RKUL: Time Well Spent 08/08/2022

The Summer Drought Edition

Your time is finite. Your phone and the internet stand ready to help you squander it. Here are my latest picks for spending it well instead. Feel free to add more in the comments. 

Books, what else?

Now and then readers ask for books that will give them some tools to understand the basic foundations underlying my most quantitative posts. I have recommended technical population genetics textbooks before…and I know these have benefited many readers. Still, I realize that level of granularity is overkill for a larger faction of my readers. If you are not a scientist or engineer and want some familiarity with population genetics, John H. Gillespie’s Population Genetics: A Concise Guide will give you that. Biology graduate students are routinely assigned this, but it’s short, and the mathematical level doesn’t go beyond algebra (even here you can often ignore the equations). Nevertheless, it will ground you in enough 20th-century population genetics that you will know the Hardy-Weinberg Equilibrium and why it matters. 

Gillespie doesn’t touch on genomics because that’s a 21st-century field. Matt Ridley’s Genome: The Autobiography of a Species in 23 Chapters is all about genomics, but it was written in 1999 in anticipation of the human genome’s imminent publication. Because of its relative antiquity, there is much wrong in the book (he proved too bullish on candidate gene studies, for example). However, it is still an excellent and readable introduction to the field in broad strokes. Many people in genomics today credit their entry into the field to this particular book (also, you can listen to my podcast with Ridley last year where I got to ask him about how he feels about Genome more than twenty years on).

In the wake of Ridley’s success as an author popularizing evolutionary genetics, 2001 brought us The Cooperative Gene: How Mendel's Demon Explains the Evolution of Complex Beings by another Oxford-trained zoologist, Mark Ridley (yes, no relation). Though many likely purchased this book thinking the author was Matt Ridley not Mark Ridley, The Cooperative Gene is well worth a read as it digs deep into Mendel’s laws, particularly the law of segregation, which underpins the evolution of complex life forms. This isn’t a textbook, but a popular book that takes science seriously enough to plausibly unpack the logic at the heart of genetics’ and evolutionary biology’s intersections. You won’t become an evolutionary geneticist reading The Cooperative Gene, but you’ll see how they think.

Sticking to Oxford evolutionary biologists, Marek Kohn’s A Reason for Everything is an intellectual history of the adaptationist tradition that runs from Alfred Russell Wallace to Richard Dawkins today and has all been centered around Oxford University. Kohn takes a somewhat critical stance, probably justified given neutral theory and contemporary molecular evolution, which challenged adaptationist orthodoxies. Still, in the process, he highlights the foresight of the early evolutionary biologists in anticipating what modern genomics would go on to tell us about variation in the genome (yes, natural selection is powerful and pervasive).

Speaking of modern genomics, particularly paleogenetics, anyone who reads this Substack should read David Reich’s Who We Are and How We Got Here. This book reflects Reich’s scholarship, as he and his colleagues in the field of ancient DNA are constantly transforming our understanding of the human past. Yes, I recommend this book over and over, but it’s both that good and that essential.

Of course, there is more to understanding prehistory than genetics, even if that’s my personal lodestar. I consider Dragon Bone Hill: An Ice-Age Saga of Homo erectus an unduly overlooked book from the early 21st century that highlights what paleontologists know, how they do research and the scientific trajectory of the field over the last century since the discovery of finds like “Peking Man.” “Homo erectus” is a capacious if awkward catchall category, so the topic allows the authors to wander extensively in their narrative, from one million years in the past to the last 50,000 years.

Finally, to understand the last 10,000 years, The Human Web: A Bird's-Eye View of World History is excellent. If you read this book before or after Who We Are and How We Got Here you can see how recent changes in human interconnectedness have influenced the genetic patterns that scientists are discovering and why they have changed over the last 10,000 years. Father-son duo J. R. McNeill and William H. McNeill wrote The Human Web long before the paleogenetic revolution. Still, the dynamics they outline drive the patterns of relatedness between different populations that scientists characterize.

Thought

The New Politics of Abortion. Most people in the US don’t agree with the Republican or Democratic party activists on this issue, instead holding more moderate views. Any party that tries to bring too much “moral clarity” to the issue will probably be in for a disappointment.

The monkeypox situation keeps getting worse: The virus isn't particularly deadly, but the bad public health response is terrifying. I’m of a generation where our teachers told us we’d probably get AIDS and die of the disease at some point. Reading Michael Fumento’s 1990 The Myth of Heterosexual AIDS in high school was shocking; as he outlines the reality that in developed countries the AIDS epidemic had never (and still has not) broken out into the straight population, despite years of warnings that it would. But today information isn’t so constrained and controlled by big institutions determined to stay “on message.”

The will to fight: Throughout history, the most effective combatants have powered to victory on commitment to core values and collective resolve. The author is cognitive anthropologist Scott Atran, who has long studied this topic. Raw firepower can overwhelm patriotism, but the ISIS conquest of Mosul reminds us that small but more cohesive forces have not infrequently dispatched well-armed soldiers.

The Second Anglo-Indian Empire Will we see the Modi-fication of the Tory Party? I say probably not, but I like that Ed West isn’t scared to “go there.”

Data

A minimal role for synonymous variation in human disease. This preprint is a rebuttal to a Nature paper, Synonymous mutations in representative yeast genes are mostly strongly non-neutral. Synonymous mutations don’t result in a change to the amino acid coded, so the prior expectation is they shouldn’t impact disease or function. The paper in Nature found something different…but a single paper doesn’t update science like this. This should remind people not to be super credulous with sensational publications in glam journals.

Dairying, diseases and the evolution of lactase persistence in Europe. Good as any theory, though still skeptical that they have the cause for lactase-persistence-selection down. Ancient DNA tells us that dairying long predated strong selection for lactase persistence, which is pretty recent. However, it began earlier in Britain than in the European continent (I don’t see them explaining this).

A Draft Human Pangenome Reference. The first human draft genome was only a few individuals (I believe all white males, including Craig Venter). So this attempt to create a more representative reference is essential and valuable.

The sequences of 150,119 genomes in the UK Biobank. These are 150,000+ high-quality whole genomes. The publication reports nearly 10,000 Africans and South Asians, meaning this might be the highest quality assembly of individuals of these ancestry clusters out there right now. Britain remains a genomic superpower.

Full epistatic interaction maps retrieve part of missing heritability and improve phenotypic prediction. Genetic interactions probably explain the missing heritability of some traits, though I now give it less importance than twenty years ago. But the great thing about modern genomics is that you can afford to focus on many things, not just the most important things. We have the resources and tools.

My Two Cents

There’s still no free lunch, free subscribers; my most in-depth pieces for this Substack are beyond the paywall. Since the last “Time Well Spent” I’ve posted two big pieces for paying subscribers.

First, another edition of the steppe series, A Hun by any other name - On the genetic trail of Europe’s enduring bête noire:

The story of these fearsome warriors of the steppe that wreaked so much havoc between the 5th and 15th centuries AD actually begins in the Far East long before Atilla, more than 2,000 years ago. Attila's empire was actually one of those rarities, a sequel that topped the original, the New Testament to the Old. Scholars have now assembled a mass of circumstantial evidence pointing to the fact that the Huns that bedeviled the Romans were actually descended from the Xiongnu Confederacy that had harried and menaced Han-dynasty China six centuries prior. 

Second, one that people have been asking for a while, Built to Last - Continuity in Japanese Genetics A nation endures across the millennia:

These results undermine the widely held working assumption that the emergence of the Yamato marked a fusion of mainland rice farmers and Jomon between 500 BC and 500 AD (the Emishi presence in the north indicates that post-Jomon societies held out far longer, in some areas in any case). Instead, at least two historic groups of rice farmers likely arrived in Japan, the first from a Siberian population that introduced rice farming but was then genetically overwhelmed by a second population with origins in Korea. The three Kofun individuals are also very similar to modern Japanese, indicating that by the historical period, the ethnogenesis of the Yamato had mostly been finalized in genetic terms.

Also, I posted a complimentary piece, I wanna be like you - What we talk about when we compare chimps to humans genetically:

Because of this apparent evolutionary proximity to humans, the utilitarian philosopher Peter Singer has been making the case for extending human rights to chimpanzees, gorillas and orangutans for over three decades. Singer outlined his argument in 1993’s The Great Ape Project: Equality Beyond Humanity. The reaction was generally positive, with Carl Sagan pointing out that we “share over 99% of our active genes with chimpanzees and gorillas…It challenges us to reassess many of our ethical assumptions.”

You’ve probably come across Sagan’s statistic before, usually stated in a form like: humans share 98 to 99 percent of our genes with chimpanzees. But where does this oft-repeated number come from? And how could Sagan confidently assert it when writing his review seven years before the first draft of the human genome was even completed in 2000? Is it even accurate?

If you want to browse my more geographically focused pieces, Dry.io has created an interactive map of them. We’ll keep adding to that page over time. Also, Dry.io set up a nice skin for my pinboard bookmarks and a page for reader-submitted links.

Discussion

All my podcasts go ungated two weeks after their Substack release. So I encourage subscribers on the free plan who’d like to automatically get them to subscribe to that podcast stream (Apple, Stitcher, and Spotify).

Here are my guests since the last Time Well Spent:

• Ed West: Albion past and future

• Ethan Strauss: the sports journalism disruptor is in the house

• Maxim Lott: getting to the truth of the matter

• Manvir Singh: beyond anthropological dreams

• And here are the currently ungated podcasts all in one place.

For subscribers, I’m now posting transcripts (automatically generated, though I have someone quickly scanning for the most egregious errors).

ICYMI

Some of you follow me on my newsletter, blog, or Twitter. But my own domain also has all of the links and updates: https://www.razib.com

You’ll find links to the few different podcasts I’ve contributed to or run, my total RSS feed, links to more mainstream or print articles when I remember to post them, my Twitter, the occasional guest appearance here and there, etc.

• Email me

• DM me

• Facebook message me

• My total feed of content

• My long-time blog, GNXP

• My Dry.io archive

• A group blog, Secular Right, vintage at this point, but worthwhile for Heather Mac Donald’s prescience

• My Indian/South Asian-focused blog, Brown Pundits

• Some of my past pieces  for UnHerd, National Review, The Manhattan Institute, Quillette, and The New York Times 

• My old podcast, The Insight

• My podcast today, Unsupervised Learning

On the blog 

Only The Inner Party:

The 1856 election shows the last time that the old alliance won out, as you can see that the Republican candidate had very little support outside of Greater New England. The combination of the moral fervor of the anti-slavery movement, which eventually won over the whole North, and the unreasonable expectations of the numerically inferior South, eventually brought the rest of the North to the Republican party.

Over to you

Comments are open to all for this post, so if you have more reading/listening suggestions or tips on who I should be talking to or what I really should be writing for you, lay it on me.