence of networks. So I will start this review by comparing the mechanisms used by natural and social scientists to explain link formation.  

August 25, 2018 at 10:32PM

When connecting the people that acted in the same movie, natural scientists do not differentiate between people in leading or supporting roles.  

But they should because it’s not often the case that these are relevant unless they are represented by the same agent or agency.
August 25, 2018 at 10:51PM

For instance, in the study of mobile phone networks, the frequency and length of interactions has often been used as measures of link weight (Onnela et al. 2007), (Hidalgo and Rodriguez-Sickert 1008), (Miritello et al. 2011).  

And they probably shouldn’t because typically different levels of people are making these decisions. Studio brass and producers typically have more to say about the lead roles and don’t care as much about the smaller ones which are overseen by casting directors or sometimes the producers. The only person who has oversight of all of them is the director, and even then they may quit caring at some point.
August 25, 2018 at 10:52PM

Social scientists explain link formation through two families of mechanisms; one that finds it roots in sociology and the other one in economics. The sociological approach assumes that link formation is connected to the characteristics of individuals and their context. Chief examples of the sociological approach include what I will call the big three sociological link-formation hypotheses. These are: shared social foci, triadic closure, and homophily.  

August 25, 2018 at 10:55PM

The social foci hypothesis predicts that links are more likely to form among individuals who, for example, are classmates, co-workers, or go to the same gym (they share a social foci). The triadic closure hypothesis predicts that links are more likely to form among individuals that share “friends” or acquaintances. Finally, the homophily hypothesis predicts that links are more likely to form among individuals who share social characteristics, such as tastes, cultural background, or physical appearance (Lazarsfeld and Merton 1954), (McPherson et al. 2001).  

definitions of social foci, triadic closure, and homophily within network science.
August 26, 2018 at 11:39AM

Yet, strategic games look for equilibrium in the formation and dissolution of ties in the context of the game theory advanced first by (Von Neumann et al. 2007), and later by (Nash 1950).  

August 25, 2018 at 10:58PM

Preferential attachment is the idea that connectivity begets connectivity.  

August 25, 2018 at 10:59PM

Preferential attachment is an idea advanced originally by the statisticians John Willis and Udny Yule in (Willis and Yule 1922), but has been rediscovered numerous times during the twentieth century.  

August 25, 2018 at 11:00PM

Rediscoveries of this idea in the twentieth century include the work of (Simon 1955) (who did cite Yule), (Merton 1968), (Price 1976) (who studied citation networks), and (Barabási and Albert 1999), who published the modern reference for this model, which is now widely known as the Barabasi-Albert model.  

August 25, 2018 at 11:01PM

preferential attachment. In the eyes of the social sciences, however, understanding which of all of these hypotheses drives the formation of the network is what one needs to explore.  

For example what drives attachment of political candidates?
August 26, 2018 at 08:15AM

Finally it is worth noting that trust, through the theory of social capital, has been connected with long-term economic growth—even though these results are based on regressions using extremely sparse datasets.  

And this is an example of how Trump is hurting the economy.
August 26, 2018 at 08:33AM

Nevertheless, the evidence suggests that social capital and social institutions are significant predictors of economic growth, after controlling for the effects of human capital and initial levels of income (Knack and Keefer 1997), (Knack 2002).4 So trust is a relevant dimension of social interactions that has been connected to individual dyads, network formation, labor markets, and even economic growth.  

August 26, 2018 at 08:35AM

Social scientist, on the other hand, have focused on what ties are more likely to bring in new information, which are primarily weak ties (Granovetter 1973), and on why weak ties bring new information (because they bridge structural holes (Burt 2001), (Burt 2005)).  

August 26, 2018 at 09:45AM

heterogeneous networks have been found to be effective promoters of the evolution of cooperation, since there are advantages to being a cooperator when you are a hub, and hubs tend to stabilize networks in equilibriums where levels of cooperation are high (Ohtsuki et al. 2006), (Pacheco et al. 2006), (Lieberman et al. 2005), (Santos and Pacheco 2005).  

August 26, 2018 at 09:49AM

These results, however, have also been challenged by human experiments finding no such effect (Gracia-Lázaro et al. 2012). The study of cooperation in networks has also been performed in dynamic settings, where individuals are allowed to cut ties (Wang et al. 2012), promoting cooperation, and are faced with different levels of knowledge about the reputation of peers in their network (Gallo and Yan 2015). Moreover, cooperating behavior has seen to spread when people change the networks where they participate in (Fowler and Christakis 2010).  

Open questions
August 26, 2018 at 09:50AM

References

1.
Hidalgo CA. Disconnected, fragmented, or united? a trans-disciplinary review of network science. ANS. 2016;1(1). doi:10.1007/s41109-016-0010-3
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👓 A Blended Family: Her Mother Was Neanderthal, Her Father Something Else Entirely | New York Times

Read A Blended Family: Her Mother Was Neanderthal, Her Father Something Else Entirely (nytimes.com)
Genetic analysis of bones discovered in a Siberian cave hints that the prehistoric world may have been filled with “hybrid” humans.
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👓 'I was shocked it was so easy': ​meet the professor who says facial recognition ​​can tell if you're gay | The Guardian

Read 'I was shocked it was so easy': ​meet the professor who says facial recognition ​​can tell if you're gay by Paul Lewis (the Guardian)
Psychologist Michal Kosinski says artificial intelligence can detect your sexuality and politics just by looking at your face. What if he’s right?

How in God’s name are we repeating so many of the exact problems of the end of the 1800’s? First nationalism and protectionism and now the eugenics agenda?

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👓 The stress of the fathers: epigenetics | The Economist

Read The stress of the fathers: epigenetics (Economist Espresso)
Abused or neglected children are more likely to have health problems as adults.

It seems like this has been known for a while or at least I’ve read relate research.

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🎧 ‘The Daily’: The Hunt for the Golden State Killer | New York Times

Listened to ‘The Daily’: The Hunt for the Golden State Killer by Michael Barbaro from nytimes.com

Paul Holes was on the verge of retirement, having never completed his decades-long mission to catch the Golden State Killer. Then he had an idea: Upload DNA evidence to a genealogy website.

On today’s episode:

• Paul Holes, an investigator in California who helped to crack the case.

Background reading:

• A spate of murders and rapes across California in the 1970s and 1980s went unsolved for decades. Then, last week, law enforcement officials arrested Joseph James DeAngelo, 72, a former police officer.

• Investigators submitted DNA collected at a crime scene to the genealogy website GEDmatch, through which they were able to track down distant relatives of the suspect. The method has raised concerns about privacy and ethics.

A stunning story with some ingenious detective work. I worry what the potential privacy problems are off in the future, though one of the ideas here is that it actually helps protect the privacy of some individuals who are wrongly and maliciously accused and thus saves a lot of time and money.

The subtleties will be when we’re using this type of DNA evidence more frequently for lower level crimes while at the same time the technology gets increasingly cheaper to carry out.

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👓 How Many Genes Do Cells Need? Maybe Almost All of Them | Quanta Magazine

Read How Many Genes Do Cells Need? Maybe Almost All of Them (Quanta Magazine)
An ambitious study in yeast shows that the health of cells depends on the highly intertwined effects of many genes, few of which can be deleted together without consequence.

There could be some interesting data to play with here if available.

I also can’t help but wonder about applying some of Stuart Kauffman’s ideas to something like this. In particular, this sounds very reminiscent to his analogy of what happens when one strings thread randomly among a pile of buttons and the resulting complexity.

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👓 Mutating DNA caught on film | Science | AAAS

Read Mutating DNA caught on film by Elizabeth Pennisi (Science | AAAS)
Study in bacteria shows how regularly DNA changes and how few of those changes are deadly

This is a rather cool little experiment.

h/t to @moorejh via Twitter:

Bookmarked on March 16, 2018 at 12:15PM

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👓 The First Species to Have Every Individual’s Genome Sequenced | The Atlantic

Read The First Species to Have Every Individual’s Genome Sequenced by Ed Yong (The Atlantic)
It’s an endearing, giant, flightless, New Zealand parrot, and it’s a poster child for the quantified-self movement.

Kakapo

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👓 White nationalists are flocking to genetic ancestry tests — but many don’t like their results | Stat News

Read White nationalists are flocking to genetic ancestry tests. Some don’t like what they find by Eric Boodman (Stat News)
It was a strange moment of triumph against racism: The gun-slinging white supremacist Craig Cobb, dressed up for daytime TV in a dark suit and red tie, hearing that his DNA testing revealed his ancestry to be only “86 percent European, and … 14 percent Sub-Saharan African.” The studio audience whooped and laughed and cheered. And Cobb — who was, in 2013, charged with terrorizing people while trying to create an all-white enclave in North Dakota — reacted like a sore loser in the schoolyard. “Wait a minute, wait a minute, hold on, just wait a minute,” he said, trying to put on an all-knowing smile. “This is called statistical noise.”
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👓 EXCLUSIVE: First human embryos edited in U.S., using CRISPR | MIT Technology Review

Read EXCLUSIVE: First human embryos edited in U.S., using CRISPR by Steve Connor (MIT Technology Review)
Researchers have demonstrated they can efficiently improve the DNA of human embryos.
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