Scientific American: Denying evolution is white supremacy

August 22, 2021 • 9:30 am

As we’ve seen, the once-respectable journal Scientific American is circling the drain, with an increasing surfeit of articles pushing a particular ideological point of view—a woke one. Well, this article, by writer Allison Hopper, has a bit of science in it, but it’s mixed with politics in such a toxic way that it’s almost funny. It’s full of unsupported assumptions and false claims, is based on no logic at all, and is false in its main claim for two reasons.  Those of you who still subscribe to this rag may want to either write the editor, Laura Helmuth, or cancel your subscription.

Laura had a distinguished career before she took over this journal (she has a Ph.D. from Berkeley in neuroscience and has edited or written for Science, The Washington Post, and Smithsonian). I have no idea why she lets this kind of tripe into her magazine. But she’s less to blame than the author, who doesn’t even have a coherent argument. All Hopper wants to do is show that American creationism has nothing to do with religion, but that white supremacy, not belief in God, is at the core of creationism.

Read and weep: this is a this is a three-hankie article:

Now over the last 12 years I’ve given plenty of evidence that creationism stems from religious belief: belief in the Bible for conservative Jews and Christians, and belief in the Qur’an for Muslims, with both books having their own creation stories. For one thing, I’ve never met a creationist who wasn’t motivated by religion, and all creationist organizations, including the Discovery Institute, are at bottom manifestations of religious belief, regarding evolution as inimical to belief in God. This is so obvious that only someone with a bizarre agenda could deny it.

Well, Hopper does deny it.  She says that the roots of creationism really lie in white supremacy and not religion. Here’s the logical connection that leads her to that conclusion.

a. If two falsities are in the Bible, they can be connected as causal.
b. Two falsities that Hopper deals with are Biblical creationism as limned in Genesis, and the claim that humans started out with white skin and then God, marking the descendants of Cain, made them black.
c.  The supposedly black descendants of Cain have been historically portrayed as bad people, and then as black people, as the “mark” given to those descendants is said to be black skin.
d.  Therefore the Bible evinces white supremacy, since humans, made in God’s image, started out white, but a bad subset of them were turned black.
e.  In reality, human ancestors were black, so even the Bible story is wrong.
f.  The white supremacy story comes from Genesis (4:15), a book that also tells the creation story.
g.   Ergo, creationism stems from white supremacy.

(Note, as I say below, the white supremacy argument is itself based on religion!)

You’ve already noted a number of fallacies in this argument. One is that if two bad things are in the Bible, particularly in the same part of the Bible, they can be connected, and one can assert that one bad part gave rise to the other. Well, there are a number of mass killings in Genesis: beyond the extirpation of humanity by the Flood, there’s also the destruction of the Cities of the Plain, including Sodom and Gomorrah. And of course the Old Testament itself is full of genocide. By this logic, one could say that creationism stems from an impulse to murder. (Indeed, Hopper connects creationism with “lethal effects” on black people!).

The other bit of “evidence” Hopper adduces to draw creationism out of white supremacy is this (I am not making it up):

In fact, the first wave of legal fights against evolution was supported by the Klan in the 1920s.

Well that’s a strong proof, right? No matter that a lot of people who didn’t support the Klan still went after evolution in the 1920s and before.

And that’s all the evidence that Hopper has. She makes no case that creationism comes from a desire of whites to be on top save the occasional depiction of our African ancestors as white people (and, because they’re often men, this shows misogyny as well). But that claim really argues that our view of evolution comes from white supremacy!

Do you think I’m kidding? Here are a few sentences from Hopper’s article:

I want to unmask the lie that evolution denial is about religion and recognize that at its core, it is a form of white supremacy that perpetuates segregation and violence against Black bodies.

. . . At the heart of white evangelical creationism is the mythology of an unbroken white lineage that stretches back to a light-skinned Adam and Eve. In literal interpretations of the Christian Bible, white skin was created in God’s image. Dark skin has a different, more problematic origin. As the biblical story goes, the curse or mark of Cain for killing his brother was a darkening of his descendants’ skin. Historically, many congregations in the U.S. pointed to this story of Cain as evidence that Black skin was created as a punishment.

The fantasy of a continuous line of white descendants segregates white heritage from Black bodies. In the real world, this mythology translates into lethal effects on people who are Black. Fundamentalist interpretations of the Bible are part of the “fake news” epidemic that feeds the racial divide in our country.

One bit of advice for Ms. Hopper: besides the obvious one that you’re wrong about where creationism comes from, PLEASE stop using the term “black bodies” for “black people”. Yes, I know the phrase is au courant, but it dehumanizes black people in the same way that “slaves” dehumanizes “enslaved people.”  You are using racist language. And what, by the way, are the lethal effects of creationism on black people? Is Hopper speaking metaphorically or literally here?

But I digress.

Hopper is right that the Genesis account of the Bible is creationist, and says that Adam was made in God’s image. But does it say what color Adam was? I don’t think so. It’s just assumed that he was white, but on this point Scripture is silent. In fact, we don’t know, though Hopper asserts it confidently, that the earliest human ancestors were black, though humans certainly split from our closest relatives, the bonobos and chimps, in Africa, and evolved black pigmentation at some point. This is because humans probably evolved from chimplike primates (as “naked apes,” we’re outliers), and chimps happen to have white skin. As the Encyclopedia Brittanica says:

Chimpanzees are covered by a coat of brown or black hair, but their faces are bare except for a short white beard. Skin colour is generally white except for the face, hands, and feet, which are black. The faces of younger animals may be pinkish or whitish. Among older males and females, the forehead often becomes bald and the back becomes gray.

Here’s a photo from Forbes, but you can find lots of photos like this.

Old and young chimps from NBC News:

It’s entirely possible that the first members of the hominin lineage after it split from the chimp lineage had light skin, and darker skin evolved later via natural selection. If this is the case, Hopper’s argument falls apart. But it doesn’t matter, because, really, who cares besides evolutionists and anthropologists—and energetic anti-racists like Hopper—about the skin color of the earliest hominins? I’m not claiming that the earliest members of the hominin lineage were white, and I’m certainly not making a case for white supremacy, for our later hominin ancestors were surely much darker. All I’m saying is that these early hominins could have been white or gray. Hopper has no way to be sure, and in that case she has no argument.

It is likely that after several million years, hominins in Africa did evolve dark skin, and that those hominins were the ones that gave us fire, tools, and other rudiments of culture. But I don’t see how that buttresses Hopper’s argument. Even if it did, her big fallacy is not assuming that the first hominins were black, but connecting white supremacy supported by some religionists with creationism, with the former giving rise to the latter.

Why does Hopper make this argument? Because she has a goal:

My hope is that if we make the connection between creationism and racist ideology clearer, we will provide more ammunition to get science into the classroom—and into our culture at large.

Good luck with that!  Because creationism really comes from religion, and accepting evolution would overturn the faith of many Biblical literalists (about 40% of Americans), you’re not going to change their minds by telling them: “Hey! Your creationism is really a manifestation of white supremacy because the story of Adam and Eve is a tale of white supremacy!”

But were Cain’s descendants really black? Hopper assumes that they were, and that’s how many people have interpreted the story, but let’s read what the Good Book says (King James version; Genesis 4:15).

And the Lord said unto him, Therefore whosoever slayeth Cain, vengeance shall be taken on him sevenfold. And the Lord set a mark upon Cain, lest any finding him should kill him.

This is a “mark”, not dark skin, and I can’t find any scholar who interprets the Hebrew as meaning “dark skin”. Furthermore, the “mark” placed on Cain was not to identify him and his descendants as miscreants, but to protect them.  Here, from the King James Bible again, are verses 9-16 from Genesis 4:

And the Lord said unto Cain, Where is Abel thy brother? And he said, I know not: Am I my brother’s keeper?

10 And he said, What hast thou done? the voice of thy brother’s blood crieth unto me from the ground.

11 And now art thou cursed from the earth, which hath opened her mouth to receive thy brother’s blood from thy hand;

12 When thou tillest the ground, it shall not henceforth yield unto thee her strength; a fugitive and a vagabond shalt thou be in the earth.

13 And Cain said unto the Lord, My punishment is greater than I can bear.

14 Behold, thou hast driven me out this day from the face of the earth; and from thy face shall I be hid; and I shall be a fugitive and a vagabond in the earth; and it shall come to pass, that every one that findeth me shall slay me.

15 And the Lord said unto him, Therefore whosoever slayeth Cain, vengeance shall be taken on him sevenfold. And the Lord set a mark upon Cain, lest any finding him should kill him.

16 And Cain went out from the presence of the Lord, and dwelt in the land of Nod, on the east of Eden.

The “mark” is clearly given by God to protect Cain, so even if it were dark skin, for which there’s no evidence, it means that dark skin marked Cain and his descendants as people protected by God. How does that comport with Hopper’s narrative?

I’ve already gone on too long picking additional in Hopper’s Swiss cheese of a narrative, but I have one more bit of evidence that tells against her risible theory.  And that is this: historically, in the United States black people have been far more creationist than whites. If creationism draws from white supremacy, then haven’t black people heard the news?

Here are some data from a Pew Study in 2015: see bars 4-6 from the top:

So there you have it, ladies and gentlemen, brothers and sisters, comrades and friends: an insupportable argument, weakly based on erroneous science, and gracing the pages of what was once America’s premier science magazine. How low the mighty have fallen!

All I want to add in closing is that Hopper is dead wrong in claiming that the roots of creationism are not in religion, but in white supremacy. And, as the supreme irony in her argument, the “white supremacy” argument is rooted in, yes, the Bible! So even her main thesis is wrong. Yes, no matter how you slice it, even Hopper’s way, creationism is an outgrowth of religion.

In case they ditch this article, I’ve archived it here.

Jesse Singal fact-checks Science-Based Medicine again

July 18, 2021 • 9:30 am

The battle between Jesse Singal and the site Science-Based Medicine (SBM) continues. SBM originally hosted a positive review of Abigail Shrier’s book Irreversible Damage written by one of their editors, Harriet Hall, and then two other editors, David Gorski and Steven Novella (G&N), removed Hall’s review and replaced it with three pieces critical of Shrier’s thesis about the possible social origins of rapid onset gender dysphoria (ROGD) and the possible dangers of treating the syndrome with hormones and surgery when it starts in adolescence. (See the whole story in these posts.)

Although G&N claimed that they removed Hall’s review because it contained scientific errors and also glossed over Shrier’s own errors, I suspect it was also pushback from those who deemed Shrier’s book “transphobic” (it’s not).  Jesse Singal, who’s read a lot about gender dysphoria has published a critique of G&N’s stated reasons for the censorship, arguing that G&N played fast and loose with the literature themselves, mis-citing papers, engaging in confirmation bias, and so on.

Now, in four further tweets, Singal has accused A. J. Eckert (AJE), one of the people whose posts replaced Hall’s on SBM (Eckert wrote two of them), of fabricating quotes from Shrier’s book that don’t appear in it. Here are the four tweets. While these made-up quotes aren’t as potentially damaging to SBM’s reputation as is Singal’s long critique, it still shows a lack of care in SBM’s methods—something one doesn’t expect on the site, which has been careful and a valuable asset. Now, however, it may well be slanted by wokeness.

The first one deals with a phrase that, says Eckert, is used repeatedly by Shrier to characterize the social environment that, she says, pushes adolescent girls towards ROGD. Eckert says, among other things, “These [factors] are characterized as a ‘woke gender ideology,’ an oft-recited phrase that is never really defined.” In fact, Singal found that Shrier doesn’t use the phrase even once.

Singal’s second tweet notes that it was supposedly only one quote that was fabricated, but that AJE said it was “oft-recited.”

Then Singal discovers two things. First, Eckert attributes to Shrier the phrase “radical trans ideology” as characterizing what the Internet instills in some adolescent girls that get ROGD (third tweet). That phrase doesn’t appear in Shrier’s book, though AJE puts it in quotes.

Second, AJE apparently grossly mischaracterized the treatment of Lisa Littman’s study of the etiology and manifestation of ROGD published in PLoS ONe (underlined bit below).

No, Littman’s study wasn’t pulled; in fact, it’s still up at the PLoS ONE website. What happened was that the editors required some tweaks in the original version, which were made. What was pulled was a Brown University press release promoting Littman’s study. (Littman works at Brown.) And that retraction, as well as perhaps some of the changes suggested by PLoS’s editors, may have come from social-media pressure.

This last claim about pulling the study, combined with the fabricated quotations, show a lack of care of AJE and SBM, and perhaps the editors, in describing the work. I won’t call these lies or deliberate fabrications, but they do show a disturbing lack of care from a site that has spent much of its time debunking others for carelessness and duplicity.  And I’m not sure if it’s “potentially libelous”, though Eckert/G&N really should issue a couple of corrections for the site.

Judge it as you will; your mileage may vary. There will, of course, be more to come. In the meantime, Shrier’s book, now a year old, is still selling rapidly on Amazon because of all the attention that the ACLU and people like G&N give it. It’s the Streisand Effect.

h/t: cesar

More mishigas at Scientific American: A claim that opposition to evolution comes from white supremacy, not religion

July 11, 2021 • 10:00 am

As Scientific American continues its inexorable circling of the drain, it’s approaching the drainhole itself. For, from a week ago, we have an op-ed by Allison Hopper asserting that Americans’ rejection of evolution—73% of Americans are either straight-up Biblical creationists (40%) or think God helped guide evolution (33%)—is due not to religion as many suppose, but to white supremacy. It’s all about racism, Jake! (I was not the first to proposed the religion-is-the-main-cause of rejecting-evolution thesis, but laid out the case, with supporting data, in a paper in Evolution in 2012.)

Hopper rejects that thesis in her Sci Am article, saying that the idea that people reject evolution because of religion is a “lie”. To wit:

“I want to unmask the lie that evolution denial is about religion and recognize that at its core, it is a form of white supremacy that perpetuates segregation and violence against Black bodies. “

Well, she’s dead wrong about her thesis, as I’ll argue below, but also in her claim that evolution denialism “perpetuates segregation and violence against Black bodies.” It does nothing of the sort! You really have to distort your thinking to claim that people are prone to deny evolution because they’re white supremacists, much less embrace the idea that creationism (which is what I’ll call “evolution denial”, since they’re pretty much equivalent in America) creates “violence against Black bodies”. What kind of violence? Has any black person been harmed in the name of creationism? And what is it with this “black bodies” trope?  That seems to me distinctly unwoke, since the trend in “progressive” language is to emphasize the humanity of oppressed people, i.e., “enslaved persons” instead of “slaves”. Saying “black bodies” instead of “black people” clearly dehumanizes people, and I deplore it.

But I digress. Before we examine Hopper’s arguments, such as they are, here are her bona fides from the article:

Allison Hopper is a filmmaker and designer with a master’s degree in educational design from New York University. Early in her career, she worked on PBS documentaries. More recently, she’s been creating content for young people on the topic of evolution. She has presented on evolution at the Big History Conference in Amsterdam and Chautauqua, among other places.

And here’s her article, which you can read for free by clicking on the screenshot below:

Hopper is trying here to jump on the current bandwagon that everything is about race, including rejection of evolution. And, she implies, once we acquaint people with the fact that creationism is a product not of religion but of white supremacy, they’ll give up their creationism and embrace evolution.

Her argument goes like this:

1.) Many people don’t realize that all humans descend from African ancestors (true).

2.) Those African ancestors had dark skin. (Also true.) However, in their case “black” or “brown” does not equate with “oppressed”, since there were no white people to oppress them. Different species of hominin may have oppressed each other, but that had nothing to do with pigmentation.

3.) Importantly, human culture sprang from dark-skinned ancestors who had religion, language, fire, and tool use. These were the foundations, argues Hopper, for the culture we have today. It’s true that these bases (except, perhaps, for religion and language, about whose origin we know virtually nothing) probably sprang from dark-skinned ancestors. But other features of modern culture evolved in Europe and the Middle East, where natural selection had already been lightening skin color. (This constant emphasis on the overweening importance of skin color repels me.) At any rate, agriculture and its attendant amenities of civilization probably arose about 12,000 years ago in the Middle East among people who were not black (but may have been brown) and further developed by people of all colors, including whites and Asians. But who cares? Only someone obsessed with racism and determined to make it the basis for everything bad.

4.) Hopper cares, for she says that evolution’s truth dispels the Biblical story that Adam and Eve (who were supposedly white) were instrumental in creating black people, who descended from a bad person—Cain—who killed his brother. This “mark of Cain” thesis that supposedly connects creationism with white supremacy, is advanced in several ways by Hopper:

Science education in the U.S. is constantly on the defensive against antievolution activists who want biblical stories to be taught as fact. In fact, the first wave of legal fights against evolution was supported by the Klan in the 1920s. Ever since then, entrenched racism and the ban on teaching evolution in the schools have gone hand in hand. In his piece,What We Get Wrong About the Evolution Debate, Adam Shapiro argues that “the history of American controversies over evolution has long been entangled with the history of American educational racism.”

In fact, anybody who looks at the data on creationism sees immediately its connection with the Biblical creation story (not including Cain)—the view that God created everything almost instantaneously, with humans made in His/Her/Their image. Everybody promoting creationism and intelligent design is religious, and all creationist organizations are religious at bottom.

In my life I’ve met hundreds of creationists, and every one of them was religious. (David Berlinski, whom I haven’t met, may be the one exception, but that’s just one person and he may be dissimulating about religion anyway.) They make no bones about their views, either. Yet in none of these people have I heard anything about white supremacy. Sure, there may be racists among creationists—there has to be given the connection between Evangelical Christianity and the South—but you’d have to essentially make things up to argue that creationism comes from white supremacy and that its connection with religion is “a lie.” (At any rate, were Hopper’s story of Cain and Abel true, it still shows a connection between creationism and religion.)

But wait! There’s more:

The fantasy of a continuous line of white descendants segregates white heritage from Black bodies. In the real world, this mythology translates into lethal effects on people who are Black. Fundamentalist interpretations of the Bible are part of the “fake news” epidemic that feeds the racial divide in our country.

There are those “Black bodies” again.  But what are the “lethal” effects? Were black bodies really killed because white bigots and lynchers were motivated by a refusal to accept our ancient ancestry? I doubt it, and I doubt whether they were motivated by religion, either. They were motivated, I believe, by tribalism and the heritage of slavery with its attendant beliefs that blacks were inferior beings.

In fact, when Hopper talks about the dearth of children’s books on evolution, she inadvertently admits that religion (not the story of Cain and Abel!) is tilting kids towards creationism:

If you go on Amazon and look up “children’s books on evolution” you will find about 10–15 relevant titles. This is in contrast to the hundreds of children’s books on other scientific subjects such as chemistry, astronomy and other less controversial subjects. I found only one book on evolution for preschoolers, called Grandmother Fish. The author had to self-fund the book through Kickstarter.

On the other hand, there are hundreds of children’s books available on Amazon that focus on biblical origin stories. Science deniers are pumping money into a well-funded antievolution machine. In 2007, the creationists built their own Bible-themed museum and amusement park. What they understand is that to reach young children you need music, colorful characters and celebration.

Kids get their religion long before they learn evolution, and by the time they’re presented with Darwin and his successors, they’ve had at least a decade of indoctrination in the Bible, with many being Biblical literalists. They are effectively immunized against evolution. Racism is a separate issue.

In the end, Hopper argues that if we can just tell the story of evolution properly, including that we all came from Africa and our earliest ancestors were dark-skinned, creationism would go away:

. . . even in the current literature about human origins that we do have, the end point of evolution is often depicted as a white man carrying a spear. This image not only eliminates our African heritage but also erases women and children from the picture. Because evolution is foundational knowledge, we need the story to be told in many different ways, by many different voices.

As we move forward to undo systemic racism in every aspect of business, society, academia and life, let’s be sure to do so in science education as well. Embracing humanity’s dark-skinned ancestors with love and respect is key to changing our relationship to the past, and to creating racial equity in the present. These ancient people made the rest of us possible. Opening our hearts to them and embracing them as heroic, fully human and worthy of our respect is part of the process of healing from our racist history.

I wasn’t aware that the teaching of evolution was systemically racist; do teachers really deny that our ancestors were African? And does Hopper really believe that accepting that will get rid of racism? Really? Even Darwin was a monogenist, saying that all groups of humans arose from a single ancestor who probably lived in Africa. Did that get rid of racism? I don’t think so, though some people think Darwin’s monogenism was part of a strategy to combat racism.

(I can’t get over my gag reflex when hearing that we need to embrace our ancestors with “love and respect”, since I don’t know that they were either lovable or respectable)

Okay, now what’s the evidence against Hopper’s thesis? It’s strong:

a.) Ask people why they think evolution didn’t happen. Many will say because they believe the Bible or the Qur’an. Nobody will say because it shows that white people are superior. (Of course, you can say they won’t admit their bigotry.)

b.) Every creationist organization from Answers in Genesis to the Discovery Institute is based on religion, while we find no creationist organizations whose platform is white supremacy. As I said, the two are tangentially connected because of the religious and white-supremacist nature of the American South, but this is a matter of correlation, not causation.

c.) Most telling: several surveys, listed and summarized in this paper, show that blacks and Hispanics deny evolution more than do whites. This is the opposite of what Hopper predicts, but makes sense under the “religion-first” hypothesis, since blacks and Hispanics tend to be more religious than whites in general.

d.) There is a highly statistically significant negative correlation between the religiosity of 34 European countries and their acceptance of evolution, as I noted in my Evolution paper. Most of these countries are nearly all white, save France and Germany, which have high acceptance of evolution (and more black people than, say, Iceland or Demark). The US is near the bottom in accepting evolution (I’ll give the data in a minute), not because the U.S. has a higher percentage of whites than most European countries—it doesn’t—but because the U.S. is far more religious then Europe.

Here’s the correlation I found. The U.S., labeled, is next to last in accepting evolution, while below us lies only Turkey: a Muslim country that, by the way, happens to comprise many “people of color”. Note that the most religious countries, to the right, are the least accepting of evolution. I discuss issues with these data (nonindependence, etc.) in the Evolution paper.

And here are the data from Miller and Scott (2006) that I used to make the plot for my own paper:

The religiosity of these countries, which appears in the graph above, came from other sources given in my Evolution paper.

The thing to note is that virtually all these countries are white, and yet the correlation holds across them all. As I said, the countries with the highest proportion of evolution rejectors (those at the bottom)—are not only the most religious, but also probably contain the highest proportion of people of color. This is what the religious hypothesis proposes, but it goes counter to Hopper’s thesis, which predicts that the whitest countries should be the least accepting of evolution, for rejection of evolution is a sign of white supremacy. (Of course, you could argue that white supremacy will be manifested only in countries with a substantial proportion of black people, but that’s pushing it.) In fact, Hopper’s argument is a post facto confection to support anti-racism, and appears to make no predictions that seem to stand up to scrutiny.

It seems to me that Hopper is not only deeply misguided, but also motivated by ideology, tying creationism directly to white supremacy, and almost completely dismissing its connection to religion. As I always say, “You can have religion without creationism, but you can’t have creationism without religion.” Hopper seems to have deliberately ignored data inimical to her hypothesis, which of course is what one does when afflicted with the kind of confirmation bias that comes with wokeness.

And it’s just another sign that whoever’s in charge of Scientific American is letting through ill-informed and erroneous material.  What has happened to that once-respectable magazine? Is there no longer an audience for the lively yet informative articles they used to publish? Are they becoming the Evergreen State of popular science magazines?

h/t: Eli

Some thoughts on Dick Lewontin’s obituary in the New York Times

July 8, 2021 • 9:15 am

Both the online and paper editions of today’s New York Times feature fairly long obituary of The Boss: my Ph.D advisor Dick Lewontin. It was written by science correspondent Natalie Angier, and you can access it by clicking on the screenshot below.

As he headline implies, and much of the text confirms (“a gleeful gadfly”, “Not everyone was enamored of Dr. Lewontin”, etc.), the “hook” used in the piece is Lewontin’s contrarianism: his opposition to stuff like genetic determinism, IQ studies, adaptationism, and sociobiology. To my taste, it makes him seem a bit more of an academic curmudgeon than he really was, but remember that I basically lived in his lab for six years. Yes, he was captious about science, but that was great for his students, who imbibed the essentially critical attitude needed for good science. But I never saw the man get angry, nor do I think he was, as described in the first paragraph of the piece, a “caustic writer”. In my view he was not caustic, but critical. He could take you down to size, though!

But in general it’s a very good summary of his life, concentrating (as these pieces must) on his contributions to science. Angier, after all, won a Pulitzer Prize for her science reporting.  I believe some of the material came from my own more personal memorial to Dick posted the other day, like his working-class attire and his holding hands with his wife in the movies. That’s fine with me.

A few corrections and comments (quotes from the piece are indented)

Dr. Lewontin first won scientific fame in the mid-1960s for research he conducted with John Hubby at the University of Chicago that revealed far greater genetic diversity among members of the same species than anybody had suspected.

That work upended existing notions that most genetic mutations are rare, harmful and soon swept from the breeding pool. The two men’s findings showed that, to the contrary, many different forms, or alleles, of the same genes can coexist indefinitely in wild populations of organisms, be they fruit flies, zebra finches, earthworms or zebras.

It would have been useful to mention that the work with Hubby on “members of the same species” was the fruit fly species Drosophila pseudoobscura. More important, Lewontin and Hubby did experimental work only on fruit flies, and didn’t show anything about “the degree of genetic variation in zebra finches, earthworms, or zebras”. Other people did that work much later. Lewontin and Hubby’s work (and that of Harry Harris in England) did inspire that later work, though.

Going on:

He was no fan of the massive federal Human Genome Project, which set out to map the entire sequence of human DNA, and he strongly objected to the notion that DNA is the “blueprint” for a human being. He considered the perpetual debate over race, I.Q. and heritability to be an irritating scam, a recrudescence of Nazi-inflected notions of eugenics and master races.

Even to begin to figure out how big a role genes played in intellectual life, he said, would require a large number of newborn infants to be raised in tightly controlled circumstances by caretakers who had no idea where the babies came from. “We should not be surprised that such a study has not been done,” he added.

Lewontin’s opposition to the Human Genome Project was, in retrospect, a big mistake. No, it won’t answer every question we have, but already knowing the genes we have has been of immense value in medicine, in paleoanthropology, and in evolutionary genetics of humans. As for IQ (I think that’s what the article means by “how big a role genes played in intellectual life”), we now have a pretty good idea that within human populations, about 75% of the variation among adult individuals is due to variation in their genes—that is, the “heritability” of IQ within a give population is about 0.75, or 75%. We have various ways of estimating that figure and they generally are close to each other. But one shouldn’t misinterpret heritability, as I pointed out in detail in a previous post. There are a number of ways a high heritability is misused, the most invidious being to assume that high values within a population imply that difference among populations also rest on genic differences. That’s a logical and scientific error.

Lewontin’s feud with Ed Wilson over sociobiology is described in detail, and is generally accurate. Lewontin couldn’t stand Wilson. Wilson had a more charitable attitude, though he felt blindsided by Lewontin and Gould’s attacks. I lived through that period at Harvard. I was Dick’s student but also taught Ed’s Bio 1 class twice and was friends with Wilson’s collaborators, students, and postdocs. I thus shuttled between warring labs from time to time. In the end, I think, Lewontin lost that debate, as evolutionary psychology, despite some flaws, has proven to be a useful and vital field, and friendly with Wilson himself. And of course sociobiology, applied to animals in general, is well ensconced as part of organismal biology.
Part of this bit, however, seems inaccurate:

It was Dr. Lewontin’s break with another old friend, Dr. Wilson, that proved the more harrowing and long-lasting. Dr. Lewontin in 1975 attacked Dr. Wilson’s 700-page blockbuster, “Sociobiology: A New Synthesis,” as the work of a modern, industrial Western “ideologue.” Inspired by this and similar critiques, a group of demonstrators at a 1978 scientific meeting dumped a bucket of water over Dr. Wilson’s head.

The ill will persisted for many years, but friends said the two men had recently reconciled with a handshake, calling each other worthy adversaries.

I’d love to hear about that handshake, as I know nothing about it. (I assume it’s true.) As for the bucket-of-water incident, though, I believe that’s inaccurate: the stories seem to have settled on one radical science person approaching Wilson, who was sitting at a dais in a lecture room, and tossing cup of water on Wilson while saying, “Wilson, you’re all wet!” The “pitcher of ice water” poured over Wilson may well be an apocryphal tale that persists widely. I cannot be sure.

UPDATE: In a comment below, Ira Flatow says he was there and it was indeed a pitcher of water. I stand corrected.

Finally, I liked the fact that Natalie emphasized Dick’s refusal to put his name on his students’ papers:

He had habits of dress: “Khaki pants, work boots, work shirt — in solidarity with workers,” Dr. Coyne said. He had habits of principle, notably of authorship: Many senior scientists are listed as authors on research reports done entirely by their students, but Dr. Lewontin would have none of it. If you didn’t do any of the work, he insisted, you don’t get to take any of the credit.

It’s telling that at his faux-retirement dinner, when asked to say a few words, Dick talked almost entirely about how none of us, his students and colleagues, should take credit for work that we didn’t do—or didn’t do much of. That came from his egalitarianism, his spirit of fairness, and his desire to see young folk get the credit they needed to advance in science. As Sara Hrdy says in the article when criticizing Dick for being “unfair” to E. O. Wilson, “Dick was a complicated man.” I’m not sure I’d use the adjective “complicated”, for while he was a polymath and multitalented, he wasn’t that hard to figure out, even if none of us could come close to him in intellect and achievement. I’d say a “great” man, but of course I’m one of those whom Angier describes in the first sentence of this paragraph:

Many of his students and colleagues regarded him with an awe that tipped toward reverence, describing him as equally gifted at abstruse quantitative research, popular writing and public speaking; a Renaissance scholar who spoke fluent French, wrote treatises in Italian, worked with Buckminster Fuller on his geodesic domes and played chamber music on the clarinet with his pianist wife, Mary Jane. He was also a volunteer firefighter and a self-described Marxist who chopped his own wood.

In the end, Angier did a very good job, and the only reason I have quibbles is because I was so close to her subject.

To close, here are three pictures that limn the man’s life. First, two photos of a very young Lewontin; these were taken at the Cold Spring Harbor population-genetics meetings in 1955, when Dick would have been 26. I never saw him wear a bowtie, and rarely a tie.

This is a picture that all his students knew about and got a huge kick from. Cold Spring Harbor labels it “Richard Lewontin; E. B. Ford (eating clams at Neptune’s Cave)”. Ford, of course, was a famous British ecological geneticist.

And a photo I’ve shown before: Lewontin on his 90th birthday in 2019. It was taken by Andrew Berry:

 

John Horgan makes a strawman argument against “consilience”

June 27, 2021 • 9:30 am

The science writer John Horgan became well known for his 1996 book The End of Science, in which he claimed that the era of “fundamental science”—the kind of science that yielded big discoveries like the structure of DNA, evolution, and quantum mechanics—was coming to an end. That is, all the paradigm-changing views of the universe had already been made.

Since then, of course, we’ve learned about dark matter, dark energy, the Higgs Boson, gotten indications that quantum mechanics may have fundamental flaws, and so on. String theory, though it may be untestable and thereby die, became a big deal. Now you may say that Horgan’s right—that these discoveries aren’t “fundamental”—but I’d never bet on humanity reaching the end of world-changing scientific discoveries about the universe. Still, in 2015 Horgan defended his earlier conclusion in the pages of Scientific American.   He wasn’t calling for science to stop, of course, but promoting the depressing conclusion that we’d found out pretty much all the “fundamental” truths we’d ever get.

I think he was and is wrong.

Now, also in the pages of Scientific American, Horgan has a new “opinion” piece that is again a bit of science-dissing in that it’s the usual criticism of “scientism”, which he defines as science overstepping its boundaries and impinging on “other ways of knowing”, like religion (!) and the “knowledge” we get from psychedelic visions.

But Horgan’s main target is “consilience,” a term used by E. O. Wilson, who wrote a book by that title proposing a sweeping project: the absorption of all forms of “knowing” and endeavor into science. That would include morality, art, psychology, literature, philosophy, and so on. All knowledge would and should, claimed Wilson, be analyzed using the toolkit of science, leaving no room for the humanities as we know them.

Click on the screenshot to read:

My first response is one I made in my exchange with Adam Gopnik at Letter on “ways of knowing”: religion (see Horgan’s title) is not a “way of knowing”, and neither is ingestion of ayahuasca (which Horgan tried and is regularly used by shamans to derive “visions” that Horgan sees as “ways of knowing”).

Horgan says these mystical  drug-induced visions  are ones “in which we seem to glimpse truths normally hidden behind the surface of things.” I’ve recounted my own LSD-induced vision in which my hidden truth, which I wrote down on a piece of paper because it sounded so profound, turned out to be “the walls are fucking brown.” And if you do glimpse truths when you’re on drugs, they’re either private experiences or other claims that, when you’ve come down, must be verified with the toolkit of science. “The universe is one” is not a truth except in the trivial sense that it’s all made of matter and energy.

Since my views on the ambit of science (construed broadly) have been set out in the exchange with Gopnik, I won’t repeat my arguments here, but I deny Horgan’s claim that there are “ways of knowing” about the cosmos that do not employ the empirical toolkit of science. (See also pp. 185-196 in my book Faith Versus Fact.).

But I do agree with Horgan that the Grand Project to subsume art, literature, philosophy and morality completely into the “harder” sciences is futile. The thing is, hardly any scientist I know agrees with Wilson or with Horgan’s characterization. Yes, Sam Harris does think that science can determine what is right and wrong to do, but few agree with him about that (I dissent as well). And even the most “scientistic” scholar I know, Steve Pinker, doesn’t entertain the notion that full consilience is feasible. As Pinker said in the New Republic:

Demonizers of scientism often confuse intelligibility with a sin called reductionism. But to explain a complex happening in terms of deeper principles is not to discard its richness. No sane thinker would try to explain World War I in the language of physics, chemistry, and biology as opposed to the more perspicuous language of the perceptions and goals of leaders in 1914 Europe. At the same time, a curious person can legitimately ask why human minds are apt to have such perceptions and goals, including the tribalism, overconfidence, and sense of honor that fell into a deadly combination at that historical moment.

In the last sentence Pinker raises a point that is the subject of one of the best short pieces he’s written, the one below from The New Republic (click on screenshot; this piece was later attacked by New Republic editor Leon Wieseltier):

You should read this article as a palliative for Horgan’s, as Pinker is calling not for the ingestion of all other disciplines by science, but an expansion of the humanities by using the toolkit of science. Surely science can inform morality, art, analysis of literature, politics and history.  Here’s part of Pinker’s view:

Diagnoses of the malaise of the humanities rightly point to anti-intellectual trends in our culture and to the commercialization of our universities. But an honest appraisal would have to acknowledge that some of the damage is self-inflicted. The humanities have yet to recover from the disaster of postmodernism, with its defiant obscurantism, dogmatic relativism, and suffocating political correctness. And they have failed to define a progressive agenda. Several university presidents and provosts have lamented to me that when a scientist comes into their office, it’s to announce some exciting new research opportunity and demand the resources to pursue it. When a humanities scholar drops by, it’s to plead for respect for the way things have always been done.

Those ways do deserve respect, and there can be no replacement for the varieties of close reading, thick description, and deep immersion that erudite scholars can apply to individual works. But must these be the only paths to understanding? A consilience with science offers the humanities countless possibilities for innovation in understanding. Art, culture, and society are products of human brains. They originate in our faculties of perception, thought, and emotion, and they cumulate and spread through the epidemiological dynamics by which one person affects others. Shouldn’t we be curious to understand these connections? Both sides would win. The humanities would enjoy more of the explanatory depth of the sciences, to say nothing of the kind of a progressive agenda that appeals to deans and donors. The sciences could challenge their theories with the natural experiments and ecologically valid phenomena that have been so richly characterized by humanists.

In some disciplines, this consilience is a fait accompli. Archeology has grown from a branch of art history to a high-tech science. Linguistics and the philosophy of mind shade into cognitive science and neuroscience.

And of course even religion has been altered by science (I wouldn’t use the word “enriched”), at least in terms of science disproving some of the foundational claims of religion, like the existence of a creation event of biological life by God, the existence of Adam and Eve, the Exodus, and so on. In that sense, any morality that gets its force from from religion loses considerable ground.

But on to Horgan.

First, I again deny that there are ways of knowing about the universe (which is, after all, what Horgan means by “fundamental knowledge”) that do not require the empirical toolkit of science: observation, testing, doubting, predicting, and so on.

But Horgan has other points to make. First, he doesn’t think consilience is possible. Here’s he’s probably right, for we simply will never have the knowledge to connect all human endeavors through scientific hypotheses. Some depend on unknowable historical or evolutionary events, others on knowledge inaccessible to us. Even if, in principle, all phenomena reduce to the motions of molecules, we will never be able to scientifically explain why Tolstoy wrote Anna Karenina the way he did or why it affects each of us differently. And no scientist I know, save perhaps Ed Wilson, thinks that we should try to do this, though there are Darwinian analysis of parts of literature.

But Horgan goes further, arguing that we haven’t even achieved consilience within scientific disciplines. Physicists are still arguing about quantum mechanics and string theory, we don’t yet have a unification of all fundamental physical forces (gravity stubbornly refuses to consiliate), we don’t understand how physical processes in the brain produce consciousness, and even evolutionary biologists still argue about the importance of group selection.  But the existence of unsolved problems, some of which will never be solved, does not support Horgan’s argument that greater consilience isn’t feasible. We simply can’t imagine what science will find in the next few centuries and, as Pinker notes, consilience is being achieved in archaeology and linguistics.

It turns out that Horgan thinks consilience is unfeasible for this reason:

If consilience entails convergence toward a consensus, science is moving away from consilience.

I’d take issue with that, too. Scientists are a lot more in agreement on matters of truth than they were 200 years ago. We have a consensus about the major features of evolution, about the structures of molecules, about how DNA and metabolism work, about the age of the Universe, about who were the ancestors of humans, and what the fundamental particles were. Of course we’ll never agree on everything, but to say that “science is moving away from consilience” in effect says that we know less than we used to. And that’s not the case. We have a lot more consensus than we used to. When I was young, there was a big argument about whether the continents moved. We now know that they do.

Further, Horgan asserts that besides being unfeasible, consilience is undesirable. He says he once thought it was desirable, but realized that a pluralism of “ways of knowing” is extremely valuable. Horgan’s argument for pluralism comes from his view that it brings to bear more “ways of knowing” on unsolved questions. But his claim here is weak:

But increasingly, I see pluralism as a valuable, even necessary counterweight to our yearning for certitude. Pluralism is especially important when it comes to our ideas about who we are, can be and should be. If we settle on a single self-conception, we risk limiting our freedom to reinvent ourselves, to discover new ways to flourish.

Wilson acknowledges that consilience is a reductionistic enterprise, which will eliminate many ways of seeing the world. Consider how he treats mystical visions, in which we seem to glimpse truths normally hidden behind the surface of things. To my mind, these experiences rub our faces in the unutterable weirdness of existence, which transcends all our knowledge and forms of expression. As William James says in The Varieties of Religious Experience, mystical experiences should “forbid a premature closing of our accounts with reality.”

. . . Wilson is a gracious, courtly man in person as well on the page. But his consilience project stems from excessive faith in science, or scientism. (Both Wilson and Pinker embrace the term scientism, and they no doubt think that the phrase “excessive faith in science” is oxymoronic.) Given the failure to achieve consilience within physics and biology—not to mention the replication crisis and other problems—scientists should stop indulging in fantasies about conquering all human culture and attaining something akin to omniscience. Scientists, in short, should be more humble.

And that’s it. (The relevance of the “replication” crisis is obscure, and at any rate isn’t ubiquitous.) It’s all about the “other ways of knowing”. Horgan has a long digression about a shaman’s drug-induced vision of snakes, which, in fact, Wilson says could be genetically ingrained in our psyche. Further, we may learn how drugs like ayahuasca unleash our neurons to produce these visions of evolution-installed fears. A shaman’s vision is not immune to the tools of science.

At any rate, look at Horgan’s last sentence above: “Scientists, in short, should be more humble.”  Where have you heard that before? That’s right—from theologians. Although I believe Horgan is a nonbeliever, here he’s being soft on belief, implying, as he did in the title, that religion has something to say about the nature of truth and scientists should give theologians a break. Well, the nature of religion may tell us why it exists and makes certain claims, but that involves a scientific analysis of religion—an analysis Horgan spurns. You know who needs to be humble? The religionists, because they harbor far less doubt than do scientists!

As Horgan says:

Wilson needn’t have worried. Scientific omniscience looks less likely than ever, and humans are far too diverse, creative and contrary to settle for a single worldview of any kind. Inspired by mysticism and the arts, as well as by science, we will keep arguing about who we are and reinventing ourselves forever.

Well, there’s nothing wrong with much of that: worldviews include subjective issues from outside science, and of course we’ll keep on with these futile arguments about “who we are” (arguments, by the way, that might be partly settled by evolutionary biology and evolutionary psychology!). But this is not the point. The point Horgan makes is that there are other ways of knowing what is true about the world beyond science, and science should stop sticking its damn nose into the tent of the humanities. But this is a straw man. Almost nobody claims that literature, music, and art will or should be completely subsumed by science (though they are, at bottom, consistent with it), but on the other hand Pinker is right in claiming that we should not tell scientists to stop impinging on the humanities.

I’ll end with Pinker’s closing of his lovely New Republic article, in which he answers critics who say that the invasion of humanities by scientific practices is “naive and simplistic”:

And the critics should be careful with the adjectives. If anything is naïve and simplistic, it is the conviction that the legacy silos of academia should be fortified and that we should be forever content with current ways of making sense of the world. Surely our conceptions of politics, culture, and morality have much to learn from our best understanding of the physical universe and of our makeup as a species.

Sometimes when I read Horgan, and see his endless criticisms about the limits of science, his concentration on scientific disagreements and ignoring genuine consiliences, and his claim that science is but one of many “ways of knowing”, I wonder if the man—despite being a teacher of science writing—really likes science.

h/t: Hos

Carl Zimmer on governments ignoring and abusing science

February 11, 2021 • 9:15 am

by Greg Mayer

[Addendum— I’ve only just realized (1005 h) that Jerry posted on this same piece by Carl Zimmer back in 2017. Great minds think alike! But the relevance to today is, I think, even more striking.]

A few days ago I happened to run across an old blog post by the eminent science writer Carl Zimmer, in which he recounts the Lysenko affair and the lessons to be learned from it. Posted in 2017, the lessons he identifies are eerily prescient in light of the U.S. government’s (i.e., Trump’s) response to the coronavirus pandemic:

— A government decided that an important area of research, one that the worldwide scientific community had been working on for decades, was wrong. Instead, they embraced weak evidence to the contrary.

— It ignored its own best scientists and its scientific academies.

— It glamorized someone who opposed that mainstream research based on weak research, turning his meager track record into a virtue.

— It forced scientists to either be political allies or opponents.

— It personally condemned scientists who supported the worldwide consensus and spoke out against the government’s agenda, casting them as bad people hell-bent on harming the nation.

— The damage to the scientific community rippled far, and lasted for years. It showed hostility to scientists from other countries, isolating them from international partnerships. It also created an atmosphere of fear that led to self-censorship.

— And by turning away from the best science, the Trump administration did harm to its country.

It all seems very relevant, and his third item practically screams, “Scott Atlas!” He wrote the piece in 2017 in the context of climate change policy, but the relevance to today must have been evident to Carl, too; the reason I came across the 4-year old post is because he had moved it to near the top of his blog, where I came across it while looking for other things on his website.

The blog post is based on a talk Zimmer gave at a conference on “Science, Journalism, and Democracy: Grappling With A New Reality” at Rockefeller University on how science journalism can deal with the “confusing swirl of reality, misinformation, and so-called fake news” that is “[t]he current media landscape”. Carl’s talk can be seen on YouTube (below).

Shabby science reporting in the New York Times

January 10, 2021 • 11:00 am

I’ve noticed lately that the quality of science writing in newspapers has declined, even in The New York Times, which used to have some really good writing, especially by Carl Zimmer, who doesn’t seem to appear in its pages so often.

_____________________

CORRECTION:  Zimmer is still writing prolifically in the NYT, but covering a beat—vaccination—that I’d missed, (mis)leading me to believe that he was engaged in activities other than writing for the NYT. He’s asked me to correct this in a comment below, so I’ll just add his comment here:

If you had bothered to look at my author page at the Times, you’d see that I have been busier than ever there as I help cover the science of the pandemic. Over the past 10 months, I’ve written 93 stories about Covid-19, which comes to about two articles a week. Please correct your post. You are misleading your readers about my work. https://www.nytimes.com/by/carl-zimmer

I guess he was peeved. The misstatement was my fault, of course, and I’ve fixed it, but I have to say that this is a rather splenetic reply from someone whose work I’ve always praised.

_____________________

Rather, in place of long-form biology and physics, a variety of people now write for the Times‘s biological “Trilobite” column, and seem to take a more gee-whiz approach to science, producing short columns that are also short on information.

Part of the problem may be that many of these columns are written by freelancers who haven’t spent most of their writing career dealing with biology. My general impression is that the NYT is starting to reduce its coverage of science. That would be a damn shame since it was the only major paper to have a full science section (I don’t get the paper issues any longer, so I don’t know if they still have the Tuesday science section I’d read first).

The sloppy writing seems to be the case with this week’s column, a column reporting a new genome-sequencing study in Nature of monotremes: the platypus and the echidna (“spiny anteater”). I have only scanned the paper briefly, and will read it thoroughly, but on reading the NYT’s short summary I spotted two errors—not outright misstatements of fact, but statements that are incomplete descriptions of the truth, and where an extra word or two would have made the column not only more accurate, but more interesting.

Here’s the article (click on the screenshot):

 

Maybe I’m being petulant, but here are two quasi-misstatements in the piece. First, this one (emphases are mine):

When the British zoologist George Shaw first encountered a platypus specimen in 1799, he was so befuddled that he checked for stitches, thinking someone might be trying to trick him with a Frankencreature. It’s hard to blame him: What other animal has a rubbery bill, ankle spikes full of venom, luxurious fur that glows under black light and a tendency to lay eggs?

The facts: Only the males have ankle spurs, and of course only the males have venom. (This probably shows that the trait is used not for defense against predators, but for male-male competition during mating.) Females have no venom and have rudimentary spur nubs that drop off before maturing. Of course, females have the genes for producing ankle spurs and venom, as those genes don’t know which sex they’ll wind up in—just like human males have genes for vaginas and breasts and human females carry genes for penises. But the sex-development pathway prevents the expression of venom and spurs in females, just as it prevented me from developing a vagina.

The sex-limitation of the spurs isn’t mentioned in the Nature piece, but every biologist who knows their platypuses also knows that only the males have venom spurs. And, by the way, the echidna has some genes that used to produce venom, but they’re non-expressed “pseudogenes” that have become inactivated. That shows that the ancestral monotreme was almost certainly venomous (this isn’t mentioned in the NYT piece, either).

About those egg-yolk genes:

For instance, many birds and insects have multiple copies of a gene called vitellogenin, which is involved in the production of egg yolks.

Most mammals don’t have the vitellogenin gene, said Dr. Zhang. But the new genomes reveal that platypuses and echidnas have one copy of it, helping to explain their anomalous egg-laying — and suggesting that this gene (and perhaps the reproductive strategy itself) may have been something the rest of us lost, rather than an innovation of the monotremes. 

Well, yes, mammals do have the vitellogenin gene. In fact, our own species has three of them, but, as in other mammals they’re pseudogenes—genes that are there in the genome but are broken and not expressed. Humans and other placental mammals don’t require egg yolk because we’re nourished through the placenta, not yolks in shells. The platypus has two vitellogenin genes (described in the Nature paper as “genes”, so the statement that platypuses and echnidas have “one copy” is misleading)—they’re just not “functional” genes.

Now you may say this is quibbling, but it’s not. First of all, the statement that playtpuses have one copy of the egg yolk gene is wrong. They have two, but one doesn’t function. More important, the statement that there are nonfunctional yolk genes in all mammals says something powerful about evolution, something that I discuss in my book Why Evolution is True.  Those “vestigial” and nonfunctional genes are evolutionary remnants of our ancestors who did produce egg yolk. Why else would they be there in our genome, doing nothing? Chickens, who of course evolved from reptiles, as we did, have all three vitellogenin genes in working order.

Another error, then, is the statement “suggesting that this genes. . . may have been something the rest of us lost.” No, we didn’t lose it; it’s still there in our genomes. And there’s no “suggestion” about it: it’s sitting there in our DNA, has been sequenced, and has been shown to be nonfunctional. Finally, we KNOW that this gene is NOT an innovation of the monotremes, and have known that for a long time (e.g., see here). It was inherited from their reptilian ancestors.

This isn’t flat out erroneous science reporting, but it’s incomplete science reporting—the summary of a paper phoned in to the NYT. (I also find the Time’s summary curiously devoid of what’s really new in the paper; at least half of it reprises what we already knew.) More important, the reporter missed a good chance to give some powerful evidence for evolution, both in ourselves and in monotremes, whose genomes harbor some dead egg-yolk genes that are active in our avian and reptilian relatives. And yes, those echidnas have dead genes for venom.

h/t: Gregory

Why we shouldn’t be worried (yet) about the new strain of Covid-19

December 23, 2020 • 10:30 am

Reader Jim Batterson sent me this 25-minute video with the comment:

I know you prefer to read rather than watch a video, but I wanted to make you aware of a 24-minute YouTube video from Vince Racaniello, a virologist at Columbia University who leads a cast of virology geezers and one younger immunologist in a weekly zoomcast production of “This Week in Virology”.  He did this standalone presentation to rant a bit on the way that this latest variant in the UK is being hyped to the world. I think he does a pretty good job for any viewer who has had a biology course in the past five or so years.
The point is that viruses are mutating constantly, and yet none the coronavirus mutations have yielded a new “strain”—that is, a mutant type that has new biological properties. The property touted for the new virus is its purportedly increased “spreadability”, but, as Racaniello notes repeatedly, that simply hasn’t been demonstrated. As he shows, you can get some variants spreading more widely than others simply by accident: the variant may not have any effect on spreadability itself but can increase in frequency as a byproduct of “superspreader events”—the main way the virus spreads—because only a small subset of all viruses get passed to other humans.

Racaniello then shows the changes in the new mutant “strain”, noting that only one of the several mutants in the spike protein is even a candidate for a change in spreadability, but there is not an iota of evidence that any of those mutations actually make the strain more spreadable.  Nevertheless, all of us are inundated with media scare stories about this “superspreader virus”.

Racaniello’s point is that though there are epidemiological data showing a correlation between the presence of the mutant in some areas and a greater spread of the virus, that’s just  a correlation without evidence of causation. And there could be several causes, including accidents. To show this mutant is a “super virus”, you simply have to do lab experiments; epidemiological correlations show nothing.

Racaniello doesn’t rule out that this mutant spreads faster than its ancestors, but he’s not convinced it is, and doesn’t think that we yet have a reason to be concerned. In fact, he suggests that the changes in the new strain may make it less spreadable. Let me add that Racaniello knows what he’s talking about, as he’s co-author on a well known textbook of virology.

Like all good scientists, Racaniello isn’t declaring that this virus is “neutral” compared to its competitors—he’s simply saying that we don’t have any data suggesting it’s more nefarious. In fact, the same story happened earlier with a different mutant that spread widely, but nothing ever came of that.  We need experimental cell-culture data from the lab on viral shedding, and that doesn’t exist.

His final comment:

“We should move on from the scary headlines, and get ahead with vaccination programs, which are underway—and that is going to be the way we get away from this pandemic.”

Anyway, this is a good and clear mini-lecture, and listening to it should calm you down a bit if the media have gotten you worried.

The intellectual vacuity of New Scientist’s evolution issue: 4. The supposed importance of genetic drift in evolution

September 29, 2020 • 10:45 am

Genetic drift is the random change in frequencies of alleles (forms of a gene, like the A, B, and O alleles of the Landsteiner blood-group gene) due to random assortment of genes during meiosis and the fact that populations are limited in size. It is one of only a handful of evolutionary “forces” that can cause evolution—if you conceive of “evolution,” as many of us do, as “changes in allele frequencies over time” (“allele frequencies” are sometimes called “gene frequencies”). Other forces that can cause evolutionary change are natural selection and meiotic drive.

Genetic drift certainly operates in populations, for it must given that populations are finite and alleles assort randomly when sperm (or pollen) and eggs are formed. The question that evolutionists have been most concerned with is this: “How important is genetic drift in evolution?”  We know that, if populations are sufficiently small, for instance, drift can actually counteract natural selection, leading to high frequencies of maladaptive genes. This is what has happened in small human isolates, such as religious communities like the Amish and Dunkers.  It’s not clear, though, that this has happened with any appreciable frequency in other species.

Drift was once implicated by Sewall Wright, a famous evolutionist, in his well-known “shifting balance theory of evolution“, which maintained that drift was essential in producing many adaptations in nature. That theory was once influential, but has now fallen out of favor, and I take credit for some of that (see my collaborative critiques here and here).

Related to this are various theories that see genetic drift and its maladaptive effects as crucial in forming new species (e.g., the “founder-flush” theory of speciation). In my book with Allen Orr, Speciation, we analyze these ideas in chapter 11 and conclude that drift has been of minimal importance in speciation compared to natural selection.

Finally, genetic drift was an important part of Steve Gould’s theory of punctuated equilibrium, for it was the force that allowed isolated populations to undergo random phenotypic change, tumbling them from one face of “Galton’s polyhedron” to another. This was one of the explanations for why change in the fossil record was jerky. Well, the fossil record may well be punctuated, but Gould’s theoretical explanation was pretty soundly dismantled by population geneticists, including several of my Chicago colleagues (see this important critique).

While one can cite examples of genetic drift operating in nature, like the expected loss of genetic variation in very small populations, in my view it hasn’t been of much importance in speciation, morphological and physiological evolution, or in facilitating adaptive evolution by pushing populations through “adaptive valleys.” Even the view that it has made species vulnerable to extinction by reducing the pool of genetic variation needed to adapt to environmental change has been exaggerated. I know of no extinctions caused by genetic drift, though I haven’t checked on the cheetah example lately (they were said to be highly inbred because of small populations, but I’m not sure that this is what makes them vulnerable to extinction). In fact, for conservation purposes, I believe the importance of loss of genetic variation through drift has been much less than the importance of reduced population size itself that makes populations vulnerable to extinction because individuals can’t find mates or overgraze their environment, or simply because if you’re a small population, random fluctuations in numbers are more likely to make you go extinct. This is demographic rather than genetically based extinction.

But drift has been important in molecular evolution, causing a turnover of gene variants over long periods of time. If those variants are “neutral”—that is, they are equivalent in their response to natural selection—then they will turn over at a roughly linear rate with time, and the changes can be used as a sort of “molecular clock” to estimate divergence times between species. This kind of molecular divergence has been used to construct family trees of species as well as to estimate the times when species diverged. This is a fairly new usage, for such molecular tools and estimates have been available only since the 1960s.

On to the New Scientist bit about drift in its latest issue, a special on evolution.

The 13-point section about how new findings will expand our understanding of evolution includes section 9 about drift, called “Survival of the luckiest.” It first recounts, accurately, how drift operates, but then exaggerates its importance by mentioning two studies of urban populations of animals, populations that in principle should show more drift than wild populations because populations living in cities are small and fragmented. The section says nothing about any of the things I just told you, which is what evolutionists have really been concerned about with respect to genetic drift.

Here’s the entirety of how New Scientist says drift is revising our view of evolution (the author of this section is Colin Barass):

Biologists have known about genetic drift for a century, but in recent years they realised that it could be especially common in urban settings where roads and buildings tend to isolate organisms into small populations. A 2016 study of the white-footed mouse, Peromyscus leucopus, in New York supported the idea. Jason Munshi-South at Fordham University, New York, and his colleagues discovered that urban populations have lost as much as half of their genetic diversity compared with rural populations.

Last year, Lindsay Miles at the University of Toronto Mississauga, Canada, and her colleagues published a review of evidence from about 160 studies of evolution in urban environments, in organisms ranging from mammals and birds to insects and plants. Almost two-thirds of the studies reported reduced genetic diversity compared with rural counterparts, leading the researchers to conclude that genetic drift must have played a role. “Genetic drift can definitely be a significant driver of evolution,” says Miles.

These findings have big implications, because populations lose their ability to adapt and thrive if they lack genetic diversity for natural selection to work on. Of course, genetic drift isn’t confined to urban settings, but given how much urbanisation is expected to grow, the extra threat it poses to wildlife is concerning. It highlights the need to create green corridors so that animals and plants don’t become isolated into ever-smaller populations.

I don’t think those findings do have “big implications”, because the important of reduced genetic variation in urban environments is unclear, particularly when the genes assayed have no clear connection with natural selection. And the import of losing half of your genetic diversity is also questionable: after all, a single fertilize female contains half of the “heritability” of an entire population. Everything rests on whether evolution by natural selection depends on very low-frequency genetic variants, present only in big populations, and we don’t really know if this is the case.  And the above study is in white-footed mice, only one species among millions, and only for populations in urban environments. That’s not to denigrate it, just to point out that its relevance to nonurban nature is unclear and its relevance to evolution is equally unclear.

You can read the Miles et al. study at the link (here), and having read it, I wasn’t impressed, since the authors themselves don’t come to nearly as strong a conclusion as does New Scientist. Here’s from the paper’s conclusions:

Although our review of the literature with quantitative analyses of published urban population genetic data sets demonstrates trends towards increased genetic drift and reduced gene flow, these patterns were not significant and were not universally seen across taxa. In fact, over a third of published studies show no negative effects of urbanization on genetic diversity and differentiation, including studies supporting urban facilitation models at a much higher proportion than previously realized. How populations and species respond to urbanization clearly depends on the natural history of the taxa investigated, the number and location of cities being sampled, and the molecular techniques used to characterize population genetic structure.

In other words, although two-thirds of the studies showed reduced variation or increased inter-population differentiation, these patterns were not significantly different from non-urban populations.  And if those differences were not significant, you needn’t start speculating about genetic drift. The authors conclude simply that different species show different genetic patterns when living in urban environments.

Miles’s statement that “genetic drift can definitely be a significant driver of evolution” is ambiguous, because she doesn’t say what she means by “significant” or by “evolution” (is she talking just about patterns of molecular evolution, like genetic diversity, or other types of evolution?)

New Scientist, in other words, fails to make the case that genetic drift has changed our view of how evolution operates, much less that it’s modified the modern synthetic theory of evolution. We already knew that small populations lose genetic variation because of genetic drift, and that’s been standard lore for decades. The real novel claims about drift—that it facilitates adaptive evolution, that it’s an important driver of speciation, and that it explains punctuated patterns in the fossil record—have disappeared because of the absence of both data and theory supporting those claims.

I am weary of going after New Scientist, and this may be my last critique of that issue. But be aware that virtually every one of the other nine points is exaggerated as well. Move along folks—nothing to see here.

The intellectual vacuity of New Scientist’s evolution issue: 3. The supposed importance of epigenetics in evolution

September 28, 2020 • 11:00 am

I’ll continue on with New Scientist‘s 13-section claim that the modern theory of evolution needs a reboot (see previous posts here and here), though I don’t know how much longer I can stand their uninformed palaver written by incurious journalists. Today we’l take up section 4: “There is more to inheritance than just genes”, which emphasizes the importance of epigenetic changes in evolution. The article appeared in this special issue of the rag magazine:

As I’ve written many times before, epigenetic changes are not good candidates for an inherited basis for evolutionary change, mainly because the vast majority of epigenetic modifications of DNA—usually via methylating DNA bases—disappear within one generation, as the DNA effaces the epigenetic markers during sexual reproduction. A few epigenetically produced traits can persist for a few generations, but that’s not a good basis for permanent evolutionary change, and certainly not a general explanation of adaptation. In fact, we know the genetic basis of adaptation in many cases, and it’s nearly 100% due to changes in the DNA sequence, not to epigenetic modification of the DNA sequence. (Lactose tolerance in pastoral human populations is one example.)

To support the claim that epigenetics is important in evolution, author Carrie Arnold mentions the shopworn example of pregnant Dutch women, deprived of food by the Nazis, giving birth to children who became unhealthy adults, with high levels of obesity, diabetes, and so on. Besides this not being an example of adaptive evolutionary change, it’s still not certain that the changes in the kids were produced by epigenetic modification of the DNA. The pregnant mothers were the ones who passed on the traits, and the fetuses could have been affected by the mother’s physiology, not by changes in her DNA. (It’s telling that the children of undernourished fathers alone didn’t show the changes.) There may have been some epigenetic changes, or maternal effects, in that the grandchildren seem to be affected too, but that’s where the train of changes comes to a stop.

Then Arnold mentions an experiment with which I wasn’t familiar, but supposedly demonstrated epigenetic changes that persisted for many generation—25, to be precise:

Subsequent studies in plants and animals suggest that epigenetic inheritance is more common than anyone had expected. What’s more, compared with genetic inheritance, it has some big advantages. Environments can change rapidly and dramatically, but genetic mutations are random, so often require generations to take hold. Epigenetic marks, by contrast, are created in minutes or hours. And because they result from environmental change, they are often adaptive, boosting the survival of subsequent generations.

Take the pea aphid. It is capable of both sexual and asexual reproduction, and comes in two varieties: winged and wingless. When scientists exposed a group of genetically identical pea aphids to ladybirds, the proportion of winged aphids increased from a quarter to a half. This adaptation, which helped them escape the predatory ladybirds, persisted for 25 generations. The aphid DNA didn’t mutate, the only change was epigenetic.

So I “took” the pea aphid, reading the paper that supposedly showed persistent epigenetic variation over 25 generations. Click on the screenshot below to get the paper (from the journal Heredity):

It’s a long and somewhat tedious read, but there are two points to make.

1.) The plastic response to the predator—growing wings (an adaptation that’s genetically encoded)—did not persist for 25 generations on its own. In fact, if you remove the predator, the stimulus for growing wings, the population becomes wingless again within a single generation. So we do not have a case of epigenetic markers persisting on their own for many generations, much less two generations.

2.) There is no evidence that the production of winged forms is caused by epigenetic modification of the DNA, and the authors admit this.

In other words, everything that Arnold says or implies about this experiment is misguided.

The experiment was started with a single clonal population of aphids, that is, parthenogenetically produced individuals from a single female. The population thus lacked genetic variation except for new mutations that could have occurred after the experiment started. One part of the population was the experimental section, exposed to predatory ladybirds. That one produced winged individuals immediately at a proportion of about 50% of the population. This proportion remained stable for 27 generations. Producing wings in the presence of predators is adaptive, of course, as you can flee them, and not producing wings when the predator is absent is also presumably adaptive, as there’s a metabolic and reproductive cost of producing wings you don’t use. Thus the switching between wings and winglessness is an adaptive plasticity, and is presumably coded (not epigenetically!) in the aphids’ DNA.

The control line, lacking ladybirds, stayed at about 25% winged individuals for 25 generations.

At three intervals, the authors took aphids from the experimental line and put them in an environment without predators. If the epigenetic markers persisted in the absence of the predator, and through meiosis, you’d expect these “reversion” lines to still show a higher frequency of winged individuals. They didn’t. They basically reverted to the control level of winglessness within a single generation, presumably because the switch for growing wings (ladybirds) wasn’t there.

So what we see is that to get the adaptive trait, wings, to persist, you need the stimulus to be there constantly. The presence of the predator somehow induces the aphids to grow wings, just as the presence of fish in a pond causes some rotifers to grow fish-repelling spines. And when you take the predator away, the aphids switch back to the wingless form. Here’s a plot showing the frequency of wings in the experimental population (red line), in the control predator-less population,  (black line) and the reverted population in which predators were removed (blue line):

(From paper): Proportions of winged adult aphids (mean ± SE) across generations of the experimental evolution with predators (in red), without predators (in black) and in branch lines for which predators were removed after generations 3, 13, and 22 (in blue). “*” or “NS” denote the significance (P < 0.05, or P > 0.05, respectively) of differences between controls (without predator, black dots) and branch lines after predator removal (blue dots). The vertical black dotted line indicates the time of initial predator introduction in the treatment lines

Unlike the Dutch situation, or others that report persistence of environmentally induced changes for a few generations, in this case the induced change, the presence of wings, reverts to control levels within a generation. We do not see the kind of trait persistence here that epigenetics advocates tout as important in making the phenomenon important in evolution.

And indeed, we don’t even know if the switch from winglessness to wings is an epigenetic change, as opposed to some chemical change that occurs in the aphids when they sense the presence of predators that turns on “wing-making genes”. (That’s how it works in rotifers: when a fish eats a rotifer, it releases chemicals into the water that induce the other rotifers to produce spines. That’s not an epigenetic modification of the DNA.) If you think that any environmental change is “epigenetic”, then yes, this one could be, but that’s not the way the cool kids construe “epigenetic” these days. It’s taken to mean “alterations of the DNA structure”, which is what journalist Arnold means by mentioning “epigenetic marks [that] are created in minutes or hours.”

There’s one twist in the experiment as well: in the lines subject to predators, the plasticity of individuals became reduced; that is, they were less likely to respond to changes in predators with changes in wings. The paper’s authors impute this to epigenetics, but it could well be due to selection occurring on mutations that arose in the predator lines. That is, since predation was omnipresent, there was less selection pressure to maintain a “switching system,” and your plasticity could erode. To maintain a switch between wings and winglessness, the lineage has to experience periodic bouts of predation alternated with bouts of no predation. So the loss of plasticity itself also says nothing about whether epigenetic markers were accumulating in the DNA.

And, at the end, the paper’s authors admit that we don’t know whether this switch is due to epigenetic modification of the DNA, as the New Scientists reporter claims.  From the Heredity paper:

We can thus tentatively attribute the decline in plasticity observed in lines that were exposed to predators for many generations to the action of some non-genetically transmitted information (i.e. information not encoded in the DNA sequence). The hypothesis that observed phenotypic changes were caused by reversible epigenetic changes is thereby more likely but in order to be confirmed, this hypothesis would require to be backed up by molecular analyses.

I can find nothing in this paper that even suggests that epigenetic changes were happening to the aphids’ DNA, much less any kind of inherited changes that persist for more than one generation. This paper is certainly not an example of what New Scientist says it is.

This is the third buzzwordy phenomenon tendered by New Scientist as an exciting new finding that can modify the Modern Evolutionary Synthesis. And it’s the third one that is wrong. I am growing weary, and will see if I need to persist in debunking further claims in the article. Rest assured, though, that most of them are even weaker than the three I’ve discussed. But what does New Scientist care? They want clicks, not accuracy, and I fear that I’m wasting my time. I’d rather write about the new paper on consciousness in crows.

At least the New Scientist article admits that epigenetics is controversial:

The extent of epigenetic inheritance is contested. Some sceptics point out that, during mammalian reproduction, the creation of sperm and egg cells involves erasing epigenetic markers. Others argue that epigenetic transmission across generations is extremely widespread and useful. In plants, for example, it can account for differences in fruit size, flowering time and many other survival-boosting traits.

Yes, but it’s because the transmission across generations lasts about two or three generations at most that is why epigenetic modification by itself is not a good candidate for the “replicator” that produces adaptive evolution.

Lunchtime!