📑 Solomon Golomb (1932–2016) | Stephen Wolfram Blog

Annotated Solomon Golomb (1932–2016) by Stephen Wolfram (blog.stephenwolfram.com)

As it happens, he’d already done some work on coding theory—in the area of biology. The digital nature of DNA had been discovered by Jim Watson and Francis Crick in 1953, but it wasn’t yet clear just how sequences of the four possible base pairs encoded the 20 amino acids. In 1956, Max Delbrück—Jim Watson’s former postdoc advisor at Caltech—asked around at JPL if anyone could figure it out. Sol and two colleagues analyzed an idea of Francis Crick’s and came up with “comma-free codes” in which overlapping triples of base pairs could encode amino acids. The analysis showed that exactly 20 amino acids could be encoded this way. It seemed like an amazing explanation of what was seen—but unfortunately it isn’t how biology actually works (biology uses a more straightforward encoding, where some of the 64 possible triples just don’t represent anything).  

I recall talking to Sol about this very thing when I sat in on a course he taught at USC on combinatorics. He gave me his paper on it and a few related issues as I was very interested at the time about the applications of information theory and biology.

I’m glad I managed to sit in on the class and still have the audio recordings and notes. While I can’t say that Newton taught me calculus, I can say I learned combinatorics from Golomb.

👓 Engineering bioinformatics in seconds, not hours | Ryan Barrett

Read Engineering bioinformatics in seconds, not hours by Ryan BarrettRyan Barrett (snarfed.org)

It was winter 2014. Pharrell had just dropped Happy, the Rosetta probe landed on a comet, President Obama was opening diplomatic relations with Cuba

…and here at Color, the bioinformatics team had a problem. Our pipeline — the data processing system that crunches raw DNA data from our lab into the variants we report to patients — was slow. 12 to 24 hours slow.

This wasn’t a problem in and of itself — bioinformatics pipelines routinely run for hours or even days — but it was a royal pain for development. We’d write new pipeline code, start it running, go home, and return the next morning to find it had crashed halfway through because we’d missed a semicolon. Argh. Or worse, since we hadn’t launched yet, our live pipeline would hit similar bugs in production R&D samples, which would delay them until we could debug, test, and deploy the fix. No good.

👓 Twins get some 'mystifying' results when they put 5 DNA ancestry kits to the test | CBC

Read Twins get some 'mystifying' results when they put 5 DNA ancestry kits to the test (CBC)
Last spring, Marketplace host Charlsie Agro and her identical twin sister, Carly, bought DNA ancestry kits from five of the most popular companies in the industry. Find out why some of the results they received left a team of computational biologists at Yale University baffled.

I would expect some reasonable variation between companies, but far, far less within a particular company. In all though, the article does a good job of explaining some of the basics of what is going on here.

🎧 “The Daily”: The Ethics of Genetically Editing Babies | New York Times

Listened to "The Daily": The Ethics of Genetically Editing Babies from New York Times

A scientist in China claimed to have created the world’s first gene-edited human beings. How should the U.S. respond?

👓 I’ve always known that my family was Irish descended in some way. | Charlie Owen

Read a post by Charlie OwenCharlie Owen (sonniesedge.co.uk)
I've always known that my family was Irish descended in some way. We're too prone to doughiness and large multi-generational households to be anything but that. What with Brexit looking to be an absolute shitshow and me wanting to, you know, STILL BE EUROPEAN, I thought it'd be worth looking into my...

👓 Mainstream Media Is Blowing Its Coverage Of Elizabeth Warren's DNA Test | HuffPost

Read Mainstream Media Is Blowing Its Coverage Of Elizabeth Warren's DNA Test (HuffPost)
Tribal leaders and Native people say the senator is an ally — and they support her look at her ancestry. But hardly anyone asked them.

👓 James Watson Won’t Stop Talking About Race | New York Times

Read James Watson Won’t Stop Talking About Race (nytimes.com)
The Nobel-winning biologist has drawn global criticism with unfounded pronouncements on genetics, race and intelligence. He still thinks he’s right, a new documentary finds.

👓 The year ahead: genetics | Economist Espresso

Read The year ahead: genetics (Economist Espresso)
Soon two American biotechnology firms hope to offer couples undertaking in vitro fertilisation the chance to screen embryos before they are implanted. Pre-implantation genetic diagnosis is already widely used to test for chromosomal abnormalities or specific genetic disorders. But MyOme and Genomic Prediction plan to reconstruct the whole sequence of an embryo’s genome using just a few cells from a biopsy and genetic sequences of both parents. They can then, in theory, calculate the risk the embryo will develop a wide range of different diseases in later life—including ailments that are extraordinarily complicated, involving thousands of genetic variants. By selecting between different embryos, those undergoing IVF can optimise the health of their progeny in a way that those who conceive naturally cannot. That raises ethical concerns. Although both firms will screen embryos for disease risk only, there is no reason why traits such as height or intelligence might not be selected in the same way.

👓 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….

👓 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.

👓 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.

👓 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

👓 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.

👓 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