Category: human biology

Mayan human sacrifices from ancient bones show genetic relatedness among those killed (and other stuff)

June 17, 2024 • 9:30 am

This new paper in Nature gives a rare picture of human sacrifice among ancient Mayans from the Yucatán peninsula in Mexico.  Paleoanthropologists had found remains before, mostly children, preserved by being tossed in sacred cenotes (wells), but this group of 64 ancient individuals was not only collected, but their DNA was analyzed from the ear bones, giving surprising results about genetic relatedness.

As with the Aztecs, human sacrifice was a fixture of ancient Mayan society, though the people killed (in this case, children) were probably captives rather than residents of the place where the killers lived. Sacrifice could have occurred via either decapitation, extraction of the heart from living individuals, or killing with arrows.

Click below to read the piece, or find the pdf here.  

The figure below shows where the remains were found: in a chultún (an underground cistern) next to an airport runway near the ancient Mayan city of Chichén Itzá (now a World Heritage Site), which flourished between about 600 and 1200 A.D. This map gives the location:

(From the paper) a, Location of the Maya region in the Americas. b, Geographical locations of Chichén Itzá and Tixcacaltuyub in the Yucatan Peninsula. c, Stratigraphy for the chultún and the adjacent cave in which the burial was found (adapted from ref. 4). d, Location of the chultún within the archaeological site of Chichén Itzá and its relation to El Castillo (adapted from ref. 10). Modern roads are marked in light grey; the chultún abuts an airport runway.

They found the bones of 64 individuals, carbon-dated as being from the 7th to the 12 centuries AD. How did they know how many individuals were represented in their sample? Because they recovered 64 left petrous parts, the bit of the skull’s temporal bone that surrounds the inner ear (this bone, sequestered away from the outside of the skull, is often used to extract ancient DNA).  64 left petrous bones means 64 individuals.

First, every one of the individuals was a male between 3 and 6 years old, showing that the Mayans preferred to sacrifice young boys. Why? It’s not clear, but there’s speculation that sacrifices helped local maize crops flourish (the method of sacrifice wasn’t specified in the paper).  However, other sacrificed individuals recovered, as in the famous sacred cenote, have been mixtures of males and females, but also overrepresented with children. The authors don’t speculate why, in this location, only boys were killed.

The ancestry of the sacrificed individuals was compared among each other, as well as to 68 individuals of Mayan descent living the nearby town of Tixcacaltuyub. One surprising finding was that those sacrificed included two pairs of identical (monozygotic) twins (easily seen in DNA, which is identical among two different earbones).  The authors note that twins held a special position in Mayan mythology.  But, as the plot of “pairwise mismatch rates” shows below), 11 pair of individuals were “close relatives”, represented by the hollow diamonds (the twins, with a mismatch rate of zero, are the two pairs of twins.  The authors speculate (see below) that the individuals came from a single big event of mass killing.

The paper doesn’t say how “close” the “close relatives were”, or whether they were contemporaneous, like brothers, but given the age of the individuals, it seems likely that the related pair members came from the same family.

(From paper): e, Genetic pairwise mismatch rate (PMR) for child pairs in the chultún identifies 11 close relative pairs (hollow diamonds), including two pairs of monozygotic twins (highlighted in grey). A low overall PMR for unrelated individuals (black triangles) confirms low genetic diversity in the population; only pairs with PMR < 0.20 are visualized in the plot. See Supplementary Fig. 2 for individual annotations.

The comparison of the DNA of the sacrificed children with that of living people in Tixcacaltuyub, as in the principal-component cluster graph below, showed that the sacrificed individuals )”YCH”, dark purple stars) fell into a cluster of Native Americans, other Mayan individuals, people from Belize, and individuals from the nearby town (“TIX”, light blue stars), and were considerably different from individuals in Africa, Asia, and Oceania, as expected. (This shows diagnostic genetic differences between geographic groups, demonstrating that the idea of “races”—defined as “diagnostically genetically differentiated populations”—is not purely a social construct, but contains biological information.)  However, the ancient sacrificed individuals, which also had a dollop of genes from the Caribbean, didn’t particularly cluster with the present day Mayans living nearby, who had their own admixture of genes from Africa and Europe, perhaps reflecting turnover of populations over time. In the sixteenth century there was a big poulation bottleneck, perhaps due to diseases introduced by Europeans. In fact, this bottleneck reduced the population of what is now Mexico by 90%!)

(From paper): (From paper): a, PCA showing ancient Chichén Itzá (YCH) individuals and present-day Tixcacaltuyub (TIX) in a worldwide PCA plot.

One other bit of information. We are able, looking at contemporary DNA sequences of a population, to judge whether natural selection is acting on genes or groups of genes. If variable genes such as the HLA (“human leukocyte antigen”) genes involved in immune response show coordinated variation (that is, variant “A” of one gene tends to co-occur with variant “B” of another gene in individuals), this gives evidence that selection is acting on groups of genes—in this case genes affecting immunity. The authors identified several HLA variants that look like they were subject to selection, and also tested some by making copies of sequences of some HLA variants and seeing how strongly they bound to proteins derived from Salmonella bacteria (strong binding means that the HLA proteins were reacting and presumably neutralizing the bacterial proteins). The authors suggest that the selection acting to promote the rise in frequency of some HLA variants was due to typhoid or paratyphoid-like infections.

The upshot:  Although the data from HLA genes does indicate that there was selection for immunity in both ancient and historic times, what I find most interesting is that the sacrifice involved children, all male children, and many were close relatives. This, at least, gives us a pretty strong sociological picture of one aspect of ancient Mayan culture. To quote the authors,

In comparing the subadults in the chultún to other ancient and present-day populations in the Maya region, we find evidence of long-term genetic continuity, which also suggests that the sacrificed children and sibling pairs at Chichén Itzá were obtained from nearby ancient Maya communities. Among present-day individuals at TIX, we detect evidence of European and African admixture since the Contact period.

and

Overall, 25% of the children had a close relative within the assemblage, suggesting that the sacrificed children may have been specifically selected for their close biological kinship. Moreover, this may underestimate the true number of relatives present in chultún as only 64 of the estimated 106 individuals in the chultún had a preserved petrous portion of the left temporal bone available for analysis. The further finding that the closely related children in each set seem to have consumed a similar diet and died at a similar age suggests that they have been sacrificed during the same ritual event as a pair or twin sacrifice.

and, finally,

The discovery of two sets of identical twins, as well as other close relatives, in a ritual mass burial of male children suggests that young boys may have been selected for sacrifice because of their biological kinship and the importance of twins in Maya mythology. We show that, at a genome-wide level, the present-day Maya of Tixcacaltuyub exhibit genetic continuity with the ancient Maya who once inhabited Chichén Itzá and we demonstrate through several lines of evidence the involvement of the HLA region in a pathogen-driven selection event(s) probably caused by infectious diseases brought into the Americas by Europeans during the colonial period.

The interest of the Mayans in identical twins reminds me of Josef Mengele in Auschwitz, who also took a particular interest in twins, but in his case he did gruesome experiments on them before killing them.

New paper doubts estimates of how often women hunted in hunter-gatherer societies

March 4, 2024 • 11:45 am

Twitter is good for some stuff, and the best are 1.) cat and duck pictures and 2.) finding out about new science papers, often before they’re published.  Remember the conflict last year about the frequency of women hunting in hunter-gatherer societies (see my posts here). The original paper in PLoS One by Anderson et al. claimed that not only did women engage in hunting in these societies more often than we thought (79% of a sample of such societies showed women participated in hunting), but they also hunted big game more often than we thought. The paper was meant to dispel “The myth of man the hunter” (part of its title) and was clearly meant to promulgate some kind of sex equity in hunting, though a separation of gender roles doesn’t demean women.

The paper was criticized a lot for using biased data (see the set of links above), and the bias, it seemed, either intentionally or fortuitously dispelled what was seen as a misogynistic view: men hunted and women stayed home to grow food, mend things, and take care of the children. It was certainly treated in the popular literature as a blow to both misogyny and the view that sexes had “roles” consistent across societies.

Then I saw this tweet by Alexander, who does cognitive and behavioral neuroscience, and it pointed to a not-yet-published paper on BiorΧiv whose claims, when you read it blow Anderson et al. out of the water.  Now remember, it isn’t yet peer-reviewed, but its accusations—there are 15 authors—are devastating. If it’s true, Anderson et al. are guilty of incredibly sloppy scholarship.  And also perhaps ideologically-biased scholarship, since every error or miscoding they used biased the results in favor or women hunting more frequently or taking larger game.

First, the tweet.

Click below to see the pdf of the paper:

Venkataraman et al. find that the paper commits every error that it was possible to make in the paper: leaving out important papers, including irrelevant papers, using duplicate papers, mis-coding their societies, getting the wrong values for “big” versus “small” game, and many others.

Rather than go through the mistakes, I’m just going to show you the last three paragraphs of Venkataraman et al., which summarize the errors they found in Anderson et al.  Read it. If they’re even close to being right, PLoS ONE should retract the Anderson et al. paper.

We have outlined several conceptual and methodological concerns with Anderson et al.’s (2023) analysis. Specifically, Anderson et al.’s (2023) analysis is not reproducible because their sampling criteria are not clear and 35% of the societies in their sample do not come from DPLACE, the database they claim was the source of all the societies in their sample. Moreover, these 35% were not included in their analysis, and authoritative sources on hunting in the societies in the Anderson et al. (2023) sample were not consulted. Additionally, there are at least 18 societies in D-PLACE with information on hunting that were inexplicably omitted from their analysis, none of which provide evidence for women hunters.

Finally, there were numerous coding errors. Of the 50/63 (79%) societies that Anderson et al. (2023) coded as ones in which women hunt, for example, our re-coding found that women rarely or never hunted in 16/50 (32%); we also found 2 false negatives. Overall, we found evidence in the biased Anderson et al. (2023) data set that in 35/63 (56%) societies, women hunt “Sometimes” or “Frequently”. Moreover, compared to the 17/63 (27%) societies in which women were claimed to hunt big game regularly, our re-coding found that this was true for only 9/63 (14%). A precise estimate of women’s hunting in foraging societies must await a future thorough and unbiased analysis of the ethnographic record (see, e.g., [10]), but it is certainly far less than the Anderson et al. (2023) estimate and is very unlikely to overturn the current view that it is relatively uncommon.

The fundamental issue is that women’s hunting is not a binary phenomenon, and treating it as such, especially with a very low threshold for classifying a society as one in which women hunt, obfuscates gendered divisions of labor within groups. Anthropologists have long recognized that the nature of cooperation in foragers is complex and multi-faceted, and women’s and men’s subsistence activities play important and often complementary roles. Moreover, women’s hunting has been studied for decades, and anthropologists have a good understanding of when and why it occurs. Yet, to focus on hunting at the expense of other critical activities – from gathering and food processing, to water and firewood collection, to the manufacture of clothing, shelters, and tools, to pregnancy, childbirth, nursing, childcare, and healthcare, to education, marriages, rituals, politics, and conflict resolution – is to downplay the complexity, and thereby the importance of women’s roles in the foraging lifeway. To build a more complete picture of the lives of foragers in the present and the past, it serves no one to misrepresent reality. In correcting the misapprehension that women do not hunt, we should not replace one myth with another

The truth is the truth, and, as Venkataraman et al. note repeatedly, the truth does not work to the detriment of women in these societies, who, with a frequent division of labor, work at least as hard as do the men.

h/t: cesar

Gene flow from Neanderthals and Denisovans to “modern” humans, and vice versa

February 26, 2024 • 10:45 am

Today I’ll try to summarize another paper that is difficult for one reason: figuring out how the authors (including Nobel laureate Svante Pääbo) sussed out which genes originated in Neanderthals and Denisovans (both lineages now extinct) and which in their sister lineage: the separate lineage leading to modern humans.  (All three lineages shared a common ancestor.) As we know, the modern human genome contains a lower percentage of genes that originated in Neanderthals, and this is also true for genes that originated in Denisovans (the latter are found more often in modern populations from Oceania, Asia, and in native North Americans).

As for the two extinct lineages, both derived from a single ancestor that, according to the paper below, left Africa for Eurasia about 600,000 years ago. That traveling lineage then split at an uncertain time to give rise to the Neanderthals, who went extinct about 35,000 years ago, and to the Denisovans (known from but a handful of teeth and bones), who went extinct around the same time as did Neanderthals. In the meantime, the lineage that gave rise to us—”modern” humans—stayed in East Africa, leaving for  Eurasia about 60,000 years ago, and some individuals in this group lived near the already-present Neanderthals and Denisovans.

Although human paleobiologists, who love to identify new species, call the Denisovans and Neanderthals species different from modern humans (i.e, different from “Homo sapiens“), I’m stubborn and consider all three groups members of the same biological species. That’s because there’s evidence of gene flow among all the groups: from Neanderthals and Denisovans to modern humans, from modern humans to Neanderthals, and even from Denisovans to Neanderthals and vice versa. Because these archaic genes persist in modern humans, the hybrids between the lineages must have been fertile to allow such backcrossing. Since we have populations who lived at least partly in the same area and produced fertile hybrids, they can be considered biological species, though perhaps biological species in statu nascendi.

Here’s a diagram of the three lineages from the paper whose title is below. The arrows show the direction of gene exchange and some examples of variants transferred by hybridization.

(from paper): Figure 1. Schematic illustration of the history of archaic and modern humans and DNA sequence evolution Derived mutations are highlighted. The occurrence of gene flow between groups is illustrated by arrows. The archaic groups contributed both derived and ancestral variants to modern humans. Note that the extent, number of gene flow events, and when they occurred are only partially known.

You can read the paper below by clicking on the title. The object of the paper is to answer this question:

Which genes were transferred between the lineages, and what effect did they have on the individuals who carried them?

Now, of course, the first question is “How do we know which genes actually originated in one of the three lineages after it split off from the others, and how do we know in which direction that gene was transferred to another lineage.”  This is not an easy question, and I asked my friend Phil Ward, an entomologist and systematist who works at UC Davis. I’ve put his explanation below the fold in case you want to know.

I trust the authors’ determinations of which genes originated where, and which ones were introduced into a given lineage by hybridization; after all, this is Pääbo and his group!  So I’ll just give a list of a few of genes transferred, which way they went, and what they appear to do in modern populations. Let me add two things. First, while it’s easy to find out what a gene does (it can be tested in cell culture or by inserting it in mice), it’s not so easy to determine what effect it has on the phenotype or reproduction of modern humans.

Second, the paper is quite “adaptationist”, with the authors suggesting reasons why a transfer might have been adaptive. (If it was really bad for the carrier, it would have disappeared from the population.) However, very few of the transferred genes are present in very high frequency in modern humans or Neanderthals, and so, if they had a really beneficial effect on reproduction or survival, one would expect that they would be “fixed” (present in every individual) or at least high frequency.  Since that’s not usually the case, the authors float hypotheses that transferred genes are good in some populations but not others. This seems to some extent like post facto rationalization based on a diehard adaptive viewpoint.

On to the genes! Indented sections are mine except for doubly-indented sections, which are excerpts from the paper:

Mutations in the Neanderthal lineage that got in modern humans via hybridization. 

Genes affecting fatty acid and lipid metabolism.  These genes appear to increase the risk of type 2 diabetes, so they’re not good for us.

Genes increasing sensitivity to pain (a sodium-channel gene in the nervous system). This gene appears to have a salubrious effect, because it’s associated with an increase in lifespan (genes that decrease pain sensitivity can allow you to suffer injuries and infections without noticing them, which is why sufferers from Hansen’s disease, lacking pain sensitivity, lose digits and other body parts). But if the gene is so good for us, why is it present in so few of us (0.4% of people in the UK)?

Genes affecting gestation. We received a progesterone receptor-variant that mutated in Neanderthals and that actually increases the frequency of premature births.  Here’s how the authors explain its persistence at high frequencies in both Neanderthals and modern human populations (some of the latter have a frequency of the gene of 20% or higher):

Since [this variant] is associated with an increased risk of premature births in present-day humans, it has been suggested to represent an evolutionary disadvantage to Neandertals, especially in the absence of modern medical care.  However, the Neandertal variants are also associated with an approximately 15% decreased risk for bleeding and miscarriages early in pregnancy as well as with having more siblings.  It is therefore tempting to speculate that it represents an evolutionary trade-off where the Neandertal variants rescues pregnancies that would otherwise have resulted in miscarriages, but the price paid is that some of these pregnancies result in premature births. Notably, two different versions of the Neandertal progesterone receptor gene have been contributed to modern humans, and both have risen in frequency, as shown by an increase in their occurrence in skeletal remains of individuals over the past 10,000 years.  Both Neandertal versions result in higher expression of the progesterone receptor and may thus mediate a higher progesterone effect during pregnancies. This is compatible with the finding that progesterone administration lowers miscarriage rates in women who previously experienced miscarriages  and suggests that increased progesterone effects mediated either by higher hormone levels or by higher receptor levels may protect at-risk pregnancies.

It’s okay to speculate, but perhaps there are other effects of the gene that we don’t know about, and are the bad effects of premature births overcome by the beneficial effects on bleeding and reduced early miscarriage? What we have here is a reflection of the author’s view that the transferred genes must in general have a net positive effect on reproduction, even if they can’t demonstrate it.

Genes affecting the immune system. Many of the genes we got from Neanderthals appear to interact with viruses and are at high frequencies in humans; the authors thus speculate that they spread to ward off infections and still do so in modern populations.  Also, some of the variants have big differences in frequency between populations, which the authors attribute to population-specific infections. Further, some of the variants may cause autoimmune disease (again, we know little about their effects on modern humans, which may be small.)  But they speculate that the existence of so many Neanderthal variants in modern humans strongly suggest that they spread in our lineage via selection for disease resistance.

Mutations in the Denisovan lineage that got in modern humans via hybridization. 

Genes affecting adaptation to high altitude. Here, taken from the paper, is the best example of a gene entering the modern human genome that is likely to have spread by natural selection. This example is pretty well known.

High altitude adaptation

One striking example of Denisovan influence on present-day populations is a 33-kb Denisovan DNA segment on chromosome 2 that occurs at an allele frequency of over 80% among Tibetans, while being absent or very rare in other Asian populations. It encodes EPAS1, a transcription factor induced by hypoxia that is involved in adaptation to low oxygen levels. Denisovans were present on the Tibetan high plateau; some of them may thus have been adapted to life at high altitudes and presumably contributed this genetic predisposition to modern humans as they arrived in the region.

We also received genes involved in producing adaptation to low temperature by “inducing brown fat”: these too seem to have spread in cold-climate populations by natural selection:

Cold adaptation and facial morphology:

Another example of a Denisovan genetic contribution is a 28-kb segment on chromosome 1, carrying the genes WARS and TBX15. It is present in almost 100% of Greenlandic Inuit and several other populations. The Denisovan variants affect the expression of genes that may influence adaptation to low temperatures, possibly by inducing brown fat.

At the end, the authors discuss genes that emerged in modern humans and found their way into Neanderthal lineages, including variants affecting purine (nucleotide) biosynthesis, preventing oxidative stress, gene splicing, and chromosome segregation.  The authors then present a “combinatorial view” of the modern human genome, noting that we’re likely to contain a variety of variants coming from our now-extinct ancestors, but different modern individuals have different combinations. Here’s that view from the paper’s abstract:

We propose that the genetic basis of what constitutes a modern human is best thought of as a combination of genetic features, where perhaps none of them is present in each and every present-day individual.

_________

Reference: Zeberg H, Jakobsson M, Pääbo S. The genetic changes that shaped Neandertals, Denisovans, and modern humans. Cell. 2024 Feb 14:S0092-8674(23)01403-4. doi: 10.1016/j.cell.2023.12.029. Epub ahead of print. PMID: 38367615.

Click “read more” to see the method for determining where a mutation originated and which way it was transferred:

Continue reading “Gene flow from Neanderthals and Denisovans to “modern” humans, and vice versa” →

The biology of quitting: when you should hold ’em and when you should fold ’em

April 20, 2023 • 12:30 pm

Someone called this Big Think piece to my attention because some quotes from me are in it. And they are, but that’s not the important part, which is the evolutionary biology of giving up, and I guess I’m the Expert Evolutionist in this take.  The piece is by Julia Keller, a prolific author and journalist who won a Pulitzer Prize for feature writing in 2004, and this is an excerpt from her new book  Quitting: A Life Strategy: The Myth of Perseverance and How the New Science of Giving Up Can Set You Free. which came out April 18.

Although I had some association with Julia when she wrote for the Chicago Tribune (I think she helped me get a free-speech op-ed published), I don’t remember even speaking to her on this topic, but it must have been quite a while back. At any rate, I certainly want to be set free from my maladaptive compulsions, which include persisting when I should give up, so I’ll be reading her book.

Click on the screenshot to read:

The science involved is largely evolutionary: it pays you to give up when you leave more offspring by quitting than by persisting. Or to couch it more accurately, genes that enable you to assess a situation (consciously or not) and give up at the right point—right before the relative reproductive gain from persisting turns into a relative loss compared to other gene forms affecting quitting—will come to dominate over the “nevertheless she persisted” genes.  Keller engages the reader by drawing at the outset a comparison between Simone Biles stopping her gymnastic performance in the 2021 Tokyo games, and, on the other hand, a honeybee deciding whether or not to sting a potential predator of the nest.

If the bee does sting, she invariably dies (her innards are ripped out with the sting), and can no longer protect the nest. But if that suicidal act drives away a potential predator, copies of the “sting now” gene are saved in all the other nest’s workers, who are her half sisters. (And of course they’re saved in her mother—the queen, the only female who can pass on her genes.) If a worker doesn’t sting, every copy of that gene might be lost if the nest is destroyed, for if the nest goes, so goes the queen, and every gene is lost.  On the other hand, a potential predator might not actually prey on a nest, so why give up your life if it has no result? You have to know when stinging is liable to pay off and when it isn’t.

Inexorably, natural selection will preserve genes that succeed in this reproductive calculus by promoting stinging at the right time and place—or, on the other hand refraining from stinging if it’s liable to have no effect on colony (ergo queen) survival.  And in fact, as you see below, honeybees, while they surely don’t consciously do this calculus, they behave as if they do, and they do it correctly.  Often natural selection favors animals making “decisions” that cannot be conscious, but have been molded by selection to look as if they were conscious. 

As for Simone Biles, well, you can read about her. Her decision was clearly a conscious one, but also bred in us by selection—selection to avoid damaging our bodies, which of course can severely limit our chance to pass on our genes. This is why we usually flee danger when there is nothing to gain by meeting it. (She did have something to gain—gold medals—which is why she’s like the bees.)

Why do young men street race their cars on the street, a dangerous practice? What do they have to gain? Well, risk-taking is particularly prevalent in postpubescent males compared to females, and I bet you can guess why.

I’ll first be a bit self aggrandizing and show how I’m quoted on evolution, and then get to the very cool bee story. It’s a short piece, and you might think of other “quitting vs. non quitting” behaviors of animals that could have evolved. (Hint: one involves cat domestication.)

“Perseverance, in a biological sense, doesn’t make sense unless it’s working.”

That’s Jerry Coyne, emeritus professor at the University of Chicago, one of the top evolutionary biologists of his generation. [JAC: a BIT overstated, but I appreciate it.] I’ve called Coyne to ask him about animals and quitting. I want to know why human beings tend to adhere to the Gospel of Grit—while other creatures on this magnificently diverse earth of ours follow a different strategy. Their lives are marked by purposeful halts, fortuitous side steps, canny retreats, nick‑of‑time recalculations, wily workarounds, and deliberate do‑overs, not to mention loops, pivots, and complete reversals.

Other animals, that is, quit on a regular basis. And they don’t obsess about it, either.

In the wild, Coyne points out, perseverance has no special status. Animals do what they do because it furthers their agenda: to last long enough to reproduce, ensuring the continuation of their genetic material.

We’re animals, too, of course. And despite all the complex wonders that human beings have created—from Audis to algebra, from hot-fudge sundaes to haiku, from suspension bridges to Bridgerton—at bottom our instincts are always goading us toward the same basic, no‑nonsense goal: to stick around so that we can pass along little copies of ourselves. [JAC: note how this is an individual-centric view rather than the correct gene-centric one, but it’s good enough.] It’s axiomatic: the best way to survive is to give up on whatever’s not contributing to survival. To waste as few resources as possible on the ineffective. “Human behavior has been molded to help us obtain a favorable outcome,” Coyne tells me. We go for what works. We’re biased toward results. Yet somewhere between the impulse to follow what strikes us as the most promising path—which means quitting an unpromising path—and the simple act of giving up, something often gets in the way. And that’s the mystery that intrigues me: When quitting is the right thing to do, why don’t we always do it?

Well, who ever said that every aspect of human behavior was molded by natural selection? Please don’t think that I was implying that it was, as we have a cultural veneer on top of the behaviors conditioned by our genes. In this piece Keller doesn’t get to the subject of why we don’t quit when we should. I’m sure that’s in the book.

Now the very cool bee story:

Justin O. Schmidt is a renowned entomologist and author of The Sting of the Wild, a nifty book about a nasty thing: stinging insects. Living creatures, he tells me, echoing Coyne, have two goals, and those goals are rock-bottom rudimentary: “To eat and not be eaten.” If something’s not working, an animal stops doing it—and with a notable absence of fuss or excuse-making. . . .

. . . For a honeybee, the drive to survive carries within it the commitment to make sure there will be more honeybees. And so she defends her colony with reckless abandon. When a honeybee stings a potential predator, she dies, because the sting eviscerates her. (Only the females sting.) Given those odds—a 100 percent mortality rate after stinging—what honeybee in her right mind would make the decision to sting if it didn’t bring some benefit?

That’s why, Schmidt explains to me from his lab in Tucson, sometimes she stands down. When a creature that may pose a threat approaches the colony, the honeybee might very well not sting. She chooses, in effect, to quit—to not take the next step and rush forward to defend the nest, at the cost of her life.

His experiments, the results of which he published in 2020 in Insectes Sociaux, an international scientific journal focusing on social insects such as bees, ants, and wasps, reveal that honeybees make a calculation on the fly, as it were. They decide if a predator is close enough to the colony to be a legitimate threat and, further, if the colony has enough reproductive potential at that point to warrant her ultimate sacrifice. If the moment meets those criteria—genuine peril (check), fertile colony (check)—the honeybees are fierce fighters, happy to perish for the greater good.

But if not… well, no. They don’t engage. “Bees must make life‑or‑death decisions based on risk-benefit evaluations,” Schmidt tells me. Like a gymnast facing a dizzyingly difficult maneuver that could prove to be lethal, they weigh the danger of their next move against what’s at stake, measuring the imminent peril against the chances of success and the potential reward. They calculate odds.

And if the ratio doesn’t make sense, they quit.

That’s a bit oversimplified, for the calculus is not only unconscious (I doubt bees can weigh threats this way), but the decision capability has been molded by competition over evolutionary time between different forms of genes with different propensities to sting or give up. Further, individual worker bees are sterile, and so what’s at stake is the number of gene copies in the nest as a whole—and especially in the queen. The asymmetrical relatedness between the queen, her workers, and their useless drone brothers (produced by unfertilized eggs) makes the calculus especially complicated.

On the other hand, explaining the gene calculus to lay readers is hard, and it might be better to read the seminal work on how this all operates: Dawkins’s The Selfish Gene. 

Here’s Schmidt’s short paper (click to read; if it’s paywalled, ask for a copy). He died just this February.

Readers’ wildlife photos

December 12, 2022 • 8:15 am

Well, this doesn’t count as wildlife, but it does refer to the excretory habits of one species of primate. As contributor Athayde Tonhasca Júnior notes, ” I strongly suspect that this subject has not been approached before in your website. . . ” Indeed!  Apparently these are loo-related photos from his travels.Athayde’s notes are indented, and you can click on the photos to enlarge them.

A visit to the toilet (room), bathroom, restroom, washroom, or lavatory, is an opportunity for reflection and introspection, or to seek refuge, peace and quiet. Indeed, British men allegedly spend seven hours per year in the toilet hiding from their wives and children (according to “research” commissioned by a bathroom furniture company). But the loo – or bog, can, head, john, or latrine – can also be a place of amusement and learning.

A flamingo on duty to check your hand-washing technique in Bologna, Italy.

Unfortunately this educative and lyrical message was removed from a dentistry practice in Perth, UK:

A health warning in Scots, which is a language, a dialect or bad English, depending on who you ask (and their political views). The UK government and the European Union recognise Scots as a minority language, but many linguists place it somewhere on a dialect continuum. To the chagrin of nationalists, Scottish heavyweights Adam Smith and David Hume considered the use of Scots as an indication of poor education.

An emergency cord is great, but what if you want to order a pizza or dry your hair while bombing the bowl? (Hotel in Padua, Italy):

My travelling companion was displeased with the facilities in a Padua cafe. Squat toilets are terrible for the elderly or disabled, but they have a great advantage: you don’t need to touch anything. You learn to appreciate them when you hear the call of nature in the back of beyond. They are also better for your health, supposedly:

A latrine in the Housesteads Roman Fort, Britain, on the northernmost edge of the Roman Empire. Year 200 AC:

Marcus: Salve, Quintus.
Quintus: Ave, Marcus. Are you well? You look a bit green around the gills.
Marcus: Tell me about it. I think that batch of garum from Rome was off.
Quintus: I hear you.
Cornelius: I hear you too, Marcus. Loud and clear! Ha-ha! Say, chaps, wouldn’t you have a spare sponge on you?

A tersorium (a sea sponge on a stick) supposedly used by the Romans to wipe themselves after using the latrine. The sponge may have been washed in a gutter with running water, or in a bucket of water, salt and vinegar. But not everyone agrees with this popular tale (kids love it). According to Gilbert Wiplinger (Austrian Archaeological Institute), the tersorium may have been nothing more than a toilet brush. Read his gripping account in the Proceedings of the International Frontinus-Symposium on the Technical and Cultural History of Ancient Baths, Aachen, Germany, 2009.

Sign in a loo in an antechamber of Perth’s Sheriff Court House. One must be at rock bottom to shoot up before facing a sheriff (a Scottish judge with powers to fine or lock you up for up to five years). For the last seven years, Scotland has maintained the unenviable first place in Europe for drug-related deaths; drugs in Scotland have a death rate almost four times the rate in the UK as a whole. These figures – together with failing education, economy and health indicators – are secondary for people in power. The one-track-mind Scottish National Party cares for little else besides breaking up the union:

Epiphany inside a loo in Perth, UK:

The facilities in the family home (today a museum) of Brazilian painter Cândido Portinari (1903-1962) in the town of Brodowski, São Paulo State, illustrate a time when homes were not cluttered with stuff and had plenty of space to spare:

Collector, philanthropist and extremely rich Ema Klabin (1907–1994) needed the loo to store some of her many priceless pieces of art. Her house in São Paulo is a museum (Fundação Cultural Ema Gordon Klabin) well worth visiting. Entrance is free:

A replica of a once common warning to men in public urinals, hotels and railroad stations in the UK. Not doing-up all the buttons of your trousers (no zippers then) was a grave indiscretion:

That’s not nice. At all:

Able young non-pregnant adults can use the loo in the petrol station across the road:

In a cafe in the Brazilian coastal city of Ubatuba, you are not allowed to flush yourself. Presumably to prevent polluting the sea:

“Use the toilet as you have committed a crime: don’t leave clues behind” (loo in a São Paulo bookshop):

Once again: are “races” social constructs without scientific or biological meaning?

July 19, 2022 • 9:20 am

Every day, it seems, I hear that “races have no biological reality or meaning; they are purely social constructs.” And that statement is somewhat misleading, for even the crudely designated races of “white, black, Hispanic, and East Asian” in the U.S. are, as today’s paper shows, biologically distinguishable to the point where if you look at the genes of an unknown person, you have a 99.86% chance of diagnosing their self-identified “race” as one of the four groups above. That is, if you ask a person how they self-identify as one of the four SIRE groups (SIRE: “self identified race/ethnicity), and then do a fairly extensive genetic analysis of each person, you find that the groups fall into multivariate clusters.

More important, there’s little deviation between one’s SIRE and which genetic cluster they fall into. Over 99% of people in the sample from this paper can be accurately diagnosed as to self-identified race or ethnicity by looking at just 326 regions of the genome.

This in turn means that there are biological differences between different SIREs, so race cannot be simply a “social construct.” This is in direct contradiction between the extreme woke view of “race”, as expressed in the Journal of the American Medical Association, a statement I discussed in an earlier post:

Race and ethnicity are social constructs, without scientific or biological meaning.

Nope, and we’ve known that statement is wrong for nearly 20 years. Of course, if you take “biological meaning” as “data show that there are a finite number of distinct groups with huge genetic differences”, then it is a correct statement. But nobody thinks that any more except for racists or those ignorant of modern population genetics in humans.

The meaning of the biological reality adduced in papers like the one we’re discussing today is this: genes can be used to diagnose biological ancestry, which is surely involved in one’s SIRE. And therefore “races” or “ethnicities” aren’t just made-up groups, but say something about the evolutionary origin of group members.

As I said, the “old concept” of races as a small number of genetic groups that differ strongly in their genes is dead. But there are still groups, and there are groups within groups, and groups within groups within groups. Thus genetic variation in our species is hierarchical, as expected if variation among groups evolved in geographically isolated populations, between which there was some but not complete mixing.

This view of human variation leads me to abandon the use of the word “race” in general and use “ethnicity” instead. I’ll use “race” in this article, though, as I’m addressing the JAMA statement above, and also using individuals’ own diagnosis of their own “race”.

I’ve emphasized this before—in August of last year. There I cited the 2002 paper of Rosenberg et al. reporting that “one can show by using data from many genes and gene sites, and clustering algorithms, that humanity can be shown to form genetic clusters that correspond to geography (different continents or subcontinents), which of course correspond to evolutionary history.” As I also said then,

. . . . the paper of Rosenberg et al.,. . .  shows that the genetic endowment of human groups correlates significantly with their geographical location (for example, if you choose to partition human genetic variation into five groups (how many groups you choose is arbitrary), you get a pretty clear demarcation between people from Africa, from Europe, from East Asia, from Oceania, and from the Americas. (To show further grouping, if you choose six groups, the Kalash people of Asia pop up). This is one reason why companies like 23 And Me stay in business.

This association of location with genetic clustering (and these geographic clusters do correspond to old “classical” notions of race) is not without scientific meaning, because the groupings represent the history of human migration and genetic isolation. That’s why these groups form in the first place. Now you can call these groups “ethnic groups” instead of “races”, or just “geographic groups” (frankly, you could call them almost anything, though, as I said, I avoid “race”), but they show something profound about human history. The statement in bold above could be used to dismiss that meaning, which is why I consider that statement misleading.

The Rosenberg et al. paper was published two decades ago, and since then we are now able to look at more genes (potentially the entire genome of individuals) and use bigger samples over smaller areas. When we do that, we’re able to see the clusters within clusters. Here’s a reference to a 2008 paper:

Even within Europe,a paper by Novembre et al. reported, using half a million DNA sites, 50% of individuals could be placed within 310 km of their reported origin and 90% within 700 km of their origin.. And that’s just within Europe (read the paper for more details). Again, this reflects a history of limited movement of Europeans between generations.

I wanted to delve a bit into the 2005 paper of Tang et al. (mentioned in my earlier post), because it concentrates on self-reported race or ethnicity, not geographic origin, but also looks at variation over space. geography. Click on the title below to read the paper (pdf here and reference at bottom).

Tang et al. got their data from a study of hypertension in which individuals gave blood and also indicated their self-identified race as one of the four groups mentioned above. Then, each of the 3,636 individuals (taken from 15 geographic locales in the U.S., and three from Taiwan) were analyzed for 326 “microsatellite” markers—short repeated segments of DNA. (These segments may not all be independent because of genetic linkage, but certainly a lot of them are independent. The authors don’t discuss this issue, which is relevant but not invalidating.)

Tang et al. then determined whether the microsatellite data fell into clusters using on multiple genes and the clustering algorithm “structure”—the method also used by Rosenberg et al. to show ethnic variation was correlated with geography. Remember, the Tang et al. study took place mostly in American populations, with each SIRE sampled from several places. But the geographic sampling within the U.S. was limited (e.g., “Hispanics” came from only one place in Texas), and this is a potential problem.

Tang et al. did indeed find clustering using multivariate analysis: here are the clusters for all sites and SIRE combinations. Note that there are four clusters: one each for self-identified Caucasians from 6 populations (upper left), East Asians from 7 populations (middle right), African-Americans from 4 populations (lower left), and self-identified Hispanics from a single location (“K” from Starr County, Texas). Clearly we need more data from self-identified Hispanics from other areas, especially because “Hispanic” can denote many diverse ancestries.

The clusters are pretty distinct. Not only do are they distinct, but they match almost perfectly an individual’s self-identified race or ethnicity. As the authors note:

Of 3,636 subjects of varying race/ ethnicity, only 5 (0.14%) showed genetic cluster membership different from their self-identified race/ethnicity. On the other hand, we detected only modest genetic differentiation between different current geographic locales within each race/ethnicity group. Thus, ancient geographic ancestry, which is highly correlated with self-identified race/ ethnicity—as opposed to current residence—is the major determinant of genetic structure in the U.S. population.

As I said earlier “there is almost perfect correspondence between what “race” (or ethnic group) Americans consider themselves to be and the genetic groups discerned by cluster algorithms.  Because these are Americans, and move around more, the genetics reflect ancestry more closely than geography, though, as Novembre et al. found, in Europe geographic origin is also important. Americans move around more than Europeans do!I

In other words, individuals within a cluster are more geographically dispersed than what Novembre et al. found, so that membership in a cluster indicates ancient ancestry, not geographic origin. For example, members of the “East Asian” cluster come from Taiwan, Hawaii, and Stanford.

But to show that there are clusters within clusters, so that “East Asian” can’t be considered a “race” in the old sense, the authors repeated the cluster analysis using only the East Asian sample, and found that those of Chinese ancestry formed a cluster distinct from those of Japanese ancestry.  This is expected if self-identified ethnicity still reflects genetic differences that evolved in Asia. You would doubtless find similar relationships if you dissected Caucasians or African-Americans by the location of their ancestors.

What this shows, then, is that in the US, and in a limited sample of populations whose members self-identified their “race” into one of four groups, those groups can be differentiated using multiple segments of the genome. Not only that, but the differentiation is substantial enough that if you had an individual’s genetic information without knowing anything about them, you could diagnose their “self identified race/ethnicity” with 99.86% accuracy.

The take-home message:

In the U.S.—and in the world if you look at the Rosenberg study—one’s self-identified race, or race (again, I prefer “ethnicity”) identified by investigators—are not purelysocial constructs. Ethnicity or race generally say something about one’s ancestry, so that those members of the same self-identified race tend to group together in a multigenic analysis.

Note that this does not mean that there is extensive genetic differentiation between self-identified races. The old conclusion from my boss Dick Lewontin that there is more variation within an ethnic group than between ethnic groups remains true. But there is enough genetic difference on average that, if you lump all the genes together, the small differences accumulate sufficiently to allow us to diagnose a person’s self-declared race. Remember, these are “self-declared” groupings, so you can’t say they are imposed on the data by investigators. (That of course doesn’t mean that they aren’t social constructs. They may be in some sense, but they’re also social constructs that contain scientific information.)

So, the big lesson is that the JAMA was wrong: if races/ethnic groups can be diagnosed with over 99% accuracy by using information from many bits of the genome, then the statement “Race and ethnicity are social constructs, without scientific or biological meaning” is simply wrong. Race and ethnicity, even when diagnosed by individuals themselves, do have scientific biological meaning: namely, they tell us about an individual’s ancestry and where their ancestors probably came from. This is true in the U.S. (this paper) or worldwide (the Rosenberg et al. paper). Further, if you look on a finer scale, as Novembre et al. did, you can even diagnose what part of Europe a European’s ancestors came from (it’s not perfect, of course, but it’s pretty good).

This is not a new conclusion, and the papers I’ve cited are older ones.  There may be newer ones I haven’t seen, but I’d be willing to bet that their results would be pretty much the same as that above. Though genetic differentiation between groups is not large, it’s sufficient to tell us where they came from, confirming that geographic origin (reflecting ancient geographic isolation) is the source of what we call ethnic or racial differences.

Just remember this: when you hear that human race/ethnicity is a purely social construct, and doesn’t say anything about biology or evolution, that’s just wrong.

I shouldn’t have to point out that these genetic differences in no way buttress racism, for we don’t even know what they mean in terms of individual traits. But they do give us insights into evolutionary history. And that is something of scientific and biological meaning.

________________________

Reference: Tang H, Quertermous T, Rodriguez B, Kardia SL, Zhu X, Brown A, Pankow JS, Province MA, Hunt SC, Boerwinkle E, Schork NJ, Risch NJ. Genetic structure, self-identified race/ethnicity, and confounding in case-control association studies. Am J Hum Genet. 2005 Feb;76(2):268-75.

Brian Greene: We don’t have free will: one idea in a wide-ranging book

July 8, 2022 • 9:20 am

Physicist Brian Greene published the book below in 2020, and it appears to cover, well, just about everything from the Big Bang to consciousness, even spiritually and death. Click image to go to the Amazon site:

Some of the book’s topics are covered in the interview below, and its breadth reminds me of Sean Carroll’s book The Big Picture: On the Origins of Life, Meaning, and the Universe Itself. I’ve read Sean’s book, which was good (though I did disagree with his free-will compatibilism), but I haven’t yet read Greene’s. If you have, weigh in below.

I’ll try to be brief, concentrating on Greene’s view of free will, which is that we don’t have it, we’re subject only to the laws of physics, and our idea of free will is an illusion stemming from our sense that we have a choice. The interview with Greene is in, oddly, the July 1 issue of Financial Review, and is paywalled, but our library got me a copy. (Judicious inquiry may yield you one, too.) You might be able to access it one time by clicking below, but otherwise ask or rely on my excerpts:

Greene also dwells on the fact that we’re the only creatures that know that we’re going to die, an idea that, he says, is “profoundly distressing” and in fact conditions a lot of human behavior. More on that below. Here are a few topics from the interview:

Free will:  Although Greene, as I recall, has floated a form of compatibilism before (i.e., our behaviors are subject to natural laws and that’s all; we can’t have done otherwise by volition at any given moment, but we still have free will), this time he appears to be a rock-hard determinist, which I like because I’m one, too. Excerpt from the interview are indented:

What’s more, beyond thoughts of death, my colleagues, according to Greene, are mistaken in their belief they are making their own choices to change their lives. Thoughts and actions, he argues, are interactions between elementary particles, which are bound by the immutable laws of mathematics. In other words, your particles are doing their thing; we are merely followers.

“I am a firm believer,” he says, “that we are nothing but physical objects with a high degree of order [remember these words, “high degree of order” – we’ll circle back to that], allowing us to have behaviours that are quite wondrous, allowing us to think and feel and engage with the world. But our underlying ingredients – the particles themselves – are completely, and always, governed by the law of physics.”

“Free will is the sensation of making a choice. The sensation is real, but the choice seems illusory. Laws of physics determine the future.”

So then, free will does not stand up against our understanding of how the universe works.

“I don’t even know what it would mean to have free will,” he adds, “We would have to somehow intercede in the laws of physics to affect the motion of our particles. And I don’t know by what force we would possibly be able to do that.”

Do you and I have no more options than say, a fish, in how we respond to the world around us?

“Yes and no,” says Greene. “All living systems, us included, are governed by the laws of physics, but the ways in which our collection of particles can respond to stimuli is much richer. The spectrum of behaviours that our organised structure allows us to engage in is broader than the spectrumof behaviours than a fish or a fly might engage in.”

He’s right, and there’s no attempt, at least in this interview, to be compatibilistic and say, well, we have a form of free will worth wanting. 

Death: From the interview:

“People typically want to brush it off, and say, ‘I don’t dwell on dying, I don’t think about it,”‘ says Greene via Zoom from his home in New York, where he is a professor at Columbia University. “And the fact that we can brush it off speaks to the power of the culture we have created to allow us to triumph over the inevitable. We need to have some means by which we don’t crumble under the weight of knowing that we are mortal.”

. . . Greene believes it is this innate fear of death twinned with our mathematically marching particles that is driving my colleagues to new horizons, and driving my decision to write this story, and your choice to read it, all bolstered by Charles Darwin’s theory of evolution.

Greene’s view appears to be that a substantial portion of human behavior is driven by a combination of two things: the “naturalism” that deprives us of free will, combined with our learned (or inborn) knowledge and fear of death. The death part is apparently what, still without our volition, forces us into action. I’m not sure why that’s true, as the explanation’s not in the interview but perhaps it’s in the book. After all, some people argue that if you’re a determinist doomed to eternal extinction, why not just stay in bed all day? Why do anything?  If we do things that don’t enhance our reproduction, it’s because we have big brains and need to exercise and challenge them. Yes, we know we’re mortal, but I’m not sure why this makes me write this website, write books, read, or do science. I do these things because they bring me pleasure. What does mortality have to do with it?

Natural selection:  According to the writer and interviewer Jeff Allen (an art director), Greene thinks that the promulgation of our mortality, as well as much of our communication, comes from storytelling, which has been instilled into our species by natural selection. Things get a bit gnarly here as the interview becomes a bit hard to follow. I’m sure Greene understands natural selection better than Allen, but Greene’s views are filtered through the art director:

Natural selection is well known for driving physical adaptation, yet it also drives behavioural change, including complex human behaviours such as language and even storytelling. Language is a beneficial attribute that helps us as a species succeed, as is the ability to tell stories, which prepare the inexperienced with scenarios that may benefit them in the future.

“Evolution works by tiny differentials in adaptive fitness, over the course of long timescales. That’s all it takes for these behaviours to become entrenched,” says Greene. “Storytelling is like a flight simulator, that safely allows us to prepare ourselves for various challenges we will face in the real world. If we fail in the simulator, we won’t die.”

Darwin’s theory of evolution is one of the recurring themes of Greene’s book.

Note in the first paragraph that evolved language and storytelling “helps us as a species succeed”. That’s undoubtedly true—though I’m yet to be convinced that storytelling is anything more than an epiphenomenon of evolved language—but whatever evolved here was undoubtedly via individual (genic) selection and not species selection. Traits don’t evolve to enable a species to succeed; they evolve (via selection) because they give their bearers a reproductive advantage. I’m sure Greene knows this, but Allen balls things up by throwing in “species success”.

Consciousness: If you’re tackling the Big Issues that deal with both philosophy and science, it’s consciousness, defined by Greene (and I) as both self-awareness and the presence of qualia, or subjective sensations (Greene calls it “inner experience”).  I’ve written about this a lot, and don’t propose to do more here. We have consciousness, we don’t know how it works, but it’s certainly a physical property of our brains and bodies that can be manipulated by physical interventions. The two issues bearing on Greene’s piece are where it came from and how will we figure out how it works. (Greene implicitly rejects panpsychism by asking “”How can particles that in themselves do not have any awareness, yield this seemingly new quality?”. That will anger Philip Goff and his coterie of panpsychists.)

I’m not sure about the answer to either., We may never know whether consciousness is an epiphenomenon of having a big brain or is partly the result of natural selection promoting the evolution of consciousness. I suspect it’s partly the latter, since many of our “qualia” are adaptive.  Feeling pain is an aversive response that protects us from bodily damage; people who lack the ability to feel pain usually accumulate substantial injuries. And many things that give us pleasure, like orgasms, do so because they enhance our reproduction. But this is just speculation.

Greene also thinks that natural selection has something to do with human consciousness, but it’s not clear from the following whether he sees consciousness as an epiphenomenon of our big brain and its naturalistic physical properties, or whether those properties were molded by natural selection because consciousness enhanced our reproduction:

“My gut feeling,” says Greene, “Is that the final answer will be the Darwinian story. Where collections of particles come together in a certain kind of organised high order ‘brain’, that brain is able to have particle motions that yield self-awareness. But it’s still a puzzle at this moment.”

Where Green and I differ is in what kind of work might yield the answer to how consciousness comes about. Greene thinks it will come from work on AI, while I think it will come, if it ever does, from neurological manipulations. Greene:

“That’s perhaps the deepest puzzle we face,” says Greene. “How can particles that in themselves do not have any awareness, yield this seemingly new quality? Where does inner experience come from?”

Greene’s suspicion is that this problem will go away once we start to build artificial systems, that can convincingly claim to have inner awareness. “We will come to a place where we realise that when you have this kind of organisation, awareness simply arises.”

In June this year, Google engineer Blake Lemoine said an AI he was working on, named LaMDA (Language Models for Dialogue Applications), got very chatty and even argued back.

I suppose this is a version of the Turing test, but it will be very, very hard to determine if an AI bot has “inner awareness”.  Hell, I don’t even know if my friends are conscious, since it depends on self-report! Can you believe any machine that says it has “inner experiences”?

With that speculation I’ll move on. Greene also muses on the origin and fate of the universe, and whether it might “restart” after it collapses, but cosmology is above my pay grade, and I’ll leave you to read about that yourself.

h/t: Ginger K.