Category: evolution

Colossal Biosciences is still pretending it’s “de-extincted” the dire wolf

June 23, 2025 • 11:45 am

If you’ve read this site at all, you’ll know that Colossal Biosciences has pretended that it’s brought an extinct species back to life: the dire wolf (Aenocyon dirus), a carnivorous denizen of the temperate regions of North and South America. The dire wolf became extinct about 10,000 years ago, when there were already humans in the Americas.

The “dire wolf” project is only one of a number of de-extinction efforts Colossal has on tap, including bringing.back the dodo, the thylacine, and, most famously, the woolly mammoth.

None of these will work. What Colossal is doing is simply inserting a small handful of genes taken from “ancient DNA” sequences of fossilized animals into a close living relative (in the case of the dire wolf, that was the gray wolf), and then rearing this tweaked gray wolf in a surrogate mother (in this case, a domestic dog). Voilà: you get a gray wolf that, if you want fame and money, you can call a “dire wolf.”

But th0se genetic “edits” comprise a pitifully small fraction of the genes in the modern relative. In the case of the dire wolf, I wrote this:

 There were indeed 20 edits in the gray wolf genome, made in 14 genes, but five of those edits weren’t taken from the ancient DNA of the dire wolf; they were taken from mutations in dogs and gray wolves that resembled what Colossal thought dire wolves looked like. (We’re still not sure.) And among those five dog/wolf mutants were the color alleles that turned the faux wolves white.

Note that gray wolves have about 20,000 genes, so a maximum of only 0.07% of the gray wolf genome had been changed to something similar to the genome of dire wolvees, and some of those changes actually came from mutations in dogs and wolves.

For example, Colossal decided to color their dire wolves white, so they found color mutations in dogs or wolves that made these canids white, and inserted those mutations into the gray wolf genome.  It is highly unlikely that ancient dire wolves really were white; Colossal probably did this because the model “Dire Wolf” in the series “Game of Thrones” was white! A white canid on the savannah or plains would stick out like a sore thumb to its prey. I know of no temperate-zone canid or felid that’s white; the only white canids we see live in the Arctic, where they turn white in the winter.

I summarized four big problems with the dire wolf project in a Boston Globe op-ed called “De-extinction is a colossal disappointment” or go here to read the several posts I’ve written here about these misleading projects.  It’s important to realize that Colossal did not de-extinct the Dire Wolf. As I wrote in the Globe:

First, and most important, “de-extinction” is not de-extinction. The company says its claim to have de-extincted the dire wolf is legitimate because its edited pups meet some of the criteria for species “proxies” established in 2016 by the International Union for Conservation of Nature. But that claim is bogus. What Colossal has made is simply a gray wolf with a handful of genetic tweaks changing its size and color.

Eventually Colossal, through its chief scientist Beth Shapiro, admitted in a New Scientist article that no, it hadn’t made dire wolves but simply slightly genetically modified gray wolves. To wit (click to read):

But, realizing that this admission undercut the “gee-whiz” aspect of “de-extinction,” Shapiro and Colossal immediately did a 180º turn and asserted that yes, they really had made dire wolves—simply because they made a gray wolf that, they assumed, would grow up looking like the ancient dire wolf (they made three of these white wolves). In other words, if they made an gray wolf that resembled in some slight degree the extinct dire wolf (and let’s ignore behavior and ecology, which are unknown for the extinct canid), then they had brought back the dire wolf.  This is, of course, arrant nonsense.

Now Colossal, in a newsletter, doubles down again, affirming that it really has brought back the dire wolf. There are two videos and enthusiastic celebration of “de-extinction”. I quote from the newsletter (I’ve bolded every reference to their claim that they do have de-extincted dire wolves):

The dire wolves are growing. Fast.

Catch up on their latest milestones and massive growth in Pupdate 002.

Colossal’s Chief Animal Officer Matt James and animal husbandry manager Paige McNickle share the newest updates on the world’s first de-extinct dire wolves. At just over 6 months old and already weighing more than 90 pounds—around 20% larger than a gray wolf of the same age—they are hitting some major milestones. The pups are headed to their first vet visit for bloodwork and CT scans, and their diet has advanced to bones, chunk meat, and organ meat, and will soon move to full carcasses to mimic natural wild feeding.

Pack dynamics are also shifting as Remus steps into the alpha role with quiet confidence, while Romulus embraces his beta energy. And with Khaleesi’s introduction on the horizon, everything could change again.

Do not miss the first major update since their de-extinction debut.

Well, of course they doubled in size: they were just pups when they were released in their Secret Pasture somewhere in America! In the video below, Colossal is also crowing that the wolves are up to 20% larger (heavier?) than gray wolves at the same age, but they don’t say that this could be due to the highly enriched diet that the three white wolves have been given. The Colossal wolves do not have to hunt, but are handed high-quality kibble, organs, and ground meat, as well as bones: Could that have made them larger?

This is disingenuous all the way home.  I have no respect for Colossal, which has allowed the “de-extinction” hype to overwhelm the science. They are shills and should be ashamed of themselves.

If you want more of this, Beth Shapiro got the most publicity possible in this day and age by touting, among other stuff, the “de-extinction” stuff on the Joe Rogan Show. Rogan!

I can’t bear to listen to all three hours of this, but perhaps a patient reader can and will report in the comments:

Evolution meetings include an ideologically-based symposium on “teaching sex and gender”. It’s a spectrum, Jake!

June 20, 2025 • 11:00 am

A while back, the Presidents of the Society for the Study of Evolution (SSE), the American Society of Naturalists (ASN) and the Society of Systematic Biologists (SSB) posted this letter on the SSE website (click title to see archived version):

The letter was a response to Trump’s Executive order on sex, which gave the biological definition of sex: a binary based on the physiological apparatus for producing gametes of different size, of which there are two forms.  This is how the “Tri-Societies Letter” (henceforth “TSL”) started:

As scientists, we write to express our concerns about the Executive Order “Defending Women From Gender Ideology Extremism And Restoring Biological Truth To The Federal Government”. That Order states first, that “there are two sexes…[which] are not changeable”. The Order goes on to state that sex is determined at conception and is based on the size of the gamete that the resulting individual will produce. These statements are contradicted by extensive scientific evidence.

The TSL, posted on the SSE webpage, asserts that sex is a multivariate trait, is not binary but a spectrum, and that this spectrum occurs in all biological species. It adds this (bolding is mine):

Scientific consensus defines sex in humans as a biological construct that relies on a combination of chromosomes, hormonal balances, and the resulting expression of gonads, external genitalia and secondary sex characteristics. There is variation in all these biological attributes that make up sex. Accordingly, sex (and gendered expression) is not a binary trait. While some aspects of sex are bimodal, variation along the continuum of male to female is well documented in humans through hundreds of scientific articles. Such variation is observed at both the genetic level and at the individual level (including hormone levels, secondary sexual characteristics, as well as genital morphology). Beyond the incorrect claim that science backs up a simple binary definition of sex, the lived experience of people clearly demonstrates that the genetic composition at conception does not define one’s identity. Rather, sex and gender result from the interplay of genetics and environment. Such diversity is a hallmark of biological species, including humans.

Note that it gives no way to determine whether an organism, including a human, is male or female! And how many sexes are there? This gives us no clue.

The letter went on to imply that all the members of the society, or at least nearly all of them, agreed with the Presidents’ views in the TSL:

Our three scientific societies represent over 3500 scientists, many of whom are experts on the variability that is found in sexual expression throughout the plant and animal kingdoms. More information explaining why sex lies along a continuum can be found here. If you wish to speak to one of our scientists, please contact any of the societies listed below.

It turned out that this was a distortion: the Societies had never polled their membership to see how many people agreed with their letter.

The result was considerable pushback against the TSL from scientists, 125 of whom wrote a letter to the Societies saying they didn’t agree with the TSL’s characterization of sex. Luana Maroja was the driving force behind this pushback, and the letter included this (I signed it, of course):

However, we do not see sex as a “construct” and we do not see other mentioned human-specific characteristics, such as “lived experiences” or “[phenotypic] variation along the continuum of male to female”, as having anything to do with the biological definition of sex. While we humans might be unique in having gender identities and certain types of sexual dimorphism, sex applies to us just as it applies to dragonflies, butterflies, or fish – there is no human exceptionalism.   Yes, there are developmental pathologies that cause sterility and there are variations in phenotypic traits related to sexual dimorphism. However, the existence of this variation does not make sex any less binary or more complex, because what defines sex is not a combination of chromosomes or hormonal balances or external genitalia and secondary sex characteristics. The universal biological definition of sex is gamete size.

You can see my other posts about this kerfuffle here.

The response from the Societies can’t be posted as we were refused permission to do so, but I characterized it this way:

. . . . this time we asked for a response and got one, signed by all three Presidents.  I can’t reprint it because we didn’t ask for permission [we later did but were refused], but some of its gist is in the response below from Luana [Maroja]. I will say that they admitted that they think they’re in close agreement with us (I am not so sure!), that their letter wasn’t properly phrased, that some of our differences come from different semantic interpretations of words like “binary” and “continuum”(nope), and that they didn’t send the letter anyway because a federal judge changed the Executive Order on sex (this didn’t affect our criticisms). At any rate, the tri-societies letter is on hold because the organizations are now concerned with more serious threats from the Trump Administration, like science funding.

The upshot was that the Societies eventually decided to remove the letter from the SSE website. What remains on the the original page is this, “This letter was originally posted on February 5th. A revised version is in progress and will be posted shortly.”

We are still waiting. I’m betting that no revision will ever appear. And it shouldn’t, for it’s not good for the premier evolution societies to pretend that biologists see sex as a spectrum.

What I’m leading up to is that, at the SSE’s annual conference taking place this month, the Society is sponsoring a three-hour symposium with four lecturers, a symposium that seems designed to reiterate the premises of the now-vanished letter. You can see the summary of this symposium by clicking on the link below to see synopses of the four lectures; then click on the bottom symposium, which looks like this:

If you go through the written summaries of the talks, you will see two themes reiterated:

1.) Biological sex is not binary but multifaceted, a “complex suite of traits across multiple organizational levels”.  No definition of biological sex appears to be given.

2.) Teaching that sex is binary harms those people who feel they’re not part of the binary, presumably nonbinary people, genderfluid people, some trans people, and the like. An important goal of teaching about sex and gender is to avoid harming people, and this form of teaching must be designed to avoid that harm.

The first point simply reiterates what was in the now-disappeared letter.  It makes the argument that many “progressive” biologists make: sex involves a combination of different traits.  This of course neglects the universality of the gametic definition, for no other definition holds for all animals and vascular plants. That’s why the definition (really a post facto observation) is used. In fact, many of those who hold to the “multifactoral” definition never even give a definition of sex, so I don’t know how they can tell that, say, a rabbit is male or female.

The second point turns biology teaching into a form of social engineering or propaganda: we must teach about sex in a way that does not harm people (i.e., offend them). I see this as distortion of biological truth in the interests of social justice, something that Luana and I discussed in our paper “The Ideological Subversion of Biology.” In fact, of course, teaching that biological sex is binary should not make anybody feel worthless or demeaned, for the dignity and rights of people depend not on biology but on morality, which is a social construct.  I have made this point endlessly and won’t repeat it here; see the end of the paper linked just above.

Some quotes from the summary and the abstracts:

Symposium summary at the beginning:

This symposium will explore the current science behind sex and gender, explore how educators can move their instruction beyond simple binary XX/XY paradigms, and provide educational materials for teaching this nuanced and difficult subject.

The non-binary nature of sex:

However, “biological sex” can describe a complex suite of traits across multiple organizational levels, including chromosomal inheritance, physiology, morphology, behavior, etc. To capture the full range of sex variability and diversity, we must critically assess our research approaches for studying sex associated traits. In this talk, I will provide practical guidance for conceptual frameworks, experimental designs, and analytical methods for studying and teaching the biology of sex. I invite fellow scientists and educators to conscientiously apply these inclusive approaches, to advance our biological understanding of sex and to encourage academically and socially responsible outcomes of our research.

. . . . Biology is the study of the diversity of life, which includes diversity in sex, gender, sexual behavior, and sexual and romantic orientations. However, the few existing studies of biology textbooks and classrooms suggest that many textbook authors and classroom instructors represent only a narrow swath of this diversity which can lead to an over emphasis on binary sex, conflation of sex and gender, and reinforcement of essentialisms.

Biological sex is a complex and highly variable trait; however, overly simplistic explanations are common in undergraduate biology classrooms. Here we test the impact of an accurate approach to teaching about the diversity of biological sex in organismal biology (‘treatment’ lecture) and compare this approach to a ‘traditional’ lecture section of the same introductory biology course.

The harm of teaching sex “wrongly”.

Although science is thought to be objective and free of emotion, many people are uncomfortable talking about the biology of sex. That discomfort and fear leaves room for hostile attacks on the science of sex to easily propagate through political and social channels. This creates unique challenges for educators in this area. In this presentation, I will discuss the biological basis of sex and sexual diversity from the perspective of a developmental biologist. The hierarchical nature of development connects genetics to phenotypes. Development dictates how sexual diversity emerges within species. The evolution of development dictates how sexual diversity arises among species. I will use development to demonstrate how biologists can distill complexity down into understandable chunks to address the most pervasive misconceptions about sex, especially those actively being used to take away
people’s rights.

. . . To more fully characterize the current range of narratives about sex, gender, sexual behavior, and orientation (SGBO narratives) present in undergraduate biology courses, we interviewed a national sample of 53 biology majors whose genders do not align with the sex they were assigned at birth (i.e., trans-spectrum students) about the SGBO narratives they encountered in biology courses.

We analyzed interviews using reflexive thematic analysis with the goal of identifying SGBO narrative in biology content and how these narratives supported or harmed these students’ sense of belonging in biology classrooms.  We found five SGBO narratives that harmed trans-spectrum students’ sense of belonging.  We also found three narratives that supported trans-spectrum students’ belonging.  These narratives could manifest in the classroom in multiple ways ranging from short disclaimers to elaborate case studies. The ways the narratives manifested influenced their impact on at least some students. These narratives and how they manifest provide potential teaching suggestions to both support trans-spectrum in STEM classrooms and more accurately teach the diversity of biology of sex, gender, sexual behavior, and orientation.

(Continuing the last quote in the section just above):

. . . We show that (1) the treatment lecture has a positive impact on feelings of inclusion for LGBTQIA+ students, (2) the treatment lecture had a positive impact on LGBTQIA+ and TGNC (transgender and gender nonconforming) student experiences in the course compared to other students. . .

This is not a huge deal, but I don’t think that one should distort the most widely accepted definition of sex to avoid offending people who don’t think they adhere to it.  I can’t see any other reason for this symposium. And yes, sex is binary, and that’s universal: there are only two types of gametes, and this holds across all animals and vascular plants. It’s not only universal but useful, for the binary enables us to understand one of the most important phenomena in biology: sexual selection, a form of selection that leads to differences between males and females. Of course teachers should be sensitive to their audience and not denigrate those who feel non-binary, but they should also teach the conventional wisdom about sex, which is apparently not going to happen at this symposium.

Michael Lynch takes apart two attempts to forge new evolutionary “laws”

June 13, 2025 • 10:00 am

Biology isn’t really like physics: we don’t have “laws” that are always obeyed, but instead have generalizations, some of which hold across nearly organisms (but even the “law” that organisms have DNA as their genetic material is flouted). The only “law” I can think of is really a syllogism that Darwin used to show natural selection: a). if there is genetic variation among individuals for a trait, and b). if carriers of some of the variants leaves more copies of their genes for the trait than carriers of other variants, then c). those genes will be overrepresented in future generations, and the trait will change according to the effects of the overrepresented genes.

But even that is not a “law” but a syllogism. After all, natural selection doesn’t have to work.  There may be no genetic variation, as in organisms that are clonal, and different variants may not leave predictably different copies of themselves in future generations; such variants are called “neutral”.  So there is no “law” that natural selection has to change organisms.

In this paper (click on screenshot below, or find the pdf here), evolutionary geneticist Michael Lynch from Arizona State University goes after two papers (cited at bottom of this post) that, he says, are not only failed attempts to concoct “laws” of evolution, but are flat wrong because their proponents don’t know squat about evolutionary biology.  I’ll try to be very brief because the arguments are complex, and unless you know Lynch’s work on the neutral theory, much of the paper is a tough slog.  What is fun about the paper, though is that Lynch doesn’t pull any punches, saying outright that the authors don’t know what they’re doing.

Here’s the abstract followed by an early part of the paper, just to show you what Lynch is doing. Bolding is mine:

Abstract:  Recent papers by physicists, chemists, and geologists lay claim to the discovery of new principles of evolution that have somehow eluded over a century of work by evolutionary biologists, going so far as to elevate their ideas to the same stature as the fundamental laws of physics. These claims have been made in the apparent absence of any awareness of the theoretical framework of evolutionary biology that has existed for decades. The numerical indices being promoted suffer from numerous conceptual and quantitative problems, to the point of being devoid of meaning, with the authors even failing to recognize the distinction between mutation and selection. Moreover, the promulgators of these new laws base their arguments on the idea that natural selection is in relentless pursuit of increasing organismal complexity, despite the absence of any evidence in support of this and plenty pointing in the opposite direction. Evolutionary biology embraces interdisciplinary thinking, but there is no fundamental reason why the field of evolution should be subject to levels of unsubstantiated speculation that would be unacceptable in any other area of science.

. . . we are now living in a new kind of world. Successful politicians and flamboyant preachers routinely focus on the development of false narratives, also known as alternative facts, repeating them enough times to convince the naive that the new message is the absolute truth. This strategy is remarkably similar to earnest attempts by outsiders to redefine the field of evolutionary theory, typically proclaiming the latter to be in a state of woeful ignorance, while exhibiting little interest in learning what the field is actually about. Intelligent designers insist that molecular biology is too complex to have evolved by earthly evolutionary processes. A small but vocal group of proselytizers clamoring for an “extended evolutionary synthesis” continues to argue that a revolution will come once a critical mass of disciples is recruited (7–9), even though virtually every point identified as ignored has been thoroughly evaluated in prior research; see table 1.1 in ref. 6. More than one physicist has claimed that all of biology is simply physics. But 2023 marked a new level of advocacy by a small group of physicists, chemists, and geologists to rescue the field of evolutionary science from obfuscation, and to do so by introducing new theories and laws said to have grand unifying potential.

Note Lynch’s criticism of the “Extended Evolutionary Synthesis”, a program (and associated group of investigators) who claim revolutionary ways of looking at evolution, which, as Lynch notes, have already been discussed under conventional neo-Darwinian theory.

There are two theories Lynch criticizes in this paper

1.) Assembly theory. This is the complicated bit from the paper of Sharma et al. (see references below). It involves an equation that supposedly gives a threshold beyond which the assembly of components indicates life that evolved via natural selection (I won’t define the components, either, which aren’t important for the general reader’s purpose:

According to Walsh, this equation is totally bogus because it neglects all the forces that can impinge on gene forms during evolution. An excerpt:

However, this is not the biggest problem with assembly theory and its proposed utility in revealing the mechanistic origins of molecular mixtures. A second, more fundamental issue is that the authors repeatedly misuse the term selection, failing to realize that, even in its simplest form, evolution is a joint function of mutation bias, natural selection, and the power of random drift. There is a fundamental distinction between the mutational processes that give rise to an object and the ability of selection (natural or otherwise) to subsequently promote (or eradicate) it. In the field of evolution, drift refers to the collective influences of stochastic factors governed by universal factors such as finite population size, variation in family sizes, and background interference induced by the simultaneous presence of multiple mutations; via the generation of noise, the magnitude of drift modulates the efficiency of selection. For the past century, these processes have been the central components of evolutionary theory (reviewed in refs. 5 and 6).

Because this theory neglects forces like mutation and genetic drift that can change frequencies of gene forms beyond natural selection, Lynch deems it “a meaningless measure of the origins of complexity.”

2.) The notion that organismal complexity is an inevitable result of natural selection. This goes after the paper of Wong et al., and you should already know that this can’t be true: evolution is not, in any lineage, a march towards more and more complex species. The immediate refutation is the existence of parasites like fleas and tapeworms, which have lost many of their features to pursue a parasitic lifestyle.  If you make your living by parasitizing other organisms, natural selection can actually favor the loss of complexity. Tapeworms, for example, have lost many of their sensory systems, their digestive system, and features of their reproductive system.  By any measure of complexity, they are much simpler than their flatworm ancestors.

Lynch points this out, and adds that there are lineages of microbes (very simple one-celled organisms like bacteria) that have not become more complex over the billions of years they existed. There may have been a burst of complexity when the lineages arose, but clearly bacteria haven’t been on a one-way march to primates. They are doing a fine job as they are:

Despite their substantially more complex ribosomes and mechanisms for assembling them, eukaryotes do not have elevated rates or improved accuracies of translation, and if anything, catalytic rates and degrees of enzyme accuracy are reduced relative to those in prokaryotes (with simpler homomeric enzymes). Eukaryotes have diminished bioenergetic capacities (i.e., growth rates) relative to prokaryotes (21, 22), and this reduction is particularly pronounced in multicellular species (23). Finally, it is worth noting that numerous organisms (parasites in particular, which constitute a large fraction of organisms) typically evolve simplified genomes, and many biosynthetic pathways for amino acids and cofactors have been lost in the metazoan lineage.

Another bit of evidence against Wong et al. is that their adducing “subfunctionalization”, whereby genes duplicate and the duplicate copies assume new functions, shows some “law” of increasing complexity. (The divergence of hemoglobins occurred in this way.) But Lynch suggests that genes don’t duplicate to make an organism more complex, and, moreover, the differential functions of duplicate genes can arise from selection being relaxed:

Subfunctionalization does not arise because natural selection is striving for such an endpoint, which is an energetic and a mutational burden, but because of the relaxed efficiency of selection in lineages of organisms with reduced effective population sizes. How then does one relate gene number to functional information?

Lynch winds up excoriating these new “theories” again:

For authors confident enough to postulate a new law of evolution, surely some methodology and supportive data could have been provided. Science is littered with historical fads that became transiently fashionable, only to fade into the background, with a nugget of potential importance sometimes remaining (e.g., concepts derived from chaos theory, concerted evolution, evolvability, fractals, network science, and robustness). But usually when the latter happens, there is a clear starting point. This is not the case with the “law of increasing functional information,” which fails to even provide useful definitions of function and information.

. . . . To sum up, all evidence suggests that expansions in genomic and molecular complexity, largely restricted to just a small number of lineages (one including us humans), are not responses to adaptive processes. Instead, the embellishments of cellular complexity that arise in certain lineages are unavoidable consequences of a reduction in the efficiency of selection in organisms experiencing high levels of random genetic drift.

I would take issue only with Lynch’s claim that only a “small number of lineages” have become more complex than their ancestors.  Most multicellular organisms are this way.  In the end, though, Lynch’s lesson is that people should learn more about evolutionary theory, which has grown quite complex, before they start proposing “revolutionary laws of evolution.”

The two papers at issue (I’ve provided links.)

10. A. Sharma et al., Assembly theory explains and quantifies selection and evolution. Nature 622, 321–328 (2023).

11. M. L. Wong et al., On the roles of function and selection in evolving systems. Proc. Natl. Acad. Sci. U.S.A. 120, e2310223120 (2023). 

Possible evolution of hummingbird beaks since WWII

May 28, 2025 • 10:45 am

The report below may represent a case of rapid adaptive evolution of a trait: the beaks of Anna’s hummingbirds (Calypte anna) in California, though there are sufficient confounding factors that, were I teaching evolution, I would still use Peter and Rosemary Grant’s work on the beaks of medium ground finches in the Galápagos as my paradigm. (The Galápagos incident occurred over a single year on one small island and confounding factors are virtually nil).

First the species: a male Anna’s Hummingbird flying:

Robert McMorran, United States Fish and Wildlife Service, Public domainvia Wikimedia Commons

and a female hovering:

Mfield, Matthew Field, CC BY-SA 3.0 via Wikimedia Commons

Click below to read the article, and find the pdf here.

The authors posited that the increasing use of hummingbird feeders after WWII would select for changes in the bill length of this species because individuals who could reach and consume more nectar from newfangled feeders (which reward copious nectar swilling) would have a reproductive advantage. Their predictions were met, but there are complications.

Here’s a hummingbird feeder:

Centpacrr at English Wikipedia, CC BY-SA 3.0, via Wikimedia Commons

That’s a very common design, with the feeder filled with sweet liquid: often sugar water, which is okay but commercial nectar containing other nutritive substances is better. The paper describes the spread of feeders and the morphology of AH beaks over time, using about 400 museum specimens gathered since 1860. Feeders, though, were introduced mostly after WWII (from the paper):

Although it likely existed earlier, we report that the widespread recreational hummingbird feeding can be traced back to an article published in National Geographic in 1928 documenting how to ‘tame’ hummingbirds by making bottles of sweet liquid masquerading as flowers (Bodine 1928); this method is thought to have directly influenced the first patented hummingbird feeder in 1947 (True 1995). As a result of this newly popularized feeder, terms associated with hummingbird feeders in local newspapers increased rapidly from southern to northern California, where feeder density began its increase in the historic range accompanied by an increase of ANHU populations as they moved north.

Based on the spread of hummingbird feeders, the authors posited an evolutionary change in beak shape (remember, this is over 80 years):

We therefore expect feeders to select for increased volume with each lick resulting from increased bill length and thickness. In feeders, unlike flowers, nectar pools are not quickly depleted and therefore the short distance between the bill tip and the nectar surface remains relatively constant, such that minimizing the bill-nectar gap allows higher licking rates and extraction efficiency (Kingsolver and Daniel 1983; Rico-Guevara et al. 2015; Rico-Guevara and Rubega 2011; Kingsolver and Daniel 1983).

“Minimizing the bill-nectar gap” involves evolving longer bills. And getting more capacious bills allows you to take in more nectar in one slurp.

And this is what they found.  First, though, there are quite a few confounding factors that the authors had to consider:

  • Eucalyptus trees, an invasive species and also a source of food for Anna’s Hummingbird (called AH in this post), also spread over that period
  • Humans also spread, and urbanization spread from southern to northern California, so there is a climatic factor to consider, too. Since bills are a source of heat loss, we expect birds in colder climate sin the north to have shorter bills (and they did indeed find this)
  • Feeders could have a secondary effect by promoting fights between males, who try to monopolize the “nectar” source. It could be this fighting that would select for changes in bill shape, since bills are used in fighting. Attendant changes in female shape could simply be a byproduct of selection in males.
  • Increased urbanization itself could change beak shape, perhaps because it leads to planting of flowers that select for longer bills

Data analysis was done (this is above my pay grade) using a multivariate analysis, taking into account year, location, temperature, beak measurements, and the abundance of feeders and Eucalyptus trees. The latter two factors were estimated—not very satisfactorily—using newspaper mentions since 1880. The results were these:

  • The abundance of eucalyptus trees had a small effect on increasing bill length and thickness, but it was much smaller than. . . .
  • The density of feeders, which had a highly significant effect, increasing both bill length and thickness (bill dorsal area) in the predicted way
  • However, bill size was smaller in colder climates, representing a presumed tradeoff between acquiring nectar from feeders and conserving heat when it’s cold
  • Human population size and year also had strong effects, changing the trait in the expected direction, as one would expect if natural selection were causing evolution of bill size and shape over time
  • Feeder density had a stronger effect on population size of AHs in northern rather than southern California. From the paper:

We find that feeders and human population size are both strongly positively associated with ANHU [Anna’s Hummingbird] counts (Figure S9) and each appear to have facilitated population growth differently throughout California (Figure 1B,C). Specifically, feeder availability appears to have facilitated population growth at northern latitudes, whereas human population size appears to have contributed more strongly to population growth in ANHU’s native range in southern California. These findings corroborate work conducted by Greig et al. (2017) suggesting that hummingbirds at northern latitudes are more reliant on feeders in winter than those at southern latitudes, while ANHU population growth is supported by urbanized human environments.

Why urbanized environments select for higher hummingbird populations independently of feeders is a bit counterintuitive, but perhaps it has to do with planted gardens.

The upshot:  So, do we have an example of evolution by natural selection here, one based on the proliferation of feeders causing evolution in beak length and shape? It’s possible, but there are a lot of problems. They include a rather small sample size for a model with many covarying factors, the use of newspapers to estimate feeder and Eucalyptus density, an unexplained change in beak shape with feeder density (a constriction appears in the middle of the beak), and no solid evidence that the change is really genetic rather than a change in beak shape induced environmentally by the use of feeders.  (I’ll add, though, that increasing change in time suggests genetic evolution rather than a one-time environmental modification by using feeders.) But the Grants’ work had pretty strong evidence that the change in beak size in the Medium Ground Finch on Daphne Island was genetically based. (They did a heritability analysis.)

One way to test this hypothesis would be to take an area lacking many feeders, but having Anna’s Hummingbirds, and then saturate it with feeders (best to use commercial nectar). If you monitor the birds over a number of years, one should expect to see, in that one small area, a change in beak shape. But nobody is going to do this experiment, because they’d probably expire before it was done. The Grant’s experiment documented change in beak shape over just a single year, and is, to me, far more convincing.

Ghost clades: a gazillion taxa detected solely by sequencing DNA from the environment (including dolphins’ mouths)

May 15, 2025 • 10:00 am

Yesterday I posted about the discovery of a new member of the archaea that was found by sequencing DNA taken from inside a single eukaryotic dinoflagellate (there were three other species inside or associated with that cell, too). The DNA sequence I talked about belonged to what the authors named Candidatus Sukunaarchaeum mirabile. The circular genome of this microbe was unique in having the complete genetic apparatus for self replication (unlike viruses), but (unlike most other prokaryotes) had no genes for metabolism.  The authors theorize, and I agree, that it is likely some kind of parasite, commensal, or symbiont that is obligately associated with other species.  The question is whether, without the ability to metabolize—but with the ability to reproduce—whether Candidatus Sukunaarchaeum mirabile was alive.  I have no dog in that fight, but readers differed. It’s bloody hard to define “life”, though I like Richard Dawkin’s c0ncept that life is whatever can evolve via natural selection. And clearly Candidatus Sukunaarchaeum mirabile could.

At least one commenter deemed the DNA sequence of Candidatus Sukunaarchaeum mirabile as an artifact of “DNA contamination”, though I don’t understand how that could happen. Further, the assembly of the DNA into a genome was deemed artifactual, although again, given how the authors did this, and that the DNA was circular, I don’t understand that, either.

But, intrigued, I did a bit of digging. It turns out that there are a ton of organisms, mostly archaea and bacteria, that have been identified solely from their DNA sequences, and they cannot really be artifacts because they fall into a good phylogenetic tree. In addition, they used  16 ribosomal DNA genes, which tend to be clustered together on the chromosomes, and did multiple reads of all sequences to put together overlapping fragments to build coherent genomic sequences.

The object of the paper below was to sample the environment and, without isolating individual organisms, see how many were new to science simply by looking for novel DNA sequences.  The summary is in a rather old (2016) paper in Nature Microbiology, and I haven’t looked for any updates. The upshot, which you can see by clicking on the screenshot below or reading the pdf here, is that there are a gazillion new species, mostly prokaryotes (bacteria + archaea) that we didn’t know about before. Indeed, the new species, based on limited sampling, imply that we only know a smallish fraction of the organisms on the planet.

I call these groups “ghost clades” because they are known only from their DNA and not from physical appearance or other evidence.

 

The method:

The authors got DNA from a variety of locations (indented sections from the paper); bolding is mine:

This study includes 1,011 organisms from lineages for which genomes were not previously available. The organisms were present in samples collected from a shallow aquifer system, a deep subsurface research site in Japan, a salt crust in the Atacama Desert, grassland meadow soil in northern California, a CO2-rich geyser system, and two dolphin mouths. Genomes were reconstructed from metagenomes as described previously. Genomes were only included if they were estimated to be >70% complete based on presence/absence of a suite of 51 single copy genes for Bacteria and 38 single copy genes for Archaea. Genomes were additionally required to have consistent nucleotide composition and coverage across scaffolds, as determined using the ggkbase binning software (ggkbase.berkeley.edu), and to show consistent placement across both SSU rRNA and concatenated ribosomal protein phylogenies.

Note that they looked at only six sites, including, yes, two dolphin mouths.  Why the dolphins? I don’t know. At any rate, they they sequenced the hell out of DNA taken from these sites.  They didn’t do complete genomic sequencing, but did enough to identify individual species using DNA sequences coding for 16 different ribosomal proteins: well-known genes that produce proteins that are part of the ribosomes—the sites where DNA is translated into other proteins.  This was a ton of work because they had to put the separate sequences together into organisms. Here’s their rationale for using rDNA:

To render this tree of life, we aligned and concatenated a set of 16 ribosomal protein sequences from each organism. This approach yields a higher-resolution tree than is obtained from a single gene, such as the widely used 16S rRNA gene. The use of ribosomal proteins avoids artefacts that would arise from phylogenies constructed using genes with unrelated functions and subject to different evolutionary processes. Another important advantage of the chosen ribosomal proteins is that they tend to be syntenic and co-located in a small genomic region in Bacteria and Archaea, reducing binning errors that could substantially perturb the geometry of the tree. Included in this tree is one representative per genus for all genera for which high-quality draft and complete genomes exist (3,083 organisms in total).

The observation that rRNA genes tend to be near each other on the chromosome allows them to get a big chunk of genome.  After they sequenced these genes, they concatenated them: putting all 16 genes together into one big sequence. That big sequence was then subject to phylogenetic (“family tree”) analysis, and, lo and behold, below is the tree they got, taken from the paper (click to enlarge):

The groups that were previously unknown as organisms are indicated with red dots, and the top part of the graph comprises bacteria. The archaea are the smaller group of colored taxa at lower left, while the eukaryotic DNA (and organisms) are at lower right. Note that bacteria are by far the most common new taxa they found (red dots), but a lot of archaea were also new. There were, as expected, no new eukaryotes, as we know most of the sequences of their groups.  Also, although the authors say they can’t definitively resolve the placement of eukaryotes in the tripartite group, they do say that eukaryotes seem to have arisen from within archaea, and we now know that is true.

(From paper): The tree includes 92 named bacterial phyla, 26 archaeal phyla and all five of the Eukaryotic supergroups. Major lineages are assigned arbitrary colours and named, with well-characterized lineage names, in italics. Lineages lacking an isolated representative are highlighted with non-italicized names and red dots. For details on taxon sampling and tree inference, see Methods. The names Tenericutes and Thermodesulfobacteria are bracketed to indicate that these lineages branch within the Firmicutes and the Deltaproteobacteria, respectively. Eukaryotic supergroups are noted, but not otherwise delineated due to the low resolution of these lineages. The CPR phyla are assigned a single colour as they are composed entirely of organisms without isolated representatives, and are still in the process of definition at lower taxonomic levels. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick format in Supplementary Dataset 2.

What is most striking about the figure above is the huge radiation in purple at upper right, all of which are new taxa (I believe the authors consider them “phyla”). They call this group the Candidate Phyla Radiation, or CPR. It has hundreds of lineages new to science! And many of the archaea were new, too. Altogether, this shows that the diversity of life as judged from DNA sequences in the environment, is far greater than we knew.  But we expect that, don’t we? There are so many places bacteria can live, not that many people go looking for new ones, and they are small.

Here’s what you get when you put all the prokaryotic species into a conventional phylogenetic tree with branch lengths (click to enlarge). The CPR of bacteria is in purplish-blue at the bottom, all of which are new.

(From paper) The threshold for groups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and others are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting groups to have special taxonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives (red dots) are apparent from this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support from 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick format in Supplementary Dataset 2.

One final remark. Further “metagenomic” analysis showed that members of the CPR are unusual in that, like the new archaea species I mentioned yesterday, they have relatively small genomes and “restricted metabolic capacities.” None of the CPRs have compete citric acid cycles and also lack respiratory  chains and little or no capacity to synthesize amino acids or nucleotides. They must get these things (vital for life) from the environment, which may include these microbes living as parasites or symbionts. (That, of course, would make them harder to detect.) It’s not clear whether this loss of genetic abilities is a secondary reduction of a formerly complete set of abilities, or an early stage of building up metabolism. (Remember that our archaea discussed yesterday had no genes for metabolism.)

Here is the authors’ conclusion:

The tree of life as we know it has dramatically expanded due to new genomic sampling of previously enigmatic or unknown microbial lineages. This depiction of the tree captures the current genomic sampling of life, illustrating the progress that has been made in the last two decades following the first published genome. What emerges from analysis of this tree is the depth of evolutionary history that is contained within the Bacteria, in part due to the CPR, which appears to subdivide the domain. Most importantly, the analysis highlights the large fraction of diversity that is currently only accessible via cultivation-independent genome-resolved approaches.

All I can say are two things. First, there is surely more information now that expands these data, but I had no time last night to read more than this single paper. We may know most of the vertebrates on the planet, but as for insects, invertebrates, and bacteria, well, we don’t know jack. But that’s good! More work needed and cool things to discover!

Second, it’s a good things dolphins don’t brush their teeth. But some of them get help:

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Squeaky Clean 😁 Brushing dolphin’s teeth is a part of their daily husbandry, or health care. Maintaining healthy teeth and gums is just as important with dolphins as it is with humans. Fun Fact: Did you know dolphins only receive one set of teeth their entire life? . . . 📽By @dolphinsplus • • ————————————— 📥 Post your case on dentistry_everyday to get repost ————————————— Like & Follow for the love of dentistry and more such interesting content 💯. • Loved the outcome • Tag a Friend • ➖ dentistry_everyday • . dentistry dental dentist dentists dentalstudent dentalhygienist dentalart doctor doctors toothimplant dentalrestorations @dentistry.everyday dentalboards dentalradiography dentalveneers dentalclinic dentalclinicdesign dentalimplants teeth tooth dent dentallogo dentalassistant dentalcare dentalinstruments

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Three ecology and evolution societies finally remove their “sex definition statement” from the web

April 28, 2025 • 11:30 am

On February 6 of this year, the Presidents of three evolution/ecology societies (the Society for the Study of Evolution [SSE], the American Society of Naturalists [ASN], and the Society of Systematic Biologists [SSB]) put a letter on the SSE website. It was a reaction to a Trump executive order about the definition of sex, and the “tri-societies” statement asserted that sex is not binary (in ANY species), but was a multidimensional multifactoral “biological construct”.  I archived the letter here because I had a feeling that it would cause trouble.

It did. But first, read it below.  It was written, of course, as a kind of virtue-flaunting exercise to placate those who don’t feel that they are either “male” or “female” (“nonbinary” people). But in so doing, the three Societies promulgated a gross distortion of what many (I won’t say “most”, since I don’t know) biologists conceive of as the definition of sex, which is based on gamete size and is close to being binary as it comes. I’ve bolded bits of it below, bits that conflate sex and gender, throw in “lived experience” to add to the confusion, and claim that the nonbimodality of sex “is a hallmark of biological species,” implying that in all animals and plants the definition of sex is far more than bimodal.

Note that the members of these three societies were not polled about the so-called “scientific consensus” they assert; this is a diktat from the Presidents. Voilà: the original “tri-societies” letter:

President Donald J Trump
Washington, DC
Members of the US Congress Washington, DC
February 5, 2025

RE: Scientific Understanding of Sex and GenderDear President Trump and Members of the US Congress,

As scientists, we write to express our concerns about the Executive Order “Defending Women From Gender Ideology Extremism And Restoring Biological Truth To The Federal Government”. That Order states first, that “there are two sexes…[which] are not changeable”. The Order goes on to state that sex is determined at conception and is based on the size of the gamete that the resulting individual will produce. These statements are contradicted by extensive scientific evidence.

Scientific consensus defines sex in humans as a biological construct that relies on a combination of chromosomes, hormonal balances, and the resulting expression of gonads, external genitalia and secondary sex characteristics. There is variation in all these biological attributes that make up sex. Accordingly, sex (and gendered expression) is not a binary trait. While some aspects of sex are bimodal, variation along the continuum of male to female is well documented in humans through hundreds of scientific articles. Such variation is observed at both the genetic level and at the individual level (including hormone levels, secondary sexual characteristics, as well as genital morphology). Beyond the incorrect claim that science backs up a simple binary definition of sex, the lived experience of people clearly demonstrates that the genetic composition at conception does not define one’s identity. Rather, sex and gender result from the interplay of genetics and environment. Such diversity is a hallmark of biological species, including humans.

We note that you state that “Basing Federal policy on truth is critical to scientific inquiry, public safety, morale and trust in the government itself”. We agree with this statement. However, the claim that the definition of sex and the exclusion of gender identity is based on the best available science is false. Our three scientific societies represent over 3500 scientists, many of whom are experts on the variability that is found in sexual expression throughout the plant and animal kingdoms. More information explaining why sex lies along a continuum can be found here. If you wish to speak to one of our scientists, please contact any of the societies listed below.

Carol Boggs, PhD
President
Society for the Study of Evolution
president@evolutionsociety.org

Daniel Bolnick, PhD
President
American Society of Naturalists

Jessica Ware, PhD
President
Society of Systematic Biologists
president@systematicbiologists.org

You can see all my posts about the resulting kerfuffle here.  In short, intiially about twenty of us wrote to the three societies objecting to the letter’s scientific contentions. Eventually 125 people connected with evolution appended their names to the letter and were willing to make their objections public (see here). Richard Dawkins also got into the fray, and both he and I discovered independently that the three Presidents who signed the letter actually act as if sex were binary in their own published research. Further, two former Presidents of the SSE also publicly disagreed with the characterization of biological sex given above.

Finally, our letter signed by 125 people asked for an answer, and although we got one from the societies, we were also told we couldn’t make it public. So be it, but I did characterize the answer here, and the societies largely conceded our points. As I wrote:

. . . . this time we asked for a response and got one, signed by all three Presidents.  I can’t reprint it because we didn’t ask for permission [we later did but were refused], but some of its gist is in the response below from Luana [Maroja]. I will say that they admitted that they think they’re in close agreement with us (I am not so sure!), that their letter wasn’t properly phrased, that some of our differences come from different semantic interpretations of words like “binary” and “continuum”(nope), and that they didn’t send the letter anyway because a federal judge changed the Executive Order on sex (this didn’t affect our criticisms). At any rate, the tri-societies letter is on hold because the organizations are now concerned with more serious threats from the Trump Administration, like science funding.

It’s still on hold, but now they’ve taken it down (see below).

I closed my post this way:

I end by saying that scientific societies need not be “institutionally neutral” when they are dealing with issues that affect the mission of the societies, as the definition of sex surely does. But what’s not okay is for the societies to distort “scientific consensus” in the interest of ideology. I have no idea if the Presidents of these societies really believe what they said (as Dawkins has pointed out, all three Presidents use a binary notion of sex in their own biological work), but something is deeply wrong when you use one notion of sex in your own science and yet deny that notion when you’re telling politicians what scientists “really believe.”

It’s just wrong when three evolution societies give the public a distorted view of how biologists define “sex”, and even more wrong when they do so because they are motivated not by the search for truth but to cater to a certain ideology.

As this sad drama draws to an end, I was just informed that, after several months, the three societies have taken down their misguided diktat.  Go to this SSE website and you’ll see this note:

As they say, “a revised version is in progress and will be posted shortly.”  I look forward to the revised definition of sex!  I also note that, as far as I know, no members of the three Societies have been informed that the letter was removed (they were told that the letter was posted, but only several weeks after it went up).

I’m posting this simply as a public service, to inform members of the Societies, and others following kerfuffles about the definition of sex, that the letter was finally taken down and will be replaced. The silver lining is that although I found the original letter embarrassing to science–and just another reason for people not to trust science–the Societies are rethinking what they say about sex.  However, I doubt that the replacement letter is going to emphasize the bimodality of sex as it is defined by many biologists.  After all, the Societies have to be ideologically correct, don’t they?

h/t: Luana Maroja (who did nearly all the heavy lifting of writing responses, gathering signatures, and so on.

Now scientists are afraid to submit papers on evolution

April 15, 2025 • 11:45 am

This Washington Post article (click headline to read, or find it archived here), shows how chilled the research climate in America has become because of the Administration’s threats.  And the Admin hasn’t even said anything about evolution yet.  (Has anybody ever asked Trump or RFK Jr. whether they accept evolution?)

The threats involve not just the potential of being demonized for publishing on a subject that the administration might denigrate, but also the possibility of researchers in that area being punished because they’re foreigners.

A few quotes:

A few days before they were to submit a scientific paper together, an evolutionary biologist in Europe received an unexpected request from two co-authors in the United States.

After much thought, the co-authors said they preferred not to risk publishing at this time. One had just lost a job because of a canceled government grant; the other feared a similar fate if they went ahead with the paper. Although both were legally in the U.S., they worried they might lose their residency if their names appeared on a potentially controversial article.

The subject: evolution.

. . . .Although President Donald Trump’s executive orders have not targeted research involving evolution, the authors’ unease about publishing on the subject reflects the fear and uncertainty now rippling through the science world.

The paper “was months of work, but at the same time I know the current situation, and I’m scared for my friends in the U.S.,” said the European evolutionary biologist, who spoke on the condition of anonymity because they feared retaliation. “I told them, ‘If you think it is too dangerous, don’t do it.’ ”

Now granted, this is for a symposium volume (something that Steve Gould called the least-read form of scientific literature), with the paper and volume described in this way:

The withheld paper described ways in which evolution unfolds in both living and nonliving systems, a subject relevant to the search for life elsewhere in the universe. The authors included measurements and genomic data on different species. An example of evolution in the nonliving world would be the growth of the universe after the Big Bang, as new minerals and elements came into being, the European scientists said.

. . .The special edition of the Royal Society journal that was to have included the withdrawn paper, emerged from the Workshop on Information Selection and Evolution last October in Washington, which drew a multidisciplinary collection of 100 researchers from as far away as Japan to discuss the latest thinking on evolution.

“People were talking about the evolution of languages, the evolution of technology, the evolution of species, the evolution of minerals and atoms and planets and things like this,” Wong said. “It was just so scintillating.”

Of course there’s a big difference between biological evolution and the idea of “change”, even though people have tried to analogize them by confecting the idea of “memes” (which can’t explain the evolution of minerals, atoms, or planets), so this heterogeneity is why the volume doesn’t get my juices flowing.

But that is not the point. NO scientific paper should be withheld, or the authors forced to hide their real names, because they work and publish in a well-accepted field or are living under a government that is bludgeoning people left and right.  Every day it gets crazier, and every day science becomes subject to more censorship.