August, 2018 | Chris Aldrich

🔖 A Dynamic Network Approach for the Study of Human Phenotypes | PLOS Computational Biology

Bookmarked A Dynamic Network Approach for the Study of Human Phenotypes by César A. Hidalgo , Nicholas Blumm, Albert-László Barabási, Nicholas A. Christakis (PLOS Computational Biology)

Author Summary: To help the understanding of physiological failures, diseases are defined as specific sets of phenotypes affecting one or several physiological systems. Yet, the complexity of biological systems implies that our working definitions of diseases are careful discretizations of a complex phenotypic space. To reconcile the discrete nature of diseases with the complexity of biological organisms, we need to understand how diseases are connected, as connections between these different discrete categories can be informative about the mechanisms causing physiological failures. Here we introduce the Phenotypic Disease Network (PDN) as a map summarizing phenotypic connections between diseases and show that diseases progress preferentially along the links of this map. Furthermore, we show that this progression is different for patients with different genders and racial backgrounds and that patients affected by diseases that are connected to many other diseases in the PDN tend to die sooner than those affected by less connected diseases. Additionally, we have created a queryable online database (http://hudine.neu.edu/) of the 18 different datasets generated from the more than 31 million patients in this study. The disease associations can be explored online or downloaded in bulk.

h/t Disconnected, fragmented, or united? a trans-disciplinary review of network science by César A. Hidalgo (Applied Network Science | SpringerLink)

🔖 Network medicine: a network-based approach to human disease | Albert-László Barabási, Natali Gulbahce & Joseph Loscalzo | Nature Reviews Genetics

Bookmarked Network medicine: a network-based approach to human disease by Albert-László Barabási, Natali Gulbahce & Joseph Loscalzo (Nature Reviews Genetics | volume 12, pages 56–68 (2011))

Abstract
Given the functional interdependencies between the molecular components in a human cell, a disease is rarely a consequence of an abnormality in a single gene, but reflects the perturbations of the complex intracellular and intercellular network that links tissue and organ systems. The emerging tools of network medicine offer a platform to explore systematically not only the molecular complexity of a particular disease, leading to the identification of disease modules and pathways, but also the molecular relationships among apparently distinct (patho)phenotypes. Advances in this direction are essential for identifying new disease genes, for uncovering the biological significance of disease-associated mutations identified by genome-wide association studies and full-genome sequencing, and for identifying drug targets and biomarkers for complex diseases.

Key points

A disease phenotype is rarely a consequence of an abnormality in a single effector gene product, but reflects various pathobiological processes that interact in a complex network.

Here we present an overview of the organizing principles that govern cellular networks and the implications of these principles for understanding disease. Network-based approaches have potential biological and clinical applications, from the identification of disease genes to better drug targets.

Whereas essential genes tend to be associated with hubs, or highly connected proteins, disease genes tend to segregate at the network's functional periphery, avoiding hubs.

Disease genes have a high propensity to interact with each other, forming disease modules. The identification of these disease modules can help us to identify disease pathways and predict other disease genes.

The highly interconnected nature of the interactome means that, at the molecular level, it is difficult to consider diseases as being independent of one another. The mapping of network-based dependencies between pathophenotypes has culminated in the concept of the diseasome, which represents disease maps whose nodes are diseases and whose links represent various molecular relationships between the disease-associated cellular components.

Diseases linked at the molecular level tend to show detectable comorbidity.

Network medicine has important applications to drug design, leading to the emergence of network pharmacology, and also in disease classification.

h/t Disconnected, fragmented, or united? a trans-disciplinary review of network science by César A. Hidalgo (Applied Network Science | SpringerLink)

🔖 Brokerage and Closure: An Introduction to Social Capital by Ronald S. Burt

Bookmarked Brokerage and Closure: An Introduction to Social Capital by Ronald S. Burt (Oxford University Press)

Almost everything that happens in a firm flows through informal networks builts by advice, coordination, cooperation, friendship, gossip, knowledge, and trust. In this book, Ron Burt builds upon his celebrated work on network analyses to explain how these informal networks functions and the role of network entrepreneurs who have amassed social capital. Burt shows that social capital is a critical element in business strategy. Who has it, how it works and how to develop it have become key questions as markets, organizations and careers become more and more dependent on informal discretionary relationships. Informal relations have always mattered. What is new is the range of activities in which they now matter, and the emerging clarity we have about how they create advantage for certain people at the expense of others. This advantage is created by brokerage and closure. Brokerage is the activity of people who live at the intersecting of social worlds, who can see and develope good ideas. Closure is the tightening of coordination on a closed network of people. Brokerage and Closure explores how these elements work together to define social capital, showing how in the business world reputation has come to replace authority and reward has come to be associated with achieving competitive advantage in a social order of continuous disequilibrium.

h/t Disconnected, fragmented, or united? a trans-disciplinary review of network science by César A. Hidalgo (Applied Network Science | SpringerLink)

👓 Skim reading is the new normal. The effect on society is profound | Maryanne Wolf | The Guardian

Read Skim reading is the new normal. The effect on society is profound by Maryanne Wolf (the Guardian)

When the reading brain skims texts, we don’t have time to grasp complexity, to understand another’s feelings or to perceive beauty. We need a new literacy for the digital age writes Maryanne Wolf, author of Reader, Come Home

👓 Francis Fukuyama Postpones the End of History | The New Yorker

Read Francis Fukuyama Postpones the End of History by

Louis Menand (The New Yorker)

The political scientist argues that the desire of identity groups for recognition is a key threat to liberalism.

I can’t help but wonder what Jonah Goldberg’s review of this book will be given his prior effort earlier this year?

I’m also reminded here of Mark Granovetter’s ideas that getting a job is more closely tied to who you know. One’s job is often very closely tied to their identity, and even more so when the link that got them their job was through a friend or acquaintance.

I suspect that Fukuyama has a relatively useful thesis, but perhaps it’s not tied together as logically and historically as Menand would prefer. The difficult thing here is that levels of personal identity on large scales is relatively unknown for most of human history. Tribalism and individuality are certainly pulling at the threads of liberal democracy lately. Perhaps it’s because of unfulfilled promises (in America at least) of the two party system? Now that we’ve reached a summit of economic plenty much quicker than the rest of the world (and they’re usurping some of our stability as the rest of the world tries to equilibrate), we need to add some additional security nets for the lesser advantaged. It really doesn’t cost very much and in turn does so much more for the greater good of the broader society.

Highlights, Quotes, Annotations, & Marginalia

Fukuyama’s argument was that, with the imminent collapse of the Soviet Union, the last ideological alternative to liberalism had been eliminated. ❧

“Last” in the sense of a big, modern threat. We’re still facing the threats of tribalism, which apparently have a strong pull.
August 27, 2018 at 10:26AM

There would be a “Common Marketization” of international relations and the world would achieve homeostasis. ❧

Famous last words, right?!

These are the types of statements one must try very hard not to make unless there is 100% certainty.

I find myself wondering how can liberal democracy and capitalism manage to fight and make the case the the small tribes (everywhere, including within the US) that it can, could and should be doing more for them.
August 27, 2018 at 10:29AM

But events in Europe unfolded more or less according to Fukuyama’s prediction, and, on December 26, 1991, the Soviet Union voted itself out of existence. The Cold War really was over. ❧

Or ostensibly, until a strong man came to power in Russia and began its downturn into something else. It definitely doesn’t seem to be a liberal democracy, so we’re still fighting against it.
August 27, 2018 at 10:32AM

This speculative flourish recalled the famous question that John Stuart Mill said he asked himself as a young man: If all the political and social reforms you believe in came to pass, would it make you a happier human being? That is always an interesting question. ❧

August 27, 2018 at 10:33AM

George Kennan, who was its first chief. In July of that year, Kennan published the so-called X article, “The Sources of Soviet Conduct,” in Foreign Affairs. It appeared anonymously—signed with an “X”—but once the press learned his identity the article was received as an official statement of American Cold War policy. ❧

August 27, 2018 at 10:33AM

Fukuyama’s article could thus be seen as a bookend to Kennan’s. ❧

August 27, 2018 at 10:36AM

The National Interest, as the name proclaims, is a realist foreign-policy journal. But Fukuyama’s premise was that nations do share a harmony of interests, and that their convergence on liberal political and economic models was mutually beneficial. Realism imagines nations to be in perpetual competition with one another; Fukuyama was saying that this was no longer going to be the case. ❧

And here is a bit of the flaw. Countries are still at least in competition with each other economically, at least until they’re all on equal footing from a modernity perspective.

We are definitely still in completion with China and large parts of Europe.
August 27, 2018 at 10:38AM

Fukuyama thinks he knows what that something is, and his answer is summed up in the title of his new book, “Identity: The Demand for Dignity and the Politics of Resentment” (Farrar, Straus & Giroux). ❧

Get a copy of this to read.
August 27, 2018 at 10:39AM

The demand for recognition, Fukuyama says, is the “master concept” ❧

August 27, 2018 at 10:40AM

Fukuyama covers all of this in less than two hundred pages. How does he do it? Not well. ❧

Scathing!

Now I have to read it.
August 27, 2018 at 10:41AM

Fukuyama gives this desire for recognition a Greek name, taken from Plato’s Republic: thymos. He says that thymos is “a universal aspect of human nature that has always existed.” ❧

August 27, 2018 at 10:43AM

To say, as Fukuyama does, that “the desire for status—megalothymia—is rooted in human biology” is the academic equivalent of palmistry. You’re just making it up. ❧

August 27, 2018 at 10:45AM

Rationality and transparency are the values of classical liberalism. Rationality and transparency are supposed to be what make free markets and democratic elections work. People understand how the system functions, and that allows them to make rational choices. ❧

But economically, we know there isn’t perfect knowledge or perfect rationality (see Tversky and Khaneman). There is rarely even perfect transparency either which makes things much harder, especially in a post-truth society apparenlty.
August 27, 2018 at 10:48AM

Liberalism remains the ideal political and economic system, but it needs to find ways to accommodate and neutralize this pesky desire for recognition. ❧

August 27, 2018 at 10:50AM

Enrollment was small, around twenty, but a number of future intellectual luminaries, like Hannah Arendt and Jacques Lacan, either took the class or sat in on it. ❧

August 27, 2018 at 10:52AM

For Kojève, the key concept in Hegel’s “Phenomenology” was recognition. Human beings want the recognition of other human beings in order to become self-conscious—to know themselves as autonomous individuals. ❧

This is very reminiscent of Valerie Alexander’s talk last week about recognizing employees at work. How can liberal democracy take advantage of this?
August 27, 2018 at 10:53AM

Kojève thought that the other way was through labor. The slave achieves his sense of self by work that transforms the natural world into a human world. But the slave is driven to labor in the first place because of the master’s refusal to recognize him. This “master-slave dialectic” is the motor of human history, and human history comes to an end when there are no more masters or slaves, and all are recognized equally. ❧

August 27, 2018 at 10:55AM

Kojève’s lectures were published as “Introduction to the Reading of Hegel,” a book that went through many printings in France. ❧

Maybe it was Kojève and not Covfefe that Trump was referencing?! 😛
August 27, 2018 at 10:56AM

Encouraged by his friend Saul Bellow, he decided to turn the article into a book. “The Closing of the American Mind,” which Simon & Schuster brought out in February, 1987, launched a campaign of criticism of American higher education that has taken little time off since. ❧

August 27, 2018 at 11:00AM

In 1992, in the essay “The Politics of Recognition,” Taylor analyzed the advent of multiculturalism in terms similar to the ones Fukuyama uses in “Identity.” ❧

August 27, 2018 at 11:03AM

Fukuyama acknowledges that identity politics has done some good, and he says that people on the right exaggerate the prevalence of political correctness and the effects of affirmative action. ❧

There’s a reference to voting theory about people not voting their particular views, but that they’re asking themselves, “Who would someone like me vote for?” Perhaps it’s George Lakoff? I should look this up and tie it in here somewhere.
August 27, 2018 at 11:05AM

He has no interest in the solution that liberals typically adopt to accommodate diversity: pluralism and multiculturalism. ❧

Interesting to see an IndieWeb principle pop up here! How do other parts dovetail perhaps? What about other movements?
August 27, 2018 at 11:06AM

Fukuyama concedes that people need a sense of national identity, whether ethnic or creedal, but otherwise he remains an assimilationist and a universalist. ❧

Is it a “national” identity they need? Why not a cultural one, or a personal one? Why not all the identities? What about the broader idea of many publics? Recognition and identity touch on many of these publics for a variety of reasons.
August 27, 2018 at 11:08AM

He wants to iron out differences, not protect them. He suggests measures like a mandatory national-service requirement and a more meaningful path to citizenship for immigrants. ❧

What if we look at the shrinking number of languages as a microcosm of identity. Are people forced to lose language? Do they not care? What are the other similarities and differences.

Cross reference: https://boffosocko.com/2015/06/08/a-world-of-languages-and-how-many-speak-them-infographic/
August 27, 2018 at 11:10AM

Wouldn’t it be important to distinguish people who ultimately don’t want differences to matter, like the people involved in #MeToo and Black Lives Matter, from people who ultimately do want them to matter, like ISIS militants, Brexit voters, or separatist nationalists? And what about people who are neither Mexican nor immigrants and who feel indignation at the treatment of Mexican immigrants? Black Americans risked their lives for civil rights, but so did white Americans. How would Socrates classify that behavior? Borrowed thymos? ❧

Some importatnt questions here. They give me some ideas…
August 27, 2018 at 11:12AM

History is somersaults all the way to the end. That’s why it’s so hard to write, and so hard to predict. Unless you’re lucky. ♦ ❧

This is definitely more of a Big History approach…
August 27, 2018 at 11:12AM

🔖 The End of History? by Francis Fukuyama

Bookmarked The End of History? by Francis Fukuyama (The National Interest | No. 16 (Summer 1989), pp. 3-18)

IN WATCHING the flow of events over the past decade or so, it is hard to avoid the feeling that something very fundamental has happened in world history. The past year has seen a flood of articles commemorating the end of the Cold War, and the fact that "peace" seems to be breaking out in many regions of the world. Most of these analyses lack any larger conceptual framework for distinguishing between what is essential and what is contingent or accidental in world history, and are predictably superficial. If Mr. Gorbachev were ousted from the Kremlin or a new Ayatollah proclaimed the millennium from a desolate Middle Eastern capital, these same commentators would scramble to announce the rebirth of a new era of conflict.

And yet, all of these people sense dimly that there is some larger process at work, a process that gives coherence and order to the daily headlines. The twentieth century saw the developed world descend into a paroxysm of ideological violence, as liberalism contended first with the remnants of absolutism, then bolshevism and fascism, and finally an updated Marxism that threatened to lead to the ultimate apocalypse of nuclear war. But the century that began full of self-confidence in the ultimate triumph of Western liberal democracy seems at its close to be returning full circle to where it started: not to an "end of ideology" or a convergence between capitalism and socialism, as earlier predicted, but to an unabashed victory of economic and political liberalism.