Raghuveer Parthasarathy: Four Physical Principles and Biophysics -- Manifold podcast #11

 

Raghu Parthasarathy is the Alec and Kay Keith Professor of Physics at the University of Oregon. His research focuses on biophysics, exploring systems in which the complex interactions between individual components, such as biomolecules or cells, can give rise to simple and robust physical patterns. 

Raghu is the author of a recent popular science book, So Simple a Beginning: How Four Physical Principles Shape Our Living World. 

Steve and Raghu discuss: 

0:00 Introduction 

1:34 Early life, transition from Physics to Biophysics 

20:15 So Simple a Beginning: discussion of the Four Physical Principles in the title, which govern biological systems 

26:06 DNA prediction 

37:46 Machine learning / causality in science 

46:23 Scaling (the fourth physical principle) 

54:12 Who the book is for and what high schoolers are learning in their bio and physics classes 

1:05:41 Science funding, grants, running a research lab 

1:09:12 Scientific careers and radical sub-optimality of the existing system 

Transcript.

Resources: 

Book - https://press.princeton.edu/books/hardcover/9780691200408/so-simple-a-beginning 

Raghuveer Parthasarathy's lab at the University of Oregon - https://pages.uoregon.edu/raghu/ 

 

Raghuveer Parthasarathy's blog the Eighteenth Elephant - https://eighteenthelephant.com/

Added from comments:

key holez • 2 days ago 

It was a fascinating episode, and I immediately went out and ordered the book! One question that came to mind: given how much of the human genome is dedicated to complex regulatory mechanisms and not proteins as such, it seems unintuitive to me that so much of heritability seems to be additive. I would have thought that in a system with lots of complicated,messy on/off switches, small genetic differences would often lead to large phenotype differences -- but if what I've heard about polygenic prediction is right, then, empirically, assuming everything is linear seems to work just fine (outside of rare variants, maybe). Is there a clear explanation for how complex feedback patterns give rise to linearity in the end? Is it just another manifestation of the central limit theorem...?

steve hsu 

This is an active area of research. It is somewhat surprising even to me how well linearity / additivity holds in human genetics. Searches for non-linear effects on complex traits have been largely unsuccessful -- i.e., in the sense that most of the variance seems to be controlled by additive effects. By now this has been investigated for large numbers of traits including major diseases, quantitive traits such as blood biomarkers, height, cognitive ability, etc. 

One possible explanation is that because humans are so similar to each other, and have passed through tight evolutionary bottlenecks, *individual differences* between humans are mainly due to small additive effects, located both in regulatory and coding regions. 

To genetically edit a human into a frog presumably requires many changes in loci with big nonlinear effects. However, it may be the case that almost all such genetic variants are *fixed* in the human population: what makes two individuals different from each other is mainly small additive effects. 

Zooming out slightly, the implications for human genetic engineering are very positive. Vast pools of additive variance means that multiplex gene editing will not be impossibly hard...

This topic is discussed further in the review article: https://arxiv.org/abs/2101.05870

Complex Trait Prediction: Methods and Protocols (Springer 2022)

My research group contributed a chapter to this new book on Complex Trait Prediction (see below). The book is somewhat unique, covering applications to humans, plants, and animals all in a single volume. 

Complex Trait Prediction: Methods and Protocols (Springer Nature) 

Editors: 

Nourollah Ahmadi and Jérôme Bartholomé 

CIRAD, UMR AGAP Institut, Montpellier, France

 

About this book 

This volume explores the conceptual framework and the practical issues related to genomic prediction of complex traits in human medicine and in animal and plant breeding. The book is organized into five parts. Part One reminds molecular genetics approaches intending to predict phenotypic variations. Part Two presents the principles of genomic prediction of complex traits, and reviews factors that affect its reliability. Part Three describes genomic prediction methods, including machine-learning approaches, accounting for different degree of biological complexity, and reviews the associated computer-packages. Part Four reports on emerging trends such as phenomic prediction and incorporation into genomic prediction models of “omics” data and crop growth models. Part Five is dedicated to lessons learned from case studies in the fields of human health and animal and plant breeding, and to methods for analysis of the economic effectiveness of genomic prediction. 

Written in the highly successful Methods in Molecular Biology series format, the book provides theoretical bases and practical guidelines for an informed decision making of practitioners and identifies pertinent routes for further methodological researches. Cutting-edge and thorough, Complex Trait Predictions: Methods and Protocols is a valuable resource for scientists and researchers who are interested in learning more about this important and developing field.

Our article (pp 421–446):

From Genotype to Phenotype: Polygenic Prediction of Complex Human Traits 

T. Raben, L. Lello, E. Widen, and S. Hsu 

Decoding the genome confers the capability to predict characteristics of the organism (phenotype) from DNA (genotype). We describe the present status and future prospects of genomic prediction of complex traits in humans. Some highly heritable complex phenotypes such as height and other quantitative traits can already be predicted with reasonable accuracy from DNA alone. For many diseases, including important common conditions such as coronary artery disease, breast cancer, type I and II diabetes, individuals with outlier polygenic scores (e.g., top few percent) have been shown to have 5 or even 10 times higher risk than average. Several psychiatric conditions such as schizophrenia and autism also fall into this category. We discuss related topics such as the genetic architecture of complex traits, sibling validation of polygenic scores, and applications to adult health, in vitro fertilization (embryo selection), and genetic engineering.

Ungated arXiv version.

Previous discussion: 

From Genotype to Phenotype: polygenic prediction of complex human traits 

Clinical Applications of Polygenic Risk Scores 

See also Big Chickens.

Meghan Daum on the New Culture Wars - Manifold Podcast #32

Corey and Steve talk to Meghan Daum about her new book The Problem With Everything: My Journey Through The New Culture Wars. Meghan describes how she became aware of the "Red Pill" through what she calls "free speech YouTube" videos. The three ask whether their feeling of alienation from Gen-Z wokeness is just a sign of getting old or reflects principles of free speech and open debate. Megan argues that Gen-Z's focus on fairness leads to difficult compromises. They discuss social interactions in the pre-internet, early-internet, and woke-internet eras.

Transcript

Meghan Daum (Author Website)

Meghan Daum on Medium

The Problem with Everything: My Journey Through the New Culture Wars


man·i·fold /ˈmanəˌfōld/ many and various.

In mathematics, a manifold is a topological space that locally resembles Euclidean space near each point.

Steve Hsu and Corey Washington have been friends for almost 30 years, and between them hold PhDs in Neuroscience, Philosophy, and Theoretical Physics. Join them for wide ranging and unfiltered conversations with leading writers, scientists, technologists, academics, entrepreneurs, investors, and more.

Steve Hsu is VP for Research and Professor of Theoretical Physics at Michigan State University. He is also a researcher in computational genomics and founder of several Silicon Valley startups, ranging from information security to biotech. Educated at Caltech and Berkeley, he was a Harvard Junior Fellow and held faculty positions at Yale and the University of Oregon before joining MSU.

Corey Washington is Director of Analytics in the Office of Research and Innovation at Michigan State University. He was educated at Amherst College and MIT before receiving a PhD in Philosophy from Stanford and a PhD in a Neuroscience from Columbia. He held faculty positions at the University Washington and the University of Maryland. Prior to MSU, Corey worked as a biotech consultant and is founder of a medical diagnostics startup.

Borges, blogging, and a vast circle of invisible friends

This blog gets about 100k page views per month. My sense is that there are a lot of additional views through RSS feeds and social media (FB, G+, etc.), but those are hard to track. Most of the hits are on the main landing page, with a smaller fraction going to a specific article. I'd guess that someone hitting the landing page looks at a few posts, so there are probably at least 200k article views per month. I write somewhat fewer than 20 posts per month, which suggests that a typical post is read ~10k times. Some outlier posts get a lot of traffic from inbound links and search engine results even years after they were written. These have far more than 10k cumulative views, according to logs. From cookies, I can see that there are many thousands of regular readers (i.e., who visit at least several times a month).

Is there any better way to estimate impact/reach than what I've described above?

For comparison, I was told that a serious non-fiction book on the NY Times Best Seller list might sell ~10k copies. So it seems possible my blog has a significantly greater reach than what I could expect from writing a book. I've thought about writing books at various times, but have always been too busy. I fantasize about writing more when I retire, or later in my career :-)

When I attend meetings or conferences, I often bump into people I don't know who tell me they read my blog. This seems to be true whether the participants are scientists, technologists, investors, or academics. I'm guessing that for every person who tells me that they're a reader, there must be many more who are readers but don't volunteer the information. If you ever see me in person, please come right up and say hello! :-)

I've been told by some people that they have tried to read this blog but find it hard to understand. I suppose that regular readers are mostly well above average in intelligence.

Borges once said

... the life of a writer is a lonely one. You think you are alone, and as the years go by, if the stars are on your side, you may discover that you are at the center of a vast circle of invisible friends whom you will never get to know, but who love you. And that is an immense reward.

AI Now (O'Reilly ebook)

爱 (ài) means "love" in Chinese!  :-)

Artificial Intelligence Now
Current Perspectives from O'Reilly Media

Get the free ebook

The past year or so has seen a true explosion in both the capabilities and adoption of artificial intelligence technologies. Today’s generalized AI tools can solve specific problems more powerfully than the complex rule-based tools that preceded them. And, because these new AI tools can be deployed in many contexts, more and more applications and industries are ripe for transformation with AI technologies.

By drawing from the best posts on the O’Reilly AI blog, this in-depth report summarizes the current state of AI technologies and applications, and provides useful guides to help you get started with deep learning and other AI tools.

In six distinct parts, this report covers:

The AI landscape: the platforms, businesses, and business models shaping AI growth; plus a look at the emerging AI stack

Technology: AI’s technical underpinnings and deep learning capabilities, tools, and tutorials

Homebuilt autonomous systems: "hobbyist" applications that showcase AI tools, libraries, cloud processing, and mobile computing

Natural language: strategies for scoping and tackling NLP projects

Use cases: an analysis of two of the leading-edge use cases for artificial intelligence—chat bots and autonomous vehicles

Integrating human and machine intelligence: development of human-AI hybrid applications and workflows; using AI to map and access large-scale knowledge databases

Baby Universes in the Laboratory

This was on the new books table at our local bookstore. I had almost forgotten about doing an interview and corresponding with the author some time ago. See also here and here.

The book is a well-written overview of some of the more theoretical aspects of inflationary cosmology, the big bang, the multiverse, etc. It also fleshes out some of the individual stories of the physicists involved in this research.

Kirkus Reviews: ... In her elegant and perceptive book, Merali ... unpacks the science behind what we know about our universe’s beginnings and traces the paths that many renowned researchers have taken to translate these insights to new heights: the creation of a brand-new “baby” universe, and not an empty one, either, but one with its own physics, matter, and (possibly) life. ... Among the most significant scientific advances in the last half-century is the discovery that our universe is inflating exponentially, a theory that led to many more breakthroughs in physics and cosmology. Yet the big question—how did the universe form, triggering inflation to begin with?—remains opaque. Merali, who works at the Foundational Questions Institute, which explores the boundaries of physics and cosmology, effortlessly explains the complex theories that form the bedrock of this concept, and she brings to life the investigators who have dedicated much of their careers in pursuit of fundamental truths. She also neatly incorporates discussions of philosophy and religion—after all, nothing less than grand design itself is at stake here—without any heavy-handedness or agenda. Over the course of several years, she traveled the world to interview firsthand the most important figures behind the idea of laboratory universe creation ... and the anecdotes she includes surrounding these conversations make her portrait even more compelling.

Here are two illustrations of how a baby universe pinches off from the universe in which it was created. This is all calculable within general relativity, modulo an issue with quantum smoothing of a singularity. The remnant of the baby universe appears to outside observers as a black hole. But inside one finds an exponentially growing region of spacetime.

Foo Camp 2016

I was at Foo Camp the last few days. This year they kept the size a bit lower (last year was kind of a zoo) and I thought the vibe was a lot more relaxed and fun. Many thanks to the O'Reilly folks for running this wonderful meeting and for inviting me. My first time was 9 years ago!

I ran a session TRUMP 2016? CAN IT HAPPEN HERE? (a few people in the session caught the Sinclair Lewis reference) to get a feel for whether the tech community understands what's happening in our country. At another meeting earlier in the year I concluded

Everything at this meeting is off the record, so I can't say much about it. The one comment I'll make is that among this group of elites almost no one I've spoken to groks Trump or his appeal to a large number of Americans.

The other session I co-ran (with Othman Laraki of Color Genomics) was on genomics.

Lots of good stuff at hashtag #foocamp.

Here's a list of book recommendations from one of the sessions (James Cham).

First day of FOO Camp 2016. Whisky tasting in the Design Village soon. #foocamp pic.twitter.com/PyuNY1mG7t

— Andrew Crow (@AndrewCrow) June 11, 2016

Bourdieu and the Economy of Symbolic Exchange

From Bobos in Paradise by David Brooks. This part of Bourdieu's oeuvre is, of course, required reading for all academics. By academics, I don't just mean humanists and social scientists. Even those in the hardest of sciences and technology would benefit from considering the political / symbolic economy of their field. Why, exactly, did most positions in top theoretical physics groups go to string theorists over a 20+ year period? See String Theory Quotes , String Theory and All That , Voting and Weighing.

The Economy of Symbolic Exchange

If a university were to offer a course of study on the marketplace of ideas, the writer who would be at the heart of the curriculum would be Pierre Bourdieu. Bourdieu is a French sociologist who is influential among his colleagues but almost entirely unread outside academia because of his atrocious prose style. Bourdieu’s aim is to develop an economy of symbolic exchanges, to delineate the rules and patterns of the cultural and intellectual marketplace. His basic thesis is that all intellectual and cultural players enter the marketplace with certain forms of capital. They may have academic capital (the right degrees), cultural capital (knowledge of a field or art form, a feel for the proper etiquette), linguistic capital (the ability to use language), political capital (the approved positions or affiliations), or symbolic capital (a famous fellowship or award). Intellectuals spend their careers trying to augment their capital and convert one form of capital into another. One intellectual might try to convert knowledge into a lucrative job; another might convert symbolic capital into invitations to exclusive conferences at tony locales; a third might seek to use linguistic ability to destroy the reputations of colleagues so as to become famous or at least controversial.

Ultimately, Bourdieu writes, intellectuals compete to gain a monopoly over the power to consecrate. Certain people and institutions at the top of each specialty have the power to confer prestige and honor on favored individuals, subjects, and styles of discourse. Those who hold this consecration of power influence taste, favor certain methodologies, and define the boundary of their discipline. To be chief consecrator is the intellectual’s dream.

Bourdieu doesn’t just look at the position an intellectual may hold at a given moment; he looks at the trajectory of a career, the successive attitudes, positions, and strategies a thinker adopts while rising or competing in the marketplace. A young intellectual may enter the world armed only with personal convictions. He or she will be confronted, Bourdieu says, with a diverse “field.” There will be daring radical magazines over on one side, staid establishment journals on another, dull but worthy publishing houses here, vanguard but underfunded houses over there. The intellectual will be confronted with rivalries between schools and between established figures. The complex relationships between these and other players in the field will be the tricky and shifting environment in which the intellectual will try to make his or her name. Bourdieu is quite rigorous about the interplay of these forces, drawing elaborate charts of the various fields of French intellectual life, indicating the power and prestige levels of each institution. He identifies which institutions have consecration power over which sections of the field.

Young intellectuals will have to know how to invest their capital to derive maximum “profit,” and they will have to devise strategies for ascent—whom to kiss up to and whom to criticize and climb over. Bourdieu’s books detail a dazzling array of strategies intellectuals use to get ahead. Bourdieu is not saying that the symbolic field can be understood strictly by economic principles. Often, he says, the “loser wins” rule applies. Those who most vociferously and publicly renounce material success win prestige and honor that can be converted into lucre. Nor does Bourdieu even claim that all of the strategies are self-conscious. He says that each intellectual possesses a “habitus,” or personality and disposition, that leads him or her in certain directions and toward certain fields. Moreover, the intellectual will be influenced, often unwillingly or unknowingly, by the gravitational pull of the rivalries and controversies of the field. Jobs will open up, grants will appear, furies will rage. In some ways the field dominates and the intellectuals are blown about within it.

Bourdieu hasn’t quite established himself as the Adam Smith of the symbolic economy. And it probably wouldn’t be very useful for a young intellectual to read him in hopes of picking up career tips, as a sort of Machiavellian Guide for Nobel Prize Wannabes. Rather, Bourdieu is most useful because he puts into prose some of the concepts that most other intellectuals have observed but have not systematized. Intellectual life is a mixture of careerism and altruism (like most other professions). Today the Bobo intellectual reconciles the quest for knowledge with the quest for the summer house.

See this comment, made 11 years ago!

Steve: We are living through a very bad time in particle theory. Without significant experimental guidance all we are left with is speculation and social dynamics driving the field. I hope things will get better when LHC data starts coming in - at least, most of the models currrently under consideration will be ruled out (although, of course, not string theory :-)

I will probably write a post at some point about how scientific fields which run through fallow experimental periods longer than 20 years (the length of a person's academic career) are in danger of falling into the traps which beset the humanities and social sciences. These were all discussed by Bourdieu long ago.

James Salter, 1925-2015

"Forgive him anything, he writes like an angel."

Remember that the life of this world is but a sport and a pastime.  NYTimes obituary.

From a 2011 post:

I've been a fan of the writer James Salter (see also here) since discovering his masterpiece A Sport and a Pastime. Salter evokes Americans in France as no one since Hemingway in A Moveable Feast. The title comes from the Koran: Remember that the life of this world is but a sport and a pastime ... :-)

I can't think of higher praise than to say I've read every bit of Salter's work I could get my hands on.

See also Lion in winter: James Salter.

INTERVIEWER

But why a memoir?

SALTER

To restore those years when one says, All this is mine—these cities, women, houses, days.

INTERVIEWER

What do you think is the ultimate impulse to write?

SALTER

To write? Because all this is going to vanish. The only thing left will be the prose and poems, the books, what is written down. Man was very fortunate to have invented the book. Without it the past would completely vanish, and we would be left with nothing, we would be naked on earth.

Howard French: China's Second Continent

Another recommendation: China's Second Continent: How a Million Migrants Are Building a New Empire in Africa by Howard French (a former Africa and China correspondent for the NY Times). This is real boots on the ground reporting. French (a Mandarin speaker) spent time with Chinese immigrants across Africa, from small shopkeepers and farmers to real estate moguls and high government officials. Reviews: WSJ, NYTimes.

An interview with French on the Sinica podcast.

Exactly how exploitative are Chinese development activities on the African continent? What exactly is motivating the various resources-for-development deals inked by African governments over the last decade, and what strategies are these governments now adopting in the face of power imbalances with China? What is driving the mass migration of Chinese workers to the African continent, and why does everyone from Senegal seem to come from Henan?

This week on Sinica, we ask these questions and many more as Kaiser Kuo and Jeremy Goldkorn are joined in conversation with Howard French. If you've spent a while in China, you may have heard of Howard as the author of a well-known book on Shanghai's architectural legacy, and lecturer on the subject. What you may not know is that he is also an expert on African development, and the new author of China's Second Continent: How a Million Migrants Are Building a New Empire in Africa.

I wonder whether French is familiar with Galton's famous (and very politically incorrect; written in 1873) letter Africa for the Chinese. In some respects Galton is eerily prescient.

... The Chinaman is a being of another kind, who is endowed with a remarkable aptitude for a high material civilization. He is seen to the least advantage in his own country, where a temporary dark age still prevails, which has not sapped the genius of the race, though it has stunted the development of each member of it, by the rigid enforcement of an effete system of classical education which treats originality as a social crime. All the bad parts of his character, as his lying and servility, spring from timidity due to an education that has cowed him, and no treatment is better calculated to remedy that evil than location in a free settlement. The natural capacity of the Chinaman shows itself by the success with which, notwithstanding his timidity, he competes with strangers, wherever he may reside. The Chinese emigrants possess an extraordinary instinct for political and social organization; they contrive to establish for themselves a police and internal government, and they give no trouble to their rulers so long as they are left to manage those matters by themselves. They are good-tempered, frugal, industrious, saving, commercially inclined, and extraordinarily prolific. They thrive in all countries, the natives of the Southern provinces being perfectly able to labor and multiply in the hottest climates. ...

... The pressure of population in China is enormous, and its outflow is great and increasing. There is no lack of material for a suitable immigration into Africa. ... The Chinese have a land hunger, as well as a love for petty traffic, and they would find a field in which to gratify both of these tastes on the East African Coast. There are many Chinese capitalists resident in foreign parts who might speculate in such a system and warmly encourage it. ...

Belonging and Genocide: Hitler's Community, 1918-1945

I recommend this podcast interview with Thomas Kuhne, author of Belonging and Genocide: Hitler's Community, 1918-1945.

Kuhne claims that no German soldier ever faced court martial for refusing to kill a civilian. He estimates that (only?) about 200k German soldiers in total were involved in the killing of Jews or other civilians. But by the end of the war every German who wanted to know about "crimes in the east" could easily find out. This last observation is supported by letters and diary entries of ordinary people. Matters of national guilt or conscience weighed heavily on soldiers and ordinary Germans by the end of the war, Kuhne claims.

Kuhne makes interesting observations about the male social hierarchy within military units. Those who refused to carry out Nazi orders against civilians were regarded as weaklings, but were not subjected to direct reprisal.

There are two means to unite a people — common ideals and common crime.
—Adolf Hitler, Party Leader, Munich, 1923

If this Jewish business is ever avenged on earth, then have mercy on us Germans.
—Major Trapp, Police Officer, Poland, 1942

For there is a great, bright aspect to this war: namely a great comradeship.
—Adolf Hitler, Reich Chancellor, Berlin, 1942

We Germans are the nation that has gone for this war enthusiastically and will have to bear the consequences.
—Franz Wieschenberg, Wehrmacht Private, Eastern Front, 1944

To stick together and to fight side by side and be wounded side by side, that’s our wish.
—Kurt Kreissler, Wehrmacht NCO, Germany, 1945

Eichmann revealed

Archival work reveals that Hannah Arendt (Eichmann in Jerusalem) and many other observers were fooled by Eichmann during his trial. He was more than a cog, not merely banal, and did indeed think about his actions during the Holocaust. Bettina Stangneth's recent book, Eichmann before Jerusalem is fascinating reading.

NYTimes: ... The story of the Sassen interviews, one of the most important post-Holocaust documents, is itself a kind of cloak-and-­dagger account as Stangneth tells it, featuring hidden or lost tapes, faulty transcriptions, furtive meetings, profiteering and various other kinds of intrigue. ...

It is in these interviews and Eichmann’s own notes that he gave uninhibited vent to his version of the Holocaust and his involvement. Since he had a penchant for tailoring his endless chatting and voluminous writings to what he believed his audience desired, it may not be immediately evident why his statements in Buenos Aires should be considered more authentic than the “little man” portrait he painted in Jerusalem. The answer lies in the stance he took against what his Nazi and radical-right audience wanted to hear. For they were intent on either denying the Holocaust altogether, or outlandishly regarding it as either a Zionist plot to obtain a Jewish state or a conspiracy of the Gestapo (not the SS) working against Hitler and without his knowledge. Eichmann dashed these expectations. Not only did he affirm that the horrific events had indeed taken place; he attested to his decisive role in them. Hardly anonymous, he insisted on his reputation as the great mover behind Jewish policy, which became part of the fear, the mystique of power, surrounding him. As Stangneth observes: “He dispatched, decreed, allowed, took steps, issued orders and gave audiences.”

... Eichmann was far from a thoughtless functionary simply performing his duty. He proceeded quite intentionally from a set of tenaciously held Nazi beliefs (hardly consonant with Arendt’s puzzling contention that he “never realized what he was doing”). His was a consciously wrought racial “ethics,” one that pitted as an ultimate value the survival of one’s own blood against that of one’s enemies. ...

From a surprising admission of German inferiority — “we are fighting an enemy who ... is intellectually superior to us” — it followed that total extermination of the Jewish adversary “would have fulfilled our duty to our blood and our people and to the freedom of the peoples.” ...

Audio interview with Stangneth (NYTimes).

See also this exchange: Arendt and Eichmann (NY Review of Books), and What it was like.

How to build the future

I just bought 10 copies for my team at MSU. More here. The book is based on Thiel's Stanford class CS 183: Startup -- see course notes.

Earlier posts on Thiel.

Nicholas Wade interview: A Troublesome Inheritance

Leonard Lopate interviews Nicholas Wade (veteran genetics correspondent for the NYTimes) about his new book A Troublesome Inheritance: Genes, Race and Human History. The interview is slow at first but the second half is good.



Update: Another interview (May 9), with CBC, that gets right to the point regarding "social construction" -- the convenient but incorrect legacy of anthropologist Ashley Montagu (Israel Ehrenberg). The second guest, Stanford anthropologist Duana Fullwiley, foreshadows the counterattack on Wade.

See also this well-written essay in Time, adapted from the book.


I received a copy of A Troublesome Inheritance from the publisher. My initial impressions:

(1) The first part of the book covers well-established science concerning the genetic clustering of human populations. Some of the results will be surprising to those who have not followed the last 10 years of progress in genomics. See, e.g., here and here for my thoughts on this subject.

(2) The second part of the book covers controversial topics such as genetic group differences in behavioral and cognitive predispositions. Wade is mostly careful to present these as speculative hypotheses, but nevertheless his advocacy leaves him vulnerable to easy attack.

It will be interesting to see how this book, by a prominent science writer (indeed, the chief genetics correspondent for the paper of record), is received by the intelligentsia, the punditocracy, and actual scientists.

Additional remarks:

 

Below I have excerpted from the first link in (1) above, a post I originally wrote in 2007. I think these remarks are quite relevant to Wade's new book; note specific comments in brackets [ ... ].

... Two groups that form distinct [ genetic ] clusters are likely to exhibit different frequency distributions over various genes, leading to group differences. [ One does not require a more precise definition of "races" to get immediately to the thorny questions: two groups that differ in allele frequencies may differ statistically in phenotype! ]

This leads us to two very different possibilities in human genetic variation:

Hypothesis 1: (the PC mantra) The only group differences that exist between the clusters (races) are innocuous and superficial, for example related to skin color, hair color, body type, etc.

Hypothesis 2: (the dangerous one) Group differences exist which might affect important (let us say, deep rather than superficial) and measurable characteristics, such as cognitive abilities, personality, athletic prowess, etc.

... As scientists, we don't know whether H1 or H2 is correct, but given the revolution in biotechnology, we will eventually. Let me reiterate, before someone labels me a racist: we don't know with high confidence whether H1 or H2 is correct.

... it is important to note that group differences are statistical in nature and do not imply anything definitive about a particular individual. Rather than rely on the scientifically unsupported claim that we are all equal, it would be better to emphasize that we all have inalienable human rights regardless of our abilities or genetic makeup. [ Consider individuals, who are clearly unequal in their gifts: greater abilities should not confer greater rights! ]

... Clustering makes it possible that H2 is correct, because the alleles (genetic variants) affecting a particular phenotype will tend to have different frequencies in different groups. The average value of the trait might or might not be the same in different groups. In the case of height, enough is known to suggest that variants which lead to increased height are more frequent in northern Europe than in the south, and there is evidence that this is due to selection, not drift. [ i.e., this is evidence of recent selection driving group differences in a complex trait, controlled by thousands of loci. Wade: “Human evolution has been recent, copious, and regional.” ]

... I think it's especially important to be epistemologically careful in thinking about these matters, because of our difficult history with race. [ By articulating so many speculative theories in the second part of his book, Wade risks being perceived as not careful. ]

... I would much rather live in a world where H1 is true and H2 false. But my preference alone does not make it so. (I would also much rather live in a universe created by a loving God, and in which I and my children have eternal souls; not a cruel Darwinian universe in which our species arose merely by chance. But my preference does not make it so.)

David Epstein and self-censorship

David Epstein's new book The Sports Gene is getting a lot of attention. For example, this New Yorker review is quite good, as are these interviews: NPR, Atlantic.

Atlantic: ... I lost so much sleep over this. I literally almost backed out of writing this book, because the issues of race and gender got me so nervous. Eventually my agent and one of my colleagues convinced me to just do it, in the best way I could.

But I remember being at the 2012 American College of Sports Medicine Conference, talking to the head of the physiology department at a major research university. The head of the department was telling me that he had data on ethnic differences in response to a certain dietary supplement during an exercise program, and that he would never publish it. He didn't want to get into that issue.

I heard this a number of times: He was worried it would be extrapolated into saying somehow that there were also innate intellectual differences between black and white people. When I heard that, I said, "That is a huge problem. That means science could be disappearing into the filing cabinet, into the garbage cans, because people aren't willing to take this on."

And that's when I thought, I have to do this. I'm not going to do that same thing and leave it on the cutting-room floor.

Of course, it's all been covered on this blog already: 10,000 hours rule is nonsense (Epstein's example of the former basketball player turned high jumper who barely trained yet won the world championship is excellent), myostatin mutation, etc.

"Horses ain't like people, man, they can't make themselves better than they're born. See, with a horse, it's all in the gene. It's the fucking gene that does the running. The horse has got absolutely nothing to do with it." --- Paulie (Eric Roberts) in The Pope of Greenwich Village.

The good books

I did some unpacking today and assembled some favorite technical books (mostly physics) on one set of shelves. There are more that are still lost in boxes, but I think this is a decent collection. Surely no man can call himself educated without being familiar with the contents of a few of these books ;-)


In response to comments I'm posting some shelves of less technical books. The best way to characterize the collection below is that all of these are good, and some are among my favorites.

Click for larger images.

Financial Weaponry

Financial Weaponry, my review of George Szpiro's Pricing the Future: Physics, Finance and the 300-year Journey to the Black–Scholes Equation, is now available at the Physics World site.

I posted some excerpts earlier here.

Borges: A poet never rests

"The revelation can occur at any time. A poet never rests.

He's always working, even when he dreams.

Besides, the life of a writer is a lonely one.

You think you are alone, and as the years go by,

if the stars are on your side, you may discover

that you are at the center of a vast circle of invisible friends

whom you will never get to know, but who love you.

And that is an immense reward."

Borges' The Witness

I am ecstatic at now having thousands of books, both technical and non-technical, available in searchable formats on my laptop, tablet and iphone.

I came across this brief Borges piece, originally published in 1960, by accident while surfing through my digital book collection. A quick trip to my shelves showed that I had this in physical form, but somehow had never read it.

See also the perils of precocity.

The Witness

In a stable that stands almost in the shadow of the new stone church, a man with gray eyes and gray beard, lying amid the odor of the animals, humbly tries to will himself into death, much as a man might will himself to sleep. The day, obedient to vast and secret laws, slowly shifts about and mingles the shadows in the lowly place; outside lie plowed fields, a ditch clogged with dead leaves, and the faint track of a wolf in the black clay where the line of woods begins. The man sleeps and dreams, forgotten.

The bells for orisons awaken him. Bells are now one of evening's customs in the kingdoms of England, but as a boy the man has seen the face of Woden, the sacred horror and the exultation, the clumsy wooden idol laden with Roman coins and ponderous vestments, the sacrifice of horses, dogs, and prisoners. Before dawn he will be dead, and with him, the last eyewitness images of pagan rites will perish, never to be seen again. The world will be a little poorer when this Saxon man is dead.

Things, events, that occupy space yet come to an end when someone dies may make us stop in wonder—and yet one thing, or an infinite number of things, dies with every man's or woman's death, unless the universe itself has a memory, as theosophists have suggested. In the course of time there was one day that closed the last eyes that had looked on Christ; the Battle of Junin and the love of Helen died with the death of one man. What will die with me the day I die? What pathetic or frail image will be lost to the world? The voice of Macedonia Fernandez, the image of a bay horse in a vacant lot on the corner of Sarrano and Charcas, a bar of sulfur in the drawer of a mahogany desk?

James Salter 2

Thomas McGuane reads James Salter’s short story Last Night, and discusses it with The New Yorker’s fiction editor, Deborah Treisman.

From Last Night:

—Walter, she said.

—Yes?

—This is the right thing.

She reached to take his hand. Somehow it frightened him, as if it might mean an appeal to come with her.

—You know, she said evenly, I’ve loved you as much as I’ve ever loved anyone in the world—I’m sounding maudlin, I know.

—Ah, Marit! he cried.

—Did you love me?

His stomach was churning in despair.

—Yes, he said. Yes!

—Take care of yourself.

—Yes.

He was in good health, as it happened, a little heavier than he might have been, but nevertheless . . . His roundish, scholarly stomach was covered with a layer of soft, dark hair, his hands and nails well cared for.

She leaned forward and embraced him. She kissed him. For a moment, she was not afraid. She would live again, be young again as she once had been. She held out her arm. On the inside, two veins the color of verdigris were visible. He began to press to make them rise. Her head was turned away.

—Do you remember, she said to him, when I was working at Bates and we met that first time? I knew right away.

The needle was wavering as he tried to position it.

—I was lucky, she said. I was very lucky.

He was barely breathing. He waited, but she did not say anything more. Hardly believing what he was doing, he pushed the needle in—it was effortless—and slowly injected the contents. He heard her sigh. Her eyes were closed as she lay back. Her face was peaceful. She had embarked. My God, he thought, my God. He had known her when she was in her twenties, long-legged and innocent. Now he had slipped her, as in a burial at sea, beneath the flow of time. Her hand was still warm. He took it and held it to his lips. He pulled the bedspread up to cover her legs. The house was incredibly quiet. It had fallen into silence, the silence of a fatal act. He could not hear the wind. ...

Interview at the Harry Ransom Center (UT Austin), which houses the Salter archive.

Reynolds Price discusses Light Years at Duke.