Why Evolution is True is a blog written by Jerry Coyne, centered on evolution and biology but also dealing with diverse topics like politics, culture, and cats.
Please send in your good wildlife photos lest the feature become sporadic or—Ceiling Cat forbid—go extinct.
Today we have some nice photos by reader Mark Sturtevant; his captions are indented, and you can enlarge the pictures by clicking on them.
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This looks to be the last batch of WEIT-worthy pictures that I have from 2021.
First up are some of my favorite dragonflies, starting with the impressive royal river cruiser dragonfly (Macromia taeniolata). These are among the largest dragonflies in my area, but I am fortunate in that they are also among the most approachable. Sure, they will fly at break-neck speed as they patrol along a tree-line, as this one was, but then they hang themselves up at about eye-level, and there they sits. You may then take all the pictures you want, even at close range, and they don’t mind. The link to this species gives an idea about their size and approachability.
Next is our black saddlebags dragonfly (Tramea lacerate). Common in fields, but unlike most dragons in the skimmer family who do more perching than flying, these will fly all day, effortlessly cruising around on those overly-broad wings. But occasionally one will give me a gift by sitting on a perch as this one was at a pond near where I work. So I like them because they play hard to get.
At another park there are redbud trees, and late in the season I noticed that just about every leaf was fastened shut as shown here. What was the surprise inside?
Why, a whimsical caterpillar! A squirmy little Dr. Seussian sock. In olden times, finding an ID of something like this would be a great tedium, but now we have the BugGuide web site. A simple search in there for “caterpillar on redbud”, and immediately we learn that this is the redbud leaffolder, Fascista cercerisella.
One might think that a “March fly” would be a spring insect, but actually members of this family have several generations a year, and they emerge synchronously in large numbers. One day in November just about every leaf along a forest trail had at least one of these odd little flies. They are also known as “love bugs”, as they are often seen mating. This particular species is Bibio albipennis.
I try to carry my wide-angle macro lens when I go out, but I seldom find a scene that will work with it. Here I managed to get a picture among a group of unknown mushrooms. Sorry, I don’t know the species.
One day the wife brought home a Venus flytrap (Dionaea muscipula). A friend from down the street was visiting, and she had never seen one having a meal so I brought in a fly, slightly stunned it, and placed it as shown. As is well known, the trap is sprung if the hairs inside are triggered more than once. Our friend was pleasingly horrified at the sight of botanical carnivory.
Unfortunately, NPR has gotten hold of Agustín Fuentes, who seems to have a strong ideological slant on biology, to explain to its listeners the “problems” with using DNA tests for ascertaining your ancestry—as many of us have done with companies like 23andMe™. Sadly, Fuentes’s “criticisms” of the method and results are misguided, bespeaking either an ignorance of biology or an ideological drive to convince people that humans around the world are so similar that it’s next to useless to use DNA to find out your ancestry. (This is, of course, part of the view that “race is a social construct”, which apparently now means “ethnic groups can’t readily be identified by their DNA.”)
To cast doubt on such tests, Fuentes makes a number of claims: races (or ethnic groups) are social constructs; we don’t have enough data to reliably identify groups from their DNA (ergo we don’t have enough data to reliably determine your genetic origins); that one doesn’t expect to find genetic differences between geographically separated populations because geography is purely subjective and arbitrary; that people move around too much to reliably determine the location where one’s ancestors lived; that your genealogical history may diverge from your genetic history; and that the best that ancestry tests can do is tell you what genetic diseases you may be prone to. To sum up all the misguided information that Fuentes gave in his 14-minute interview with Regina Barber, I’ll first give one paragraph from Fuentes’s interview:
So I will tell you right now, my 23andMe tests miss a bunch of my actual kin – right? – because, like, most of your ancestors contributed no genetics to you – right? – because of the way genetics mixes down and across. And here’s the punchline for ancestry testing. It actually can tell you some information. When it comes to certain diseases, it’s actually really important to know, but it does not tell you who you are, and it actually doesn’t tell you who your ancestors are. It tells you which peoples from different places contributed to your genetics. But that is not your family, right? Your genealogy is more than just the biology.
Now we’ve met Fuentes before and I’ve taken issue with his distortions of biology (see here for some posts), especially those insisting that Darwin was a racist and that there is no such thing as a sex binary. What worries me, especially in this NPR interview, is how Fuentes, perhaps in the interest of ideology, has repeatedly misled the public. In my view, the NPR interview does damage the public understanding of an important area of modern genetics.
But hear (or read) for yourself. The short NPR show (14 minutes) can be found by either clicking on the screenshot below and then by listening to the show, or by reading the transcript here.
I had an email discussion with my colleague Luana Maroja at Williams College about this, for the two of us have co-written a paper on this and similar topics that will be out in a month. She gave me permission to use her name and her words, and so I’ll put her words in indented italics and mine flush left in roman type. Fuentes’s statements from the interview are indented in roman type.
First, a few words about the supposed inability of using DNA to determine one’s ancestors. Although it’s true that most genetic variation occurs within rather than between populations (this was first popularized by my advisor Dick Lewontin), and that 99.9% of the DNA between any pair of humans is identical, people don’t realize that that still leaves a substantial amount of genetic difference between people, and especially between populations, that can be used diagnose ancestry. We know this because the human genome has 3.3 billion base pairs, and even 99.9% identity leaves 3.3 million differences among individuals.
And research has shown that a lot of those differences occur between geographic populations. (I use either that pharse or “ethnic group” instead of “races” because we know that the classical idea of races as absolutely geographically demarcated groups, profoundly genetically differentiated,and diagnosable using few genes—is wrong.) But differences between populations become clear when you use a large group of those 3.2 million segregating base pairs (SNPs, or “single-nucleotide polymorphisms”), and these can be used to tell you where your genes come from. If it was way off the mark, companies like 23andMe would be out of business.
For example (do check out the links for yourself):
a.) Even the old and outmoded view of race is not devoid of biological meaning. A group of researchers compared a broad sample of genes in over 3,600 individuals who self-identified as either African-American, white, East Asian, or Hispanic. DNA analysis showed that these groups fell into genetic clusters, and there was a 99.84% match between which cluster someone fell into and their self-designated racial classification. This surely shows that even the old concept of race is not “without biological meaning”. But that’s not surprising because, given restricted movement in the past, human populations evolved largely in geographic isolation from one another—apart from “Hispanic”, a recently admixed population never considered a race. As any evolutionary biologist knows, geographically isolated populations become genetically differentiated over time, and this is why we can use genes to make good guesses about where populations come from.
More recent work, taking advantage of our ability to easily sequence whole genomes, confirms a high concordance between self-identified race and genetic groupings. One study of 23 ethnic groups found that they fell into seven broad “race/ethnicity” clusters, each associated with a different area of the world. On a finer scale, genetic analysis of Europeans show that, remarkably, a map of their genetic constitutions coincides almost perfectly with the map of Europe itself. In fact the DNA of most Europeans can narrow down their birthplace to within roughly 500 miles.
b.) Here’s a genetic cluster analysis (using principal-components analysis of many genes from many Italian populations, nicely separated by geography (the paper is here). This is based on only about 270 variable SNPs in 210 genes studied in 1736 individuals. Although there’s been some mixing (overlap between clusters), in general you would be able to localize where in Italy a person was from by looking at even a relatively small sample of their DNA variants. Why the different groups? They reflect the history of colonization and settlement in different parts of Italy as well as local population structure due to mating with those born close to you. Clearly, migration has not been sufficient to efface these historical differences. You get similar maps if you look at the three links above, which cover both Europe and the whole world.
c.) You can also place people pretty accurately using variation within transposable (“mobile”) genetic elements, as you can see in this figure using a cluster (principal components) analysis of MEVs, or mobile element variation. Populations fall out genetically very well according to the continent from where the individuals were sampled (the Nature paper from just 12 days ago is here). Continental areas are coded this way: AFR, African; AMR, American; EAS, East Asian; EUR, European; SAS, South Asian. And remember, this is only DNA sequences in moving elements. If you use every bit of DNA in whole genomes, you get much cleaner results.
(If you added positions of these elements, you’d get even more information, but the analysis above seems to depend on DNA sequences alone, which aren’t ideal for MEV’s because they have are so many repeats.) Still, look at how just a small sample of the genome can give you pretty good diagnostic ability.
How many SNPS do companies like 23andMe use? Over a million variable sites (see here). That gives substantial diagnostic ability to determine where one’s ancestral genes came from. Not only that, but since we know the gene order, you can use that to find your relatives, for relatives not only have similar variants, but also have the same sets of variants grouped together on their chromosomes, as “linked” gene variants aren’t broken up by recombination within a generation or two. My own 23andMe analysis found several distant cousins, and when I checked with my sister, sure enough, they were indeed my cousins. This would not be possible unless the variation had some biological significance. You can diagnose ancestry with good accuracy, but you can also find your relatives! (Because of “linkage disequilibrium” between sites, you can even “paint” the chromosomes based on geographic ancestry, showing recombination that happened in your ancestral lineage).
Now that I’ve told you the fallacy of Fuentes’s insistence that DNA testing is severely compromised because most humans are genetically identical, I’ll turn you over to Luana, who knows a lot more about this stuff than I do, as she not only does it herself, but teaches it to her undergraduates. She analyzes (her words in italics, again) a number of Fuentes’s claims, and, actually, finds the whole interview deeply misleading about DNA testing. Note that her words are reactions to what Fuentes said in the interview.
FUENTES: So here’s the deal. When you spit in a tube and send them – let’s take 23andMe – your DNA, they analyze your DNA – this little, teeny piece of it – right? – they don’t analyze all of it – and they file that in storage. It’s like, you know, a compartmentalized cluster of information. These are reference populations. These reference populations – the data they have are how they place your DNA and tell you something about it.
. . . This ability to take your spit and put it in a tube, pay someone 150 bucks and have them send you something back about your DNA – that is amazing. But what it tells you – when they send you back your results, that splash page is never accurate because the thing it should say on that splash page is, congratulations, you are 99.9% identical to every other living human. That’s not what it tells you.
LUANA: He seems to ignore that they use SNPs (single nucleotide polymorphism) rather than whole genome sequencing. Well, because they only use informative sites (SNPs)—the sites that vary among individuals and populations—and not the sites that are 99.9% identical among people, they cannot actually come back with a result saying “you are 99.9% identical to all humans”. The SNPs they actually use in determining ancestry are the variable sites alone, the 0.1% of the human genome. And because they categorize people NOT by race, but by geographic location, Fuentes’s criticism of race as a social construct also falls apart.
FUENTES: Yes. There are tens of thousands, if not hundreds of thousands of idealized reference populations in humans. So it sure as heck doesn’t tell you where you are in the human panoply of genetics.
LUANA: Then he goes on to say there would be more populations if they sequenced more people – but this is not the point. The populations nearby would still be the most genetically similar because of strong isolation by distance – so you could subdivide more (for instance, now Italians can be further subdivided between south, middle and north), but that would not change the fact that if your DNA says you are most closely related to people descending from the Italian peninsula, that doesn’t mean you may be more closely related to North Europeans, because Italians are more closely related to each other than to North Europeans.
JAC: One of the biggest flubs in Fuentes’s argument is his claim that continental areas, because (he says) they are demarcated subjectively, they aren’t really expected to have much correlation with genetic differentiation. But in fact that’s how genetic differentiation occurs: by lack of gene flow between geographically isolated populations, which causes them to evolve in different directions. He picks out the only “arbitrary” geographic division I know of between continents to make his point. But even that divide, between Europe and Asia, is not purely subjective: it’s usually at the Ural Mountains, which are a geographic barrier.
FUENTES: A reference population is a cluster of individuals who have their DNA sequenced from some geographic place – continents, big geographic space. So Africa, Asia and Europe are not biological units, right? They’re not even single geobiological patterns or areas or habitats or ecologies, right? They are geopolitical. We named them. We created these landmasses and divided them in certain ways. So for example, what is the difference between Asia and Europe?
BARBER: Other than geographic location?
FUENTES: No, when does Asia become Europe?
BARBER: Oh, I don’t know.
This is cherry-picking nonsense. Of course the geographical demarcation between Europe and Asia is somewhat arbitrary (though it does involve a mountain barrier, but this does not mean that you can’t tell a European from people in various parts of Asia). And of course the other regions: the Americas, Polynesia, Australia, Africa, and so on, are geographically isolated. The difference between Europe, Asia, and Africa, or between Australia and the Americas, is not arbitrary. Further, the presence of genetic continuity is clear in DNA information, with more significant geographic barriers usually usually leading to greater population structure.
Luana chimes in:
LUANA: Then one more bit of nonsense – because we named continental regions – it does not mean they were not “regions”. In fact, our geopolitical nomenclature usually follows geographic lines pretty closely – rivers, mountains etc. And the categories of 23andMe are not sociopolitical locations – they are geographic locations – not countries. These include the Iberian peninsula, Great Britain, east Asia etc. Not to mention that political and linguistic boundaries also have a huge effect on gene flow. I am baffled about why Fuentes is even talking about subjective “geopolitical boundaries.”
FUENTES: The problem is that they don’t actually tell you from the get-go how human you are – right? – 99.9% identical to everyone else. It’s 0.1% that varies across humans – 0.1% of our DNA. They don’t tell you sort of how that actually varies. They tell you you are X percentage African, Asian or European because we think of continents – we think of Africa, Europe and Asia as places that reflect biologies, that reflect deep lineages in humanity. And that’s not true. So the danger in these tests is reifying that. You say, like, oh, I’m 17% African. Wow, I’m 17% Black. Those two things are not the same, right? If you have 17% ancestry, let’s say, from Africa on a test from 23andMe, most – and you’re here in North America, most likely, you have some genetic ancestry in populations from West Africa, right? That’s interesting. That’s fascinating. That’s important. But that doesn’t mean you have any relation to anyone in South Africa or East Africa or Central Africa or North Africa. Africa is not a biological unit. There is no gene for race because race doesn’t come from biology. It comes from racism.
LUANA. More nonsense. He says, “But that doesn’t mean you have any relation to anyone in South Africa or East Africa or Central Africa or North Africa. Africa is not a biological unit. There is no gene for race because race doesn’t come from biology. It comes from racism.”
This is ridiculous – A sub-Saharan African population is indeed more closely related to other populations from that area than to populations from other areas, for genetic mixture between Sub-Saharan African and other groups was impeded by the Sahara. In all principal components analyses, sub-Saharan African populations appear as tight clusters, differing even from other African populations, with additional diagnostic differences seen within locations in the sub-Saharan cluster. So, I think what he means is that you won’t have close family members in Africa, for we’re talking about the kind of ancestry that dates back thousands of years, not a couple generations.
Luana found this 2011 paper from the European Journal of Human Genetics that shows the genetic structure of African and non-African populations. Notice that all sub-Saharan African populations in this principal-components analysis group together at the right (dark green), and are separate from northern African populations (orange), while European populations (blue), South Asians (pink), east Asians (light green), Pacific Islanders (yellow) and the Americas (tan). While there is some mixing, you can see that in general, the genetic clusters correspond to geographic localities, and sub-Saharan African populations are one of the most isolated of them all. (Also notice now similar this SNP map is to the map of movable genetic elements shown above: genetic information from different sources converges to a similar structure set by past population history).
(from the paper, subfigure a): Figure 1 PCA of merged HGDP and Hap Map 3 samples. Panels show the results of the PCA for the full merged set of SNPs (460 147 SNPs) (a), for random subsets of 100 000
JAC: One of Fuentes’s misleading beefs is that human migration largely nullifies any value in DNA testing:
FUENTES: But what it can tell us is where do you map related to these reference populations? What does the movement of humans look like? And the best thing they’re doing now is you can ask, sort of, well, where was I – where do my ancestors – genetic ancestors – where were they 200 years ago? Where were they 2,000 years ago? Where were they 10,000 years ago? And guess what? They’re different places. Now, humans throughout history – right? – for at least the last 3- to 500,000 years, humans and our most recent ancestors have been moving around and having sex with each other regularly. Humans do that. And that’s what we’re from.
LUANA: And then this empty statement: “Now, humans throughout history – right? – for at least the last 3- to 500,000 years, humans and our most recent ancestors have been moving around and having sex with each other regularly. Humans do that. And that’s what we’re from.” Sure, who said otherwise?? This is exactly what 23andMe gives you – the mixing, for it assumes mixed ancestry. What Fuentes is leaving out is that human populations are also quite quick to regain genetic structure after replacement events (due to the very low ancestral migration distances in our species) and after settlement, humans tended to disperse very little until the invention of rapid transportation starting with horses and now with airplanes.
JAC: One more argument Fuentes makes against assessing your ancestry via DNA testing is that his own personal ancestry changed over time as he took repeated tests. This argument implies that, say, a test you take now may be completely off the mark:
FUENTES: The cool thing about these tests is that they’re constantly updating their reference populations. So really cool part of this is that once you’ve done it, Ancestry.com, 23andMe or any of the other companies keep going back because as they expand their reference populations, lo and behold, your genes change. Everything changes about you. I – it’s basically – they just get more information, so they know better about you. So, for example, I’ve been watching myself slide around, like, the Iberian Peninsula, North Africa, way over into Arabia, down into Sudan, back up, back over. And then lately I’ve been shoved, like, way up into Russia. But what’s interesting is that you learn more and more about all of the movement of those peoples that contributed to you and how we are all mutts and how we’re all this blend of amazingness
LUANA: Finally the very thing he says:“I’ve been watching myself slide around, like, the Iberian Peninsula, North Africa, way over into Arabia, down into Sudan, back up, back over” simply shows the huge progress the sites are doing for identification. When I first sequenced my DNA, I came out as partially east Asian. Nowadays I have no East Asian, it is all Native American – in the past they did not have enough information to finely break these two related groups, now they do. This is progress. Unlike Fuentes’s insinuation, this means the dataset is getting more robust and that it’s easier to finely locate people to smaller regions.
(Luana is from Brazil but has mixed ancestry from within the Americas.)
Jerry here again: Fuentes’s presentation on this NPR show makes the listener think that the real value in DNA testing is not the “slippery” business of finding out where your ancestors come from, but what genetic diseases you have. He raises a number of “problems” with tests like those used by 23andMe, but these are not serious problems. And by concentrating on the similarity between humans, without emphasizing that there are several million sites in the DNA that can be used to diagnose ancestry as well as to find your relatives, he’s neglecting the fact that it is those millions of variable sites that are the ones that CAN BE AND ARE used to detect your ancestry—and we know now that they do so with substantial accuracy, as the data above show.
Fuentes’s deliberate neglect of genetic differentiation between populations that are geographically isolated or isolated by distance and by cultural “inbreeding”—the way we diagnose ancestry—can only be understood as an obfuscation due to either ignorance or ideology. If you adhere to a certain ideology, populations cannot be allowed to show diagnostic genetic differences because that means that populations are different, and thus that populations could be unequal. And thus they could be superior or inferior. This sliding from “difference”, which is indisputable, to “ranking”, which need not happen at all if you’re rational, is why “progressive” ideologues oppose the emphasis on diagnostic genetic differences between human populations. It is another case of reading into nature what you would like to see in nature.
And that is why Barber starts her interview with Fuentes this way.
BARBER: And aside from leaving out our similarities, most of these tests spit out results based on large, geographic locations – so continental ancestry. The problem is that these kinds of results – think African, European, South Asian – are then linked to race, a social construct.
No, we’re not talking about race or social constructs here: we’re talking about geographic populations, and which ones contributed genes to your own DNA.
Finally, because it’s so cool, here’s the genetic map of Europe compared to the geographic map, taken from the 2022 PNAS paper cited above. The genetic data, presented again as a principal components analysis on the right, are based on 5,500 individuals and 204,652 SNPs (single-nucleotide polymorphisms). Isn’t the coincidence between the genetic and geographic maps remarkable? This shows that migration has not effaced historical data, and that you don’t need obvious geographic barriers to get distinguishable clusters.
(From the paper): A sample of European structure in the UKBB. (A) The number of individuals included from each European country analyzed. Countries are grouped by geographic region; these regions are chosen as a means of group representation and do not necessarily imply historical links. Sample sizes from each region are also shown. Abbreviations are as follows: SE Europe (southeastern Europe), S Europe (southern Europe), E Europe (eastern Europe), C Europe (central Europe), N Europe (northern Europe), W Europe (western Europe), Brit. & Ire. (Britain and Ireland). (B) The sample counts for each European region. (C) The first two PCs calculated by PLINK of 5,500 European individuals. Individual genotypes are shown by letters that encode the alpha-2 ISO 3166 international standard codes and are color coded according to geographic region. The median PC for each country/region of birth is shown as a label. Plots were generated using the ggplot2 package (65) in the R statistical computing language (59).
And that, ladies and gentlemen, brothers and sisters, and comrades, is how we can make fairly accurate guesses about where your genes (and distant ancestors) come from.
UPDATE: Within a minute of pressing “post,” I got this notice from 23andMe, saying that they’d located putative relatives of mine, including one second cousin and three third cousins. I’ll check with my relatives!
You can’t make this stuff up. Here we have a doctoral student in horticulture at Cornell arguing that people’s penchant for cultivated apples as opposed to their sour wild ancestors reflects a bias against historically excluded communities. (He calls the ancestors “wild-type” apples, but I’ve never heard them called that. “Wild type” is a largely outdated term in genetics referring to the product of the most common variant of a gene. For example, if you’re dealing with the “vestigial” mutant, which shrinks the fruit fly wing down to a nubbin, the alternative gene form that produces the normal wing is called the “wild-type” allele, producing a “wild-type” phenotype with normal-sized wings. Usually we refer to the wild ancestors of a species as just “wild” apples.)
But I digress: here’s the article from Cornell’s research site about how our attitude toward apples reflects bigotry. Click to read about the stuff that you couldn’t make up.
First, a note. DNA work shows that all varieties of eating apples descend from a single species of wild apple, Malus sieversii, found in the mountains of central Asia, though there may be some genes from other Malus species. Most varieties of apples, like my favorite, the Granny Smith (crispy and tart!), have come from selective breeding of mutants arising in M. sieversii descendants, and thus could be said to belong to that species—just as all cat breeds could be said to belong to Felis silvestris lybica, the ancestral subspecies. But in the past, commercial apples have indeed been produced by crossing M. sieversii with other species of Malus, a genius that includes all the species of crabapples. These hybrids are called “applecrabs,” though I don’t think I’ve ever eaten—much less seen—one.
But I digress. The student, Andrew Scheldorf (who is said to identify as queer and uses the pronouns “he/they”), is doing the same thing, trying to produce new apple varieties at Cornell by incorporating genes from crabapples via crossing. It’s not a new method, though the article argues it is. Here’s the article’s description of Scheldorf’s work:
Have you ever tasted a wild apple? Unlike the domesticated apple, there are several species of wild apples, and most are likely to set your teeth on edge. But wild apples have evolved through natural selection over millions of years, and many are better equipped than domesticated varieties to survive in less-than-ideal conditions.
Understanding the desirable traits of wild and domesticated apples is the business of Andrew Scheldorf (he/they), a fifth-year doctoral student in horticulture. They work in the fruit physiology and climate adaptation lab in Geneva, directed by Jason Londo, School of Integrative Plant Science, Horticulture, where they study an apple tree population created by crossing the domesticated apple, Malus × domestica, with a wild species that originated in western Asia, Malus prunifolia. [JAC: that’s a crabapple species.]
The crossbred population displays a wide range of traits, some of which are prized by growers. “I look at a number of different traits in this population, including fruit size, fruit mass, sugar, acidity, tree architecture, phenolic compounds, total tannins, disease resistance, vigor, and storage ability,” Scheldorf says.
Scheldorf noticed that roughly half of the apples harvested from the population held up well during extended storage. But the other half lost soundness, becoming soft and mushy. Intrigued, Scheldorf used genotypic information and the fruit’s storage time to conduct a Genome-Wide Association Study (GWAS). Based on the results, they believe they have identified a gene that affects the shelf life of apples.
“This is a prime case in understanding what novel and useful traits can come from wild species.”
Breeders have long thought that crossing wild-type apples with the common domesticated apple would yield small, discolored, unpalatable fruit that would be of no interest to the consumer. Even if the fruit were sturdier and the trees more disease resistant, growers believed the fruit would not be marketable.
Scheldorf’s work upends conventional wisdom. “My population has shown that, with careful selection of the wild species parent—and some patience—you can get commercially viable fruit with some of the genetically and physiologically useful traits from the wild species,” they say. Their findings could be valuable both to geneticists and apple breeders. “This is a prime case in understanding what novel and useful traits can come from wild species,” Scheldorf says.
Well, so far so good, except for the mistaken claim that crossing commercial apples with crabapples is the revival of a discarded idea. It’s been done for a long time (since the 19th century), as you can see by reading about “applecrabs” (see also here), which are already sold and eaten. We already know that hybrids between domesticated and crabapples are commercially viable; you can buy the trees!
Well, I learned something. But then things go downhill as Scheldorf can’t resist analogizing the reluctance to eat sour wild apples with bigotry against marginalized people:
Scheldorf identifies as a member of the queer community. As they have sought to improve domesticated apples by drawing on the genetic diversity in wild apples, they have also felt the lack of diversity in plant science, and in science, technology, engineering, and mathematics (STEM) fields in general. They suggest that the way wild-type apples have been discounted can be seen as emblematic of how people from historically excluded communities have for centuries been shunted aside, forgotten, or disallowed in science, math, and engineering fields.
“I started to see an interesting parallel between wild apple species and historically excluded communities in STEM and academia more broadly. While both offer alternative solutions to major issues and lessons to make things more just and equitable, they both have been largely excluded from the spotlight,” Scheldorf says. “I saw how people were treating me and others in the queer community differently. In STEM we are taught to not insert ourselves into our research, don’t let your personality, your opinions, your standpoints in. Anything that does not fit the idea of a scientist is not allowed. Queer aesthetics, queer personalities—they are not super encouraged.”
No. Just no. People don’t like to eat wild apples because they are sour, not because they’re the fruit equivalent of homosexuals. Once again, things go off the rails when someone tries to claim bogus parallels between nature and human culture. Further, it doesn’t take a gay person to come up with the idea of crossing crabapples with domestic apples to create different fruits: that was done over a century ago—by William Saunders, among others.
The rest of the article is about Scheldorf’s desire to purge biology of non-inclusive language. I won’t go into it except to give one example:
Drawing upon their own experiences and their work with Biodiversify, Scheldorf is writing a paper about the distortions and misconceptions caused by gendered terms in science pedagogy. All sorts of human assumptions are embedded in words like male and female, mother and father, Scheldorf points out. “Nature is more complicated than the stereotypical gender binary,” they say. “Explaining [plant reproduction] in male and female terms makes it more difficult for the general public to understand how the mechanisms actually work.” Instead of male and female, they recommend using terms that describe anatomy: stamen-containing or pistil-containing, seed-bearing parent or pollen-bearing parent. “In all the conversations I had that were referencing this, people walked away feeling like they understood things better,” they say.
This is the same motivation that gave us the term I used in a post earlier today: “bodies with vaginas” as a substitute for “female”. Does that terminology make us understand things better? Even in the plant example, I disagree.
If you have half an hour to spare, you may want to listen to the BBC Radio 4’s version of the new article by Matthew Cobb and Nathaniel Comfort on DNA structure (with special emphasis on Rosalind Franklin’s work). If you click on the screenshot below, you can have a free listen to the show. Cobb and Comfort are joined by Angela Creager, a biomedical historian working at Princeton. First, the Beeb’s summary:
James Watson and Francis Crick, who detailed the double-helix structure of DNA in 1953, are perhaps two of the most iconic scientists of the 20th Century. Yet the story of how they made their incredible discovery is perhaps equally famous, with a notorious narrative suggesting that they only identified the structure after taking the work of Rosalind Franklin and using it without her permission.
Now, 70 years after the discovery of DNA’s structure, it is perhaps time to rewrite the tale.
New evidence has now been unearthed, in the form of an overlooked news article and an unpublished letter, that shows that Franklin was truly an equal contributor to the discovery, and Watson and Crick were not as malicious as previously assumed.
New evidence has now been unearthed, in the form of an overlooked news article and an unpublished letter, that shows that Franklin was truly an equal contributor to the discovery, and Watson and Crick were not as malicious as previously assumed. Together with Matthew Cobb of the University of Manchester, Nathaniel Comfort from Johns Hopkins University, and Angela Creager of Princeton University, Gaia Vince discusses this tantalising tale and finds out more about how this discovery could bring a whole new twist to the story of DNA.
Presenter: Gaia Vince Producer: Harrison Lewis Assistant Producer: Jonathan Blackwell
Today, as I’ve said, is the 70th anniversary of the publication of the structure of DNA, which began a scientific revolution via three papers published in Nature‘s April 25, 1953 issue: one by Watson and Crick, one by Wilkins, Stokes, and Wilson, and the third by Franklin and Gosling. As you know, Watson and Crick, who worked at the Cavendish Laboratory at Cambridge, shared the Nobel Prize in Physiology or Medicine in 1962 along with Wilkins, who had worked with Franklin at King’s College London. (I’ve always been amazed that it took them 9 years to make the award.)
As Matthew has mentioned on this site before, Rosalind Franklin certainly deserved a Prize as well (probably sharing the Chemistry Prize with Wilkins since only three awards can be given in one category). Sadly, though, Franklin died in 1958 of ovarian cancer before the Prizes were awarded. She was only 37. Here are two photos of her:
Due largely to the hyperbole of Watson’s bestseller The Double Helix, a legend arose that Franklin had been cheated of the credit that was due her. As the story goes, Watson and Crick were shown one of her X-ray crystallography photos of DNA, the famous “photo 51”, which gave them key data needed to construct their double-helix model. Franklin, many say, was robbed by the duplicity of Watson and Crick.
This story is false, as Matthew Cobb from Manchester and Nathaniel Comfort, a historian of science at Johns Hopkins, reveal in a long piece in today’s Nature (click on screenshot below). In fact, Crick never even saw photograph 51 before it was published, and although there was some rivalry between the King’s and Cavendish teams, there was also a lot of cooperation. The key to Watson and Crick’s successful model-building didn’t come from their snitching photograph 51, but in fact from a report by Max Perutz (who got the Nobel for Chemistry in 1962). As head of the Cambridge Medical Research Council (MRC) Unit, he participated, along with other MRC heads, in a scientific inspection of King’s College as a kind of informal analysis of the science going on there.
Perutz got the final report because he was on the inspection committee. And that report included details, with data, of what King’s was doing vis-à-vis DNA work Further, Franklin knew that Perutz—at Cambridge (where Watson and Crick were working)—had access to all the data in the report, and she more or less invited Crick to have a look at Perutz’s report. It was that report that gave Watson and Crick the critical data that put them on the right track to build their double-helical model of DNA, with the struts of the helix running in opposite direction and with Gs pairing with Cs and As with Ts. The article below paints a very different picture of Franklin and her relations with Watson and Crick than the one that has become lore due to what Cobb and Comfort call Watson’s “semi-fictional” portrayal in The Double Helix.. Yes, the teams were in some sense competing, but they also were collaborating, and kept track of each other’s work.
The piece was jointly written by Matthew, who’s writing a biography of Crick, and Nathaniel Comfort, who’s writing a bio of Watson. Together they ransacked the scientific archives and reached the conclusion that Franklin was in every sense a crucial collaborator in the DNA work, not somebody spurned and sidelined as “the dark lady of DNA.” Indeed, Franklin became friends with both Watson and Crick after she left King’s for Birkbeck College, and even recuperated at the Cricks’ home after her cancer operation. Here’s a bit of the Nature paper that sums up Cobb’s and Comfort’s take:
In a full description of the structure in a paper submitted in August 1953 and published in 1954, Crick and Watson did attempt to set the record straight. They acknowledged that, without Franklin’s data, “the formulation of our structure would have been most unlikely, if not impossible”, and implicitly referred to the MRC report as a “preliminary report” in which Franklin and Wilkins had “independently suggested that the basic structure of the paracrystalline [B] form is helical and contains two intertwined chains”. They also noted that the King’s researchers “suggest that the sugar-phosphate backbone forms the outside of the helix and that each chain repeats itself after one revolution in 34 Å”.
This clear acknowledgement of both the nature and the source of the information Watson and Crick had used has been overlooked in previous accounts of the discovery of the structure of DNA. As well as showing the Cambridge duo finally trying to do the right thing, It strengthens our case that Franklin was an equal member in a group of four scientists working on the structure of DNA. She was recognized by her colleagues as such, although that acknowledgement was both belated and understated. All this helps to explain one of the lasting enigmas of the affair — why neither Franklin nor Wilkins ever questioned how the structure had been discovered. They knew the answer, because they expected that Perutz would share his knowledge and because they had read Watson and Crick’s 1954 article.
Click below to read the article (it’s free):
I asked Matthew to write me a few lines about how this piece came to be, and he was more than generous: he wrote the following.
I’m writing a biography of Crick, Nathaniel Comfort is writing a biography of Watson. We first met in March 2022 and got on well together – we have been sharing information and insights ever since. This is a terrific experience as it enables us to chat about minor details and also explore interpretations. In August 2022, Nathaniel came to the UK. I encouraged him to visit Cambridge, to try and get the feel of what Watson must have felt when he went there in 1951. I decided to go down to meet him, and we agreed we would go to the Churchill College archives to see Franklin’s papers. All that material is available online (https://wellcomecollection.org/works/ka25u4ft), and we didn’t expect to find anything new. We both had our understanding of what happened in 1953, and we didn;t expect to change this. Our visit was more a kind of homage or pilgrimage – the fetishistic fun of actually touching the documents!
To our surprise, we made two discoveries, going through the material together, discussing what they meant.
– We realised why Franklin was so keen on the A form of DNA which she was studying. Not only did it provide very sharp images, it also represented the *crystalline* form of DNA – she wasn’t interested in the paracrystalline B form, which was found at higher humidity, because it seemed to her to represent the loss of order – “the stuff just dissolves” she wrote in her notes.
– We also came across a draft article for Time magazine about the discovery, which had been sent to Franklin by the journalist Joan Bruce. This was known to have existed – it was the article for which the famous photos of Watson, Crick and the DNA model were taken – but it was never published and had never been noticed, as far as we are aware. The science content of the article is confused, but it strikingly presented the discovery as the joint work of King’s and Cambridge, which, of course, it was. This was very different to the Watson and Crick centred view you get from reading Watson’s semi-fictional account in The Double Helix.
We also came across a draft article for Time magazine about the discovery, which had been sent to Franklin by the journalist Joan Bruce. This was known to have existed – it was the article for which the famous photos of Watson, Crick and the DNA model were taken – but it was never published and had never been noticed, as far as we are aware. The science content of the article is confused, but it strikingly presented the discovery as the joint work of King’s and Cambridge, which, of course, it was. This was very different to the Watson and Crick centred view you get from reading Watson’s semi-fictional account in The Double Helix.On the basis of these two discoveries, we decided to write an article for Nature, to be published on the 70th anniversary of the publication of the three articles. Our aim was to introduce these new elements and to argue (again) that the story in Watson’s account of him seeing Photograph 51 and gaining a decisive insight into the structure was hokum (this point has been made several times, with no consequence on what the general public believes!) – much more significant was a report written in December 1952, which contained data from Franklin and Wilkins and had been given to Max Perutz, the head of the Cambridge research group.After the article had been edited and was at the proof stage, we made two more discoveries:
– We found a letter from a PhD student at King’s to Crick which suggests that Franklin knew that Perutz had the relevant information and that she almost invited Crick to ask Perutz about it. This letter is very different from the competitive race that Watson portrays the discovery as. It also fits in with Franklin’s later friendship and collaboration with both Watson and Crick. We have found no evidence she felt robbed (nor was she).
– We noticed that at the Royal Society Conversazione (a kind of science fair) held in June 1953, Franklin presented the double helix as a collective work – exactly as the draft Time article suggested – with all seven authors of the Nature papers given credit.
We had to add these findings, which reinforced our argument, as best we could. Had we stumbled upon these facts earlier the article might have been a bit different, but there was only so much rewriting we could do.
We did not set out to discover anything new about an affair we thought was done and dusted, nor were we looking to exculpate Watson and Crick (nor have we done so). It has been quite a ride, but I for one will be glad to move on from 1953!
Thanks to Matthew for that. He also wrote a 23-part Twitter thread, beginning here, summarizing their views and giving lots of cool pictures. Here’s the first tweet, and just follow it down:
70 years ago, 3 papers appeared in @Nature under the title ‘Molecular structure of nucleic acids’. In an article in Nature today (link at end) @nccomfort and I shed new light on ‘what Watson and Crick really took from Rosalind Franklin’. This thread summarises our findings. 1/23 pic.twitter.com/efIG0bf1BA
A few photos. First, the infamous “photo 51”, taken by Raymond Gosling under Frankin’s supervision:
Here’s the cover of the report given to Perutz that served as a prime impetus for Watson and Crick’s construction of the DNA model:
Crick’s acknowledgment (in his lecture notes) of the importance of the MRC report in giving the dimensions of DNA (my box). Caption is Matthew’s. Note Crick’s sentence (I’ve put it in a red box), “MRC mimeographed report gave unit cell dimensions. A,B forms.” These were crucial for the model.
A letter implying that Franklin knew that Watson and Crick would see the King’s data, and wasn’t worried about it (Caption by Matthew):
We found a 1953 letter to Crick from a student at King’s, implying that Franklin knew her MRC report data would be shared with Watson and Crick, and was relaxed about this. We found no evidence that she felt robbed—and this letter suggests that she did not feel this way.
Crick lauds Franklin when he was n0minated for the Nobel (and she was dead). Caption is from Matthew:
Franklin was a brilliant scientist. Her work was an essential part of the discovery of the double helix. She did not discover the structure, but did come very close. As Crick explained when he was nominated for the Nobel Prize.
Below: Rosalind Franklin’s gravestone (she was Jewish). Note that it mentions her work on viruses but not on DNA. The grave is at “The Willesden United Synagogue Cemetery, usually known as Willesden Jewish Cemetery. . . at Beaconsfield Road, Willesden, in the London Borough of Brent, England.” Note the stones placed on the marker, a sign of respect in Jewish culture.
Finally, Matthew produced an AI-generated photo (using the My Heritage website). of Franklin showing how she might have looked and moved in real life.
A reader’s comment in a recent post brought this issue to my attention. Lots of fun!
I should have figured that once genetics became established, theologians would realize that they had a problem. Two big problems, actually. The first, which I’ve discussed before, is that we’re all supposed to be descended from a man and a woman who were a couple living at the same time and place (Adam and Eve, of course). Because this is not possible, scientifically inclined theologians have tried to save the Original Sin Couple for well over a decade. I won’t describe their solutions, but they are the subject of constant argument at the moribund BioLogos site (see here for a FAQ on Adam and Eve).
A bigger question, discussed at tedious length at the Evangelical Christian website below, is this: if Jesus was part human and part divine, but was born of a human mother (Mary), what was his genetic constitution? Clearly Joseph didn’t have a part in inseminating Mary, and if Jesus was a human, with 23 pairs of chromosome and a Y, did one set of chromosomes, containing an X, come from Mary, and the rest from God? That is, did God contribute half of Jesus’s genome, or did he create Jesus’s genome entirely?
Given the lack of evidence that a divine Jesus existed, or that even a Jesus person existed (some, like Bart Ehrman ,see Jesus as a real person but not divine: a messianic apocalyptic Jewish preacher), this argument would seem superfluous. Or trivial–like the number of angels waltzing on a pinhead. But Christians need answers, and so Finding Hope Ministries (FHM) supplies us with theirs.
Click below to read:
FHM first lists all the possibilities—eliminating the possibility Jesus was haploid, containing only 23 chromosomes from Mary, which would make the Savior inviable (and not male), but would explain the middle initial in “Jesus H. Christ”):
It seems there are only 3 options for considering the composition of Jesus’ DNA:
Jesus has 100% Mary’s DNA with a divinely created Y chromosome to make Him male. [JAC: But did God take out one of Mary’s two X chromosomes, or was he XXY, a male with Klinefelter syndrome?]
Jesus has 50% DNA from a human female (Mary) and 50% DNA from God, to replace that of a human male.
Jesus has DNA created entirely by God at the time of His conception.
Several have proposed God supplied a Y chromosome to add to the X chromosome of Mary’s egg cell (ovum), which programmed for the male gender of Jesus. In so doing God bypassed defective genetic weaknesses of the Adamic (male) genome. However, this is a fallacious argument, as 22 other chromosomes must be contributed to match the other 22 chromosomes Mary produced in her ovum cell.
God, of course, could have done anything.
FHM then analyzes the Catholic position, which they ultimately reject (their bolding):
The Roman Catholic Church embraces the second option: Jesus has 50% DNA from a human female (Mary’s) and 50% DNA from God (to replace that of a sinful human male). This enabled Mary to supply Jesus’ humanity. God the Holy Spirit miraculously encapsulated the Divine nature in Jesus human body. Mary and the Holy Spirit each contributed 50% to the end result. But doesn’t Mary fall under the category of all humans who are born sinners? Catholic theologians cite Mary’s “Immaculate conception” as contributing a sinless human nature to Jesus. Catholics believe Mary was without sin when she bore God’s Son. Mary is considered the “Holy Mother of God.” She remained a virgin after delivering Jesus (according to the Catholic church). Therefore, Roman Catholicism insists Jesus’ other brothers and sister mentioned in Scripture (James, Jude, etc) were not siblings but cousins—not birthed by the Virgin Mary. The Holy Scriptures teach Jesus’ siblings were born of Mary, who did not stay a virgin after Jesus’ birth. But the question about whether they share Jesus’ DNA remains unanswered. Let us further examine the doctrine of the Roman Catholic Church.
To ensure that Jesus was without Original Sin given that he had a human mother, Catholics adopted (in 1854!) the dogma of the Immaculate Conception: that Mary was sinless from the moment of her own conception—as sinless as the pre-serpent Adam. If so, then her offspring, Jesus, was also born without Original Sin. To ensure that Jesus’s brothers and sisters remained sinful, it was proposed that they were not the result of Mary’s insemination by God. Instead, they were “cousins,” which I presume means fathered by Joseph with another woman. Adultery!
The Catholic solution is thus this, as stated by FHM:
Catholics teach Mary was sinless and conceived in perfection. They therefore propose Mary contributed Jesus sinless human nature. Jesus’ DNA would then consist of 50% contribution from Mary, and perhaps more if God only added the ‘Y’ chromosome.
Catholic theologians admit the doctrine of Mary’s Immaculate Conception, as defined by Pope Pius IX was not overtly taught prior to the 12th century. They also agree Biblical Scripture can’t prove this teaching. But they claim the doctrine is implicitly contained in the teaching of the church Fathers.
The church Fathers, of course, didn’t know anything about heredity, much less about the Y chromosome, so I’m not sure how that solution is “implicit” in their teaching. BUT to evangelical Christians such as those from FHM, this doesn’t solve the problem. Why? For two reasons. First, as they note:
Most Protestants reject the doctrine of Immaculate Conception. They do not consider the teaching authoritative because it is not supported by Biblical Scriptures.
Indeed. The Immaculate Conception was just made up to solve the problem of getting a sinless part-human Jesus—to save the Trinity. But if you reject this construction, then you face another problem: if Jesus really did contain some of Mary’s genome, and she still had Original Sin, then Jesus would also bear Original Sin. But he couldn’t have, for then he wouldn’t be Jesus. Thus the Christians are forcd to accept the third solution—God created the entire embryo of Jesus:
It is more likely Mary nourished and “made” the infant Jesus from a single cell being conceived (created) only by God. She gave it a virgin birth, protecting it from any sinful genetic contribution from the ‘seed of man.’ But God the Holy Spirit conceived and created the initial cell of Jesus that ultimately grew into the baby child born nine months later. This was God’s miraculous conception without a man and without a woman.
. . . The Biblical record supports God intervened only once in human genealogy when Jesus became man. God picked Mary as the woman who would birth His Son because of His grace, not because He needed a sinless vessel to pass purity onto His son. Mary provided nourishment and protection for God’s Son as He developed in her uterus. The virgin birth confirmed the purity of Jesus at childbirth. So God the Holy Spirit placed a God-designed conception in the womb of Mary and she functioned as a surrogate mother. God created His human nature. Jesus existed eternally as Deity. His God nature was never created, contrary to the teaching of Mormons and Jehovah Witnesses.
They cite scripture to support this (read the article), but of course Catholics cite scripture to support their own view. The thing is, if God can create a fertilized egg containing no human genome, and then make Mary bear it for nine months, why couldn’t he have created Jesus de novo without a pregnancy? That’s another question that I’ll leave to the readers, but I suppose pregnancy is part of the story that Jesus had at least some humanlike origin.
It gets even funnier when FHM explains why Mary could not have been without sin (remember, they reject the Immaculate Conception). It involves her having mutations in her DNA, mutations caused by SIN:
Inherent sin in the human genome produces inherited physical mutations. Over many generations, the human population has experienced myriads of genetic mutations, and these defects have been incorporated into the common human gene pool, affecting every infant ever born. This is why the lifespan of men has declined from 900+ years in the pre-Flood world to 200+ years of Abraham’s contemporaries and ultimately to 70-80 years today. Mary did not live to be 900 years old. She was not martyred at a young age. Her body suffered the ravages of imperfection. She had a defective human genome and died a normal age (approximately 60) for a woman of that time.
Why sin produces mutations is unresolved, of course, and not all mutations are “defects”. But this solves the problem of a sinless Jesus born of a human mother, and kills another bird as well: the remarkable decline in human longevity since Biblical days. No more Methuselahs! How clever these theologians are! And it solves the problem of Jesus being both human and divine: the “human” bit wasn’t based on DNA, but on looking like a human and having been gestated in a human womb:
His body was truly “in the flesh,” but only “in the likeness of sinful flesh.” Jesus grew in the Mary’s womb like any other baby, yet he was different from all others. He was not genetically related to either Mary or Joseph, for both had an inherited sin nature. Jesus was sinless and without genetic flaw. He was the spotless and sacrificial Lamb of God who offered Himself as a perfect propitiation (payment satisfactory to God) for the sins of mankind.
. . .But the most amazing miracle God performed was His creation of the “second Adam” at conception. He fashioned the first Adam on the sixth day of creation as a full-grown man without sin and in God’s image. Adam was not born of a woman. He received no human DNA from earthly parents. Yet he was fully human. God created Jesus at conception in His image without any DNA contribution from earthly parents. Jesus said to his disciples:
“If you had known Me, you would have known My Father also; from now on you know Him, and have seen Him” (John 14: 7).
Problem solved! Oh, those clever Christians! They then summarize if the readers weren’t able to follow the argument:
However, the church has always taught Jesus is 100% human and 100% Deity (preexisting His incarnation as the Son of God -“the Word”). The third option presented earlier satisfies all these requirements: Jesus has DNA created entirely by God at the time of His conception. His Divine nature did not need to be created, as it was eternally present prior to His birth. God the Holy Spirit provided a human body untainted by the fallen sin-nature of Adam at conception and placed it in the uterus of a virgin, Mary. She carried this child for the nine months of a normal pregnancy as a surrogate mother. This infant had no mutations or defects because Jesus was truly created the “second Adam” in the image of God—like the “first Adam.” God created the first Adam and Eve without sin as perfect adults. Sin entered both of them at the fall, and subsequently infected the entire human race. God similarly created Jesus’s human body at conception, so He could experience everything human from the beginning to the end of a human life. Hebrews 4:15 explains: “He was at all points tempted as we are, yet without sin.” 2 Cor. 5:21 states: ” For He made him who had no sin to be sin for us. ” God became man to sacrifice Himself for the sins of mankind. The name “Jesus” means “God saves.”
Clearly the Catholics got it wrong! The clever theologians at Finding Hope Ministries have not only been able to show up those duplicitous Catholics, but found a way that Jesus can still be 100% human AND 100% divine and yet free of those sin-caused mutations. And it also explains the evolutionary reduction in human lifespan over the last two millennia! I am dumbfounded with admiration.
Can you believe that people get paid to ponder stuff like this? What’s even more incredible is that people believe these solutions.
I guess I’ve banged on about epigenetics for quite a few years here, and if there’s any lesson you should have learned, it’s that while epigenetics is of vital importance during the development of an organism, it’s vastly overrated as a cause of “intergenerational inheritance”. What mean by “epigenesis” or “epigenetics” is the attachment of methyl and acetyl groups to DNA and to the proteins (“histones”) that shepherd the DNA as it operates to create organisms. The attachment of these small molecules to DNA and proteins is in fact a major determinant of how development works—how a single, undifferentiated zygote (fertilized egg) develops into the hundreds of different types of tissues that we have.
And this epigenetic change is in fact programmed into the DNA as a way of producing this essential differentiation. There will be, say, a gene that says, “if environmental factor X is present, put a methyl group on the DNA at position Y.” Genes can do that, you know. And the position where these groups are attached either expresses genes or shut them down, which is why our tissues and cells differ in how they look and behave. They all have the same genes—it’s just that they’re differentially activated and repressed at different times and places. Epigenetics is a vital part of this gene regulation.
We’ve known this for a while, and it’s uncontroversial. What is not uncontroversial is the recent notion of “intergenerational epigenetics”: that environmental changes affecting a behavior or trait in one generation (famine or other traumas are often implicated) can be passed on not from one cell generation to another, but from one human or organismal generation to another. It’s said, for instance, that the Dutch famine during 1944 raised the death toll of offspring in the next generation. (That’s not surprising given that maternal effects in utero can affect offspring.) But it’s often said that this kind of environmental influence can be inherited across multiple generations, forming a kind of evolutionary change—almost Lamarckian in its scope. And this “transgenerational inheritance is supposed to be fairly common too.
Well it isn’t, nor is it an important “alternative” to neo-Darwinian evolutionary change. The article below by Razib Khan on his Substack site is the best discussion I know about the good and the bad stuff about the popular view of epigenetics, and is well worth reading. It explains what epigenesis is, why it’s so important in the development of organisms, and why it’s so overblown in the popular press, which loves to print stuff that smells like “Darwin was WRONG.”
Click to read:
I’m not going to summarize this except to emphasize Razib’s discussion of the problems with intergenerational (two generations) and transgeneration (three generations or more) epigenetic change. The reason why transgenerational epigenesis can’t really work is that the epigenetic marks are wiped off genes and histones during gamete formation, so induced epigenetic changes can’t be passed on. (What can be passed on is DNA that specifies that, to react to certain environmental stimuli like heat, epigenetic marks will be placed at positions X, Y, and Z.) Since female babies are born with their eggs already in place, their gametic marks aren’t wiped off until the next generation: the third.
And what about the Dutch and all that other stuff in the press about “non-Darwinian inheritance”? Well, some of it may be true (especially in plants), but Razib notes that there’s a publication bias towards positive results, which makes the probability values of the stuff that does get published dubious. Let me quote him:
How then to explain results like those from Sweden where grandfathers’ and grandmothers’ food deprivation was correlated with increased mortality of grandsons and granddaughters respectively? The p-values in these studies were below 0.05, so they were statistically significant (in other words, even if the default hypothesis is true, the probability is less than 5% that you’d get that result, so perhaps consider the alternative). Studies like this can see print because the design and results fall within scientific guidelines, so they technically meet a journal’s gatekeeping standards. But at this point, as most readers are aware, just because a study is statistically significant does not mean it will stand the test of time or its results be broadly replicable; the p-value tells you only the probability of the given outcome assuming a certain model, and sometimes unlikely things do happen. But it doesn’t tell you anything about all the comparable studies that never saw print because the statistics didn’t cooperate, nor does it reveal all the datasets selectively discarded because they turned out to be junk. A study, or studies, may show something, but the truth of a matter is established through many replications, ideally with controls for confounding variables that may be driving some of the intergenerational associations (obviously, more than genes are transmitted within families; folkways, customs and habits are acquired through imitation).
In addition, trite though the chestnut that correlation does not equal causation might be, in the case of transgenerational epigenetic transmission it cannot be avoided. Extraordinary claims contradicting over a century of established Mendelian genetics and seventy years of scientifically validated molecular biology require extraordinary evidence. In humans, many roadblocks remain to establishing that inherited characteristics in subsequent generations are due to environmental shocks in prior ones, not least that you cannot perform randomized controlled experiments. Inferences must be from observation studies, correlational or indirect (“natural experiments” like famines). Deeper digging reliability shows that cases where epigenetic marks seem to have been inherited transgenerationally actually turn out to be conditional on the existence of a conventional DNA mutation being passed on within the family. These mutations may induce a byproduct of distinctive epigenetic marks, so they are caused every generation by variants natural selection or drift favors. The causal role of the epigenetic variant in a trait may hold, but its transmission across generations due to the epigenetic mark is a mirage. Epigenetics in this case is downstream of conventional Mendelism. It is like some fine print addendum automatically regenerated anew by a DNA mutation every generation. A mere footnote to a well-characterized classical genetic process of inheritance.
In plain English, any case for the mechanism required to posit the inheritance of human epigenetic variation is a royal mess. That doesn’t mean that transgenerational epigenetic transmission doesn’t happen; it is well documented in plants and C. elegans (“worms”). A small body of candidate studies in humans also require further follow-up, but even these remain the object of strong skepticism from most biologists. Contrary to what headline writers and pop psychotherapists might like you to believe, thus far, epigenetics is terribly implausible as a factor in theories of human intergenerational trauma.
And a short summary explaining why epigenesis can’t be both important and ubiquitous:
Finally, even if transgenerational epigenetic transmission does occur, it has to be vanishingly rare and not very impactful in any studied organisms. Why? Simply because, for a century, conventional geneticists, using Mendel’s framework of mutations passed onward through pedigrees, have studied how characteristics are transmitted in the real world. If many traits were strongly dependent on (previously unnoticed) epigenetic insults in the few most recent generations, that would distort these results, and the deviations would emerge rapidly, as particularly well-studied organisms with distinctive traits might change after every novel shock. The existence of the entire field of transmission genetics negates the idea that epigenetic effects passed through families could ever be common, even in the case of plants where this is a well-known phenomenon. If epigenetic transmission was ubiquitous, then the textbooks of Mendelian genetics could never have been written. And stepping beyond basic science, applied fields like plant and animal breeding are underpinned by the Mendelian framework; epigenetic interruptions transmitted across generations could be economically disastrous, as farmers’ breeding projects would no longer yield the desired traits valuable to them.
But there are even deeper evolutionary biological reasons to be skeptical of epigenetic transmission. The persistence of fixed epigenetic marks across generations would undermine the plasticity and flexibility that epigenetics enables in individuals on a molecular scale. As a molecular mechanism, epigenetics grants cells and organisms the flexibility to adapt to short-term changed conditions and stressors; a high level of fidelity in future generations would verge on epigenetic determinism. If the duplication and passing on of DNA to future generations should be a high-fidelity process that maintains the characteristics natural selection has preferred, epigenetics should be a local adaptation mechanism that allows organisms to track environmental volatility without locking in one generation’s adaptations in perpetuity.
The excellent piece is written for the intelligent and scientifically inquisitive layperson, and you should read it to understand why epigenetic is so vital during the development of organisms, and yet so unimportant as a means of passing environmentally-induced changes across generations.
This article just appeared in the (conservative) City Journal, and is written by James Lee, a behavioral geneticist at the University at Minnesota. What Lee reports made steam issue from under my collar, for he claims that the National Institutes of Health, a U.S. government science institute, has a huge genetics and “trait” database of several million Americans. The genetic data appear to be thorough, based on genome scans, and the traits associated with each person’s genome include education, ethnicity (“race”), intelligence, income, and occupation. You can imagine how rich that dataset is for mining. And yet the NIH is restricting scientists’ access to the data to projects it apparently considers ideologically kosher.
Remember that the NIH is completely funded by the American taxpayers, so those data were accumulated with our money. To me, this means that any researcher with a valid project should have access to the data. But apparently some projects are more valid than others.
Click to read.
Here’s Lee’s description of the hard time geneticists have in getting the data when their project sounds “iffy”, and by that I mean any project that has to do with heredity and intelligence (presumably IQ or a similar measure). Note that none of the attempts to get the data have been to do projects on ethnicity and IQ, which of course are considered taboo by many (readers may want to either echo or refute that taboo). Check out the second paragraph of the excerpt below, which I’ve put in bold.
American geneticists now face an even more drastic form of censorship: exclusion from access to the data necessary to conduct analyses, let alone publish results. Case in point: the National Institutes of Health now withholds access to an important database if it thinks a scientist’s research may wander into forbidden territory. The source at issue, the Database of Genotypes and Phenotypes (dbGaP), is an exceptional tool, combining genome scans of several million individuals with extensive data about health, education, occupation, and income. It is indispensable for research on how genes and environments combine to affect human traits. No other widely accessible American database comes close in terms of scientific utility.
My colleagues at other universities and I have run into problems involving applications to study the relationships among intelligence, education, and health outcomes. Sometimes, NIH denies access to some of the attributes that I have just mentioned, on the grounds that studying their genetic basis is “stigmatizing.” Sometimes, it demands updates about ongoing research, with the implied threat that it could withdraw usage if it doesn’t receive satisfactory answers. In some cases, NIH has retroactively withdrawn access for research it had previously approved.
Note that none of the studies I am referring to include inquiries into race or sex differences. Apparently, NIH is clamping down on a broad range of attempts to explore the relationship between genetics and intelligence.
It’s hard to believe that the NIH is restricting data that might be used to show any relationship between genes and intelligence, even within one ethnic group. We already have data on genes implicated in academic achievement (which is correlated with IQ); those data are a big part of Kathryn Paige Harden‘s book The Genetic Lottery: Why DNA Matters for Social Equality, a book I reviewed for the Washington Post and also discussed on this website. As I recall, Harden’s genome-wide association study found nearly 1300 genomic sites associated with variation in academic achievement among the American European (“white”) population. Intriguingly, many of those sites were active in the brain. That in itself is of considerable interest, though Harden’s claim that this variation would help us create “level playing fields” for secondary-school students seemed unjustified. But even finding genes associated with intelligence would tell us a lot about the developmental genetics of an important human trait.
Lee also explains why the NIH should NOT be a censor of valid research projects:
What is NIH’s justification? Studies of intelligence do not pose any greater threat to the dignity of their participants than research based on non-genetic factors. With the customary safeguards in place, research activities such as genetically predicting an individual’s academic performance need be no more “stigmatizing” than predicting academic performance based on an individual’s family structure during childhood.
The cost of this censorship is profound. On a practical level, many of the original data-generating studies were set up with the explicit goal of understanding risk factors for various diseases. Since intelligence and education are also risk factors for many of these diseases, denying researchers usage of these data stymies progress on the problems the studies were funded to address. Scientific research should not have to justify itself on those grounds, anyway. Perhaps the most elemental principle of science is that the search for truth is worthwhile, regardless of its practical benefits.
NIH’s responsibility is to protect the safety and privacy of research participants, not to enforce a party line. Indeed, no apparent legal basis exists for these restrictions. NIH enforces hundreds of regulations, but you will search in vain for any grounds on which to ban “stigmatizing” research—whatever that even means.
This is a no brainer. The NIH has NO business vetting the “political correctness” of research, and since nobody is investigating The Taboo Question—racial (or “ethnic” differences in intelligence—that issue doesn’t even come up. The only reason to prohibit “genetics of IQ” studies is a strict (almost Marxist) anti-hereditarianism based on the fear that there may be a genetic basis to differences in IQ. But we already KNOW that from studies of adoptions and relatives, which show that about 50-60% of variation in IQ among people is due to variation in their genes. The NIH appears to be afraid of being canceled. That is a hell of a way to do scence!
And I can’t imagine why the NIH would even think of restricting the data for any other studies. It seems to be IQ that’s the sticking point here, and that’s unconscionable. The data belong to the American public, and to American scientists, because the American public paid for it.
I’ve always object to the demonization of research that gives results that are politically or ideologically unpalatable, but this goes beyond the pale. The government cannot withhold data paid for by us on the grounds that it might yield results that could offend people.
If a researcher has a valid reason to request these data, and the NIH refuses because of possible “stigmatizatization,” then I would say that a lawsuit is in order.
Have you been voting in Fat Bear Week? If not, today is the final day: the run-off between two heavyweights that will determine the Fattest Bear.
You probably realize that the bears get so fat in the fall because they are about to go into five months of hibernation, and need to stock up on food to sustain their metabolism as they go into winter. The Washington Post article shown below describes the remarkable phenomenon of hibernation, the potential bodily problems it poses, and new biochemical discoveries that help the bears obviate these issues and could also help immobile humans with the issue of atrophied muscles. Click to read:
Quotes from the article are indented:
But for many scientists, the true fascination of Fat Bear Week involves what happens next, when the now beachball-shaped bruins, carrying about 40 percent body fat, lumber into their dens and start hibernating. During hibernation, they remain healthy under conditions that would weaken and sicken mere humans. The bears emerge months later, lean, strong and barely affected by their months of starvation and inactivity.
Until recently, researchers could not explain how. But several fascinating new molecular studies suggest hibernation remodels bear metabolisms and gene activity in unique and dramatic ways that could have relevance for people. The fat bears can advance our understanding of diabetes, muscle atrophy, inactivity and the ingenuity of evolution.
Superficially, hibernating bears seem passive and inert. For five months or more, they do not eat, drink, urinate, defecate or move, except occasionally to turn over or shiver. Their metabolisms drop by about 75 percent. Hearts beat and lungs inflate only a few times a minute. Kidneys shut down. The bears grow profoundly insulin resistant.
If this were us, we would shed much of our muscle mass because of inactivity and probably develop diabetes, heart disease, kidney failure, frailty and other ills.
But the bears maintain their muscle and rapidly reestablish normal, healthy insulin sensitivity and organ function after hibernation.
Insulin functions to allow cells to absorb glucose from the blood to use as energy, or to convert some glucose to fat. It also helps break down fats and proteins. Normally, the onset of insulin resistance would, as the article implies, lead to diabetes and its attendant problems, but the bears are somehow able to tolerate that—as well as the muscle atrophy attendant on not moving for five months. (Muscle atrophy is a problem for people who are either paralyzed or bedridden for long periods of time.)
How do the bears do this? That’s the point of the article, which links to three scientific articles (one given below) explaining how the bears survive hibernation.
The information on fat usage came from blood samples drawn from hibernating and non-hibernating bears at Washington State University (WSU), bears trained to allow a blood draw without being anesthetized. (I guess the WSU bears also go into hibernation.)
It turns out that there is differential activation of genes in the bears during hibernation that protect them from deleterious effects of hibernation. Here are two papers cited:
By comparing the samples, [reserachers] concluded hibernation is biologically uncanny but hardly quiet. In a 2019 study, the WSU scientists and others found more than 10,000 genes in bears that work differently during hibernation vs. in autumn or spring. Many involve insulin activity and energy expenditure and most occur in the animals’ fat, which becomes quite insulin resistant during hibernation and robustly insulin sensitive immediately afterward.
Digging deeper into that process for a new study, published in September in iScience, they bathed fat cells drawn from hibernating and active bears with blood serum taken during the opposing time and watched the fat switch seasons. Fat from hibernating bears became insulin sensitive and genetically similar to fat from the active season and vice versa.
In other words, something in the blood serum of non-hibernating bears restored the insulin sensitivity of hibernating bears, and vice versa. This shows that it is something in the serum, and not in the fat, that changes during hibernation. The article continues:
Perhaps most compelling, they also identified and cross-matched hundreds of proteins in the animals’ blood and found eight that differed substantially in abundance from one season to the next. These eight proteins seemed to be driving most of the genetic and metabolic changes in the fat.
Of course correlation is not causation, and I doubt that 10,000 genes are involved in actually producing hibernation or mitigating its effects. (After all, humans have only about 25,000 protein-coding genes—more if you include as “genes” bits of DNA that do something but don’t produce proteins—and bears can’t differ that much from us. There may be changes in that many genes, but many of these may simply be side effects of natural selection changes the expression of many fewer genes.
But it’s clear that genes involved in insulin usage and sensitivity work differently in hibernating versus nonhibernating bears. What are the cues that turn these genes on and off? I doubt that we know, and the paper doesn’t say, but a good guess is that this has to do with environmental factors indicating the impending arrival of spring or fall: cues based on day length or temperature.
But what about the bears’ muscles? Why don’t they atrophy? Again, it’s due (as it must be) to differential activation of genes. And again, the gene products responsible seem to be circulated in the blood serum.
The paper below from PLoS ONE (click on screenshot to read; pdf here and reference at bottom), implicates both the blood serum and the genes involved in maintaining muscle.
The Japanese researchers bathed cultured human skeletal muscle cells in serum from either hibernating or non-hibernating black bears. What they found was significantly less degradation of protein when hibernating-bear serum was used. This appeared to be based on a gene-induced decrease in levels of two proteins and an increase in the level of another, which act in concert to preserve protein levels in the cultured cells. (The protein made in reduced amount breaks down muscle while the others promote and sustain muscle growth.) Altogether, changes in gene action appears to keep the bears’ muscles fairly intact as they go through hibernation.
Now these are cultured human cells, not bear cells, and the experiment was done in vitro rather than in vivo, but it gives a very promising lead to how bears keep their muscles strong during hibernation.
The Post article also lays out the potential uses of this information in human health.
Fat.
Potentially, these same eight proteins, which also appear in human blood, might at some point be harnessed pharmaceutically to improve insulin sensitivity or treat diabetes and other metabolic disorders in people, Kelley said. But that possibility lies far in the future and requires vastly more research with bears and us (although perhaps not in close proximity).
Muscle.
The ultimate aim of this research, [author] Miyazaki said, is to isolate and refine all of the substances and processes in hibernating bears’ blood and elsewhere in their bodies that protect them from muscle wasting, with the hope that these same elements might treat atrophy from bed rest or aging in people.
“There is probably no better way to maintain a healthy lifestyle than through physical exercise,” he said, but for people who cannot be active, for whatever reason, the internal operations of slumbering bears might someday provide respite from frailty.
It’s important to remember that these remarkable changes are certainly due to evolution via natural selection, as it’s hard to imagine a random process like genetic drift causing evolutionary changes that are certainly adaptive.
As Ernst Mayr emphasized, many important evolutionary changes in animals begin with a change in behavior. Perhaps bears in cold areas survived better if they underwent a period of low activity during winter when food is scarce (this behavioral change could reflect genetic variation), and then those quiescent bears who also had mutations affecting fat and muscle metabolism would be those most likely to survive hibernation, leaving their genes to future bear generations.
I had totally forgotten that it’s Nobel Prize season, and the first one, the Medicine or Physiology Prize, was awarded today—to the human evolutionary geneticist Svante Pääbo, a Swede. The reader who sent me the news had these immediate reactions:
Highly unusual that there is a single winner nowadays
How often has the prize gone to an evolutionary scientist (of any shape or form) ?
Probably being Swedish helped a bit!
Yes, the last “solo” prize was given in this field in 2016 to Yoshinori Ohsumi for his work on lysosomes and autophagy. As for the evolutionary biology, I’m not aware of anybody working largely on evolution who has won a Nobel Prize. The geneticist Thomas Hunt Morgan won one, but it was his students who became evolutionary geneticists. I also remember that when I entered grad school, my Ph.D. advisor Dick Lewontin was helping prepare a joint Nobel Prize nomination for Theodosius Dobzhansky and Sewall Wright, but Dobzhansky died in 1975 before it could be submitted, and posthumous Prizes aren’t given.)
Of course, Pääbo has worked on the evolution of the genus Homo, and a human orientation helps with the Prize, but his substantial contributions fully qualify him for the Big Gold Medal. As for him being Swedish, I don’t know if there’s some national nepotism in awarding prizes, but again, Pääbo’s work is iconic and no matter what nationality he was, he deserves one. And of course I’m chuffed that an evolutionary geneticist—one of my own tribe—won the Big One.
Click on the Nobel Committee’s press release or the NYT article below to read about Pääbo or go to his Wikipedia page.
NYT:
Pääbo is the leader of a large team, and has had many collaborators, but it’s clear that, if fewer than four people were to get the prize for work on human evolution, Pääbo would stand out as the main motive force, ergo his solo award. Sequencing the Neanderthal genome and estimating the time of divergence from “modern” H. sapiens (about 800,000 years)? That was Pääbo and his team. Finding the Denisovans, a separately-evolved group from Neanderthals? Pääbo and his team. Discovering that both of these groups interbred with our own ancestors, and we still carry an aliquot of their genes? Pääbo and his team. Learning that some of the introgressed genes from Denisovans have conferred high-altitude adaptations to Tibetans? Pääbo and his team. And that some Neanderthal genes confer modern resistance to infections? Pääbo and his team.
The man can truly be seen as the father of human paleogenetics—and he’s five years younger than I? Oy!
Although born in Sweden. Pääbo works mostly in Germany. Here’s his bio from the Nobel Prize Committee:
Svante Pääbo was born 1955 in Stockholm, Sweden. He defended his PhD thesis in 1986 at Uppsala University and was a postdoctoral fellow at University of Zürich, Switzerland and later at University of California, Berkeley, USA. He became Professor at the University of Munich, Germany in 1990. In 1999 he founded the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany where he is still active. He also holds a position as adjunct Professor at Okinawa Institute of Science and Technology, Japan.
A prize for work in evolutionary genetics! Well done, Dr. Pääbo!
Svante Pääbo
And a bit of biography from the NYT article:
Dr. Pääbo has a bit of Nobel Prize history in his own family: In a 2014 memoir, “Neanderthal Man,” he wrote that he was “the secret extramarital son of Sune Bergstrom, a well-known biochemist who had shared the Nobel Prize in 1982.”
It took some three decades of research for Dr. Pääbo to describe the Neanderthal genome that won him his own prize. He first went looking for DNA in mummies and older animals, like extinct cave bears and ground sloths, before he turned his attention to ancient humans.
“I longed to bring a new rigor to the study of human history by investigating DNA sequence variation in ancient humans,” he wrote in the memoir.
It would be no easy feat. Ancient genetic material was so degraded and difficult to untangle that the science writer Elizabeth Kolbert, in her book “The Sixth Extinction,” likened the process to reassembling a “Manhattan telephone book from pages that have been put through a shredder, mixed with yesterday’s trash, and left to rot in a landfill.”
