Friday: Hili dialogue

May 16, 2025 • 6:45 am

It’s Friday! It’s Friday! Gotta get down on Friday! Yep, it’s Friday. May 16, 2025, and National Barbecue Day.  Below is a stupendous barbecued beef rib with all the trimmings from one of my favorite places: Black’s in Lockhart, Texas. It was part of my first trip after the pandemic: a 2021 BBQ Tour of Texas. You can see Potato salad, beans, raw onions, jalapeño corn muffin, and sweet tea on the side (not visible).  Or get the brisket, but GO!

 

It’s also Biographer’s Day (which biographer?), National Pizza Party Day, Endangered Species Day, Love a Tree Day, National Chartreuse Day (the green version is one of my favorite liqueurs, and National Coquilles St. Jacques Day.

There’s a Google Doodle today, which takes you (click on screenshot) to another lunar game. I think Google is getting all astrology-y:

Readers are welcome to mark notable events, births, or deaths on this day by consulting the May 16 Wikipedia page.

Da Nooz:

*It looks like what I thought would be a no-brainer Supreme Court case: the birthright of citizenship, which Trump opposes, has run into some trouble. The Justices seem divided! 

The Supreme Court appeared divided after hearingarguments Thursday about the power of lower courts to issue nationwide injunctions, including rulings that have blocked President Donald Trump’s executive order restricting the guarantee of birthright citizenship nationwide.

Several liberal justices argued that Trump’s order denying automatic citizenship for U.S.-born babies is blatantly at odds with more than a hundred years of Supreme Court precedent. The court only indirectly considered the citizenship issue as it was more directly being asked to weigh the scope of nationwide injunctions. The arguments on Thursday — lasting a little more than two hours —largely focused on that issue.

The Trump administration asked the justices to scale back nationwide injunctions to apply only to the pregnant women, immigrant advocacy groups or states that challenged the ban — which opponents say conflicts with the Constitution, past court rulings and the nation’s history. More than 300 lawsuits have been filed challenging Trump’s actions, and courts in many cases have at least temporarily blocked many of his initiatives.

Solicitor General D. John Sauer told the justices that relief should be granted to people who sued, not other people, which he said “results in all these problems.” Justice Clarence Thomas, who asked the first question, said the country “survived until the 1960s” without nationwide injunctions.Justice Elena Kagan, a former solicitor general, questioned the practical effects of limiting nationwide injunctions, asking how else courts could address unconstitutional issues.

In the end the Court has to decide this one; injunctions by federal courts that apply nationwide won’t hold until the Big Court weighs in.  Either you’re a US citizen or not, and you can’t be a citizen in, say, Oregon but not Alabama. And the idea that relief applies only to those who sue is palpably stupid. It’s time for Roberts & Co. to bite the bullet. Are they afraid of striking down Trump’s orders?

*On her Broadview site, Lisa Selin Davis, who identifies as a liberal, tells us “There is a way to save PBS [Public Broadcasting System] and NPR [National Public Radio.”  And that’s to get rid of government funding and get all the money from the real public: individuals (h/t Enrico).

While I agree that Trump is depraved, I disagree that federally defunding NPR and PBS exemplifies it. Rather, I see this move as anything from reasonable to necessary. Mostly, I see it an opportunity.

Trust in the media remains at an all-time low. Many liberals understand the problem with highly biased news outlets, and regularly decry the slant of Fox or Breitbart, which baldly sell the intermeshing of editorial and news. But few of us would admit that NPR and PBS are also slanted—just in a complementary direction to our own views. (Well, not my views, but those of the people around me, aghast that someone would steal the Pride flag from in front of a brownstone, while preventing a woman from posting on the neighborhood listserv when her Israeli flag was stolen. My view is that if you’re gonna be upset about flag theft, you gotta be upset about both of those instances equally.)

Groups that comb the media for bias tend to rate NPR and PBS as left-ish, not full blown propaganda. But former NPR employee Uri Berliner wrote in The Free Press that the organization had “lost America’s trust” by representing “the distilled worldview of a very small segment of the U.S. population.”

NPR’s coverage of social and health issues has dutifully reflected the left-leaning worldviews such billionaires and their advocacy groups support. They took Dr. Rachel Levine at face value when saying that “Transgender Health Care Is An Equity Issue, Not A Political One.” A sampling of headlines: “Shifting Federal Policies Threaten Health Coverage For Trans Americans;” “New research finds trans teens have high satisfaction with gender care.” “How school systems, educators and parents can support transgender children.”

What reporters at NPR should have been doing was questioning whether the psychological and medical interventions of “gender-affirming care” added up to healthcare. They should have asked, and educated others about, what “trans” means, and where the idea of gender identity came from. They should have scrutinized the research they reported as showing interventions were successful, and not just reported the research with conclusions that affirmed their own worldviews. They should have examined the differences between adult transsexuals and young people seeking transition, and taken the idea of rapid-onset gender dysphoria seriously, rather than ignoring it. They should have explained that, no, this is not an equity issue—it’s an issue of science and of medical ethics, and it’s a cultural issue, related to how we understand, or don’t, gender… whatever the hell that word means.

Some of the bias:

· NPR refused to cover the Hunter Biden laptop story, calling it a waste of time and a distraction, despite that it was highly relevant to the presidential election.

· NPR repeatedly insisted COVID-19 did not originate in a lab and refused to explore the theory.

· The FBI, CIA, and Department of Energy have all since deemed the lab-leak theory the likely cause.

· NPR ran a Valentine’s Day feature around “queer animals,” in which it suggested the make-believe clownfish in “Finding Nemo” would’ve been better off as a female, that “banana slugs are hermaphrodites,” and that “some deer are nonbinary.”

· Research shows that “congressional Republicans faced 85% negative coverage, compared to 54% positive coverage of congressional Democrats,” on PBS’s flagship news program.

· Over a six-month period, PBS News Hour used versions of the term “far-right” 162 times, but “far-left” only 6 times.

. . . .  I’d say it’s a little more complicated when it comes to PBS, which relies more heavily on federal funding from the Corporation for Public Broadcasting than NPR does. I don’t think Masterpiece Theater and Antiques Roadshow are suffering from ultra-biased leftism, even if PBS NewsHour is. And I think Sesame Street was one of the greatest things that ever happened in television history (and I highly recommend this documentary about it). But I still don’t see a reason for all of America to subsidize such programming. Trump’s declaration is correct about this: “No media outlet has a Constitutional right to taxpayer subsidized operations, and it’s highly inappropriate for taxpayers to be forced to subsidize biased, partisan content.”

Like most Americans, I’d rather defund CPB than I would the police—and that’s not because I’ve turned right-wing. It’s because I ended up learning a lot more about race, gender, Covid, George Floyd, and many other things than my incredibly slanted liberal media gave me. Some of that knowledge came from consuming an omnivorous media diet, including certain outlets I was told would forever stain my soul if I consulted them. Mostly, I learned more because I found individuals whose reporting and analysis I could trust—the Substack model of journalism. But that’s not what I want, nor do I think most people have the time to figure out whom to trust. They want to trust a news outlet, not an newsperson.

After saying that the priorities of these venues should change, she avers that that’s nearly impossible, and so suggests this:

So here’s another version, although one that takes a similar route. If PBS and NPR want to stay open, they’re going to need to rely more on a different kind of public funding—by individual members of the public, not the money we give the government through taxes. That means they shouldn’t just appeal to a small band of educated elites who want to bask in the glow of their own certainty. They should undergo a massive ideological overhaul to more accurately reflect the views and tastes of America.

I agree. I used to listen to NPR a lot, as it’s one of the few stations I can get on my car radio, but lately I learn almost nothing by listening, and am angered that the station’s coverage is so slanted. It takes about 15 minutes of listening before you see where it’s coming from.  Now, only 10% of NPR’s total budget comes from the taxpayers, and 15% for PBS, but why not get rid of taxpayer funding altogether? If you want slanted media, that’s fine. But I’d really like a PUBLIC station that discusses all sides of the issues instead of the MSNBC of the airwaves.

*Several major league baseball players, including Pete Rose and “Shoeless” Joe Jackson, formerly placed on a list ineligible to be inducted into baseball’s Hall of Fame, have been reinstated again. Rose was banned for repeatedly betting on baseball, though not against his team (the Cincinnati Reds) when he was a player, and lying about it. He may have bet on the Reds, however, when he became manager.  Jackson was expelled for supposedly accepting bribes to throw the 1919 World Series when he played for the Chicago White Sox (this is the “Black Sox Scandal”).  Rose admitted guilt, but never admitting betting on (or against) his team; he holds several all-time records. From Wikipedia:

Rose was a switch hitter and is MLB’s all-time leader in hits (4,256), games played (3,562), at-bats (14,053), singles (3,215), and outs (10,328).[1] He won three World Series championships, three batting titles, one Most Valuable Player Award, two Gold Glove Awards, and the Rookie of the Year Award. He made 17 All-Star appearances in an unequaled five positions (second baseman, left fielder, right fielder, third baseman, and first baseman). He won two Gold Glove Awards when he was an outfielder, in 1969 and 1970. He also has the third longest hit streak in MLB history at 44, and remains the last player to hit safely in 40 or more consecutive games.

The NYT asked 12 living Hall of Famers if they thought Pete Rose should get in, even though he’s dead (article archived here).  By my count, four said “yes,” one said “no,” and the other seven either had no opinion or said it should be left up to those who vote. In my view, Rose shouldn’t get in for betting on baseball, for betting on (or against) his team, for besmirching the reputation of baseball (though players like Ty Cobb have done that, too), and because one reason he’s now eligible is because Trump raised a ruckus with the Commissioner of Baseball. Pressure from anybody shouldn’t count, only performance; but Rose’s betting and lying was part of his performance.

*Martha Nussbaum, a highly regarded professor of law and philosophy at my University, has given Judith Butler what the kids call “a sick burn” in a New Republic piece called, “The professor of parody: the hip defeatism of Judith Butler” (h/t Bryan). As I recall, she’s gone after Butler in print before. A few excerpts:

Feminist thinkers of the new symbolic type would appear to believe that the way to do feminist politics is to use words in a subversive way, in academic publications of lofty obscurity and disdainful abstractness. These symbolic gestures, it is believed, are themselves a form of political resistance; and so one need not engage with messy things such as legislatures and movements in order to act daringly. The new feminism, moreover, instructs its members that there is little room for large-scale social change, and maybe no room at all. We are all, more or less, prisoners of the structures of power that have defined our identity as women; we can never change those structures in a large-scale way, and we can never escape from them. All that we can hope to do is to find spaces within the structures of power in which to parody them, to poke fun at them, to transgress them in speech. And so symbolic verbal politics, in addition to being offered as a type of real politics, is held to be the only politics that is really possible.

These developments owe much to the recent prominence of French postmodernist thought. Many young feminists, whatever their concrete affiliations with this or that French thinker, have been influenced by the extremely French idea that the intellectual does politics by speaking seditiously, and that this is a significant type of political action. Many have also derived from the writings of Michel Foucault (rightly or wrongly) the fatalistic idea that we are prisoners of an all-enveloping structure of power, and that real-life reform movements usually end up serving power in new and insidious ways. Such feminists therefore find comfort in the idea that the subversive use of words is still available to feminist intellectuals. Deprived of the hope of larger or more lasting changes, we can still perform our resistance by the reworking of verbal categories, and thus, at the margins, of the selves who are constituted by them.

One American feminist has shaped these developments more than any other. Judith Butler seems to many young scholars to define what feminism is now. Trained as a philosopher, she is frequently seen (more by people in literature than by philosophers) as a major thinker about gender, power, and the body. As we wonder what has become of old-style feminist politics and the material realities to which it was committed, it seems necessary to reckon with Butler’s work and influence, and to scrutinize the arguments that have led so many to adopt a stance that looks very much like quietism and retreat.

. . .It is difficult to come to grips with Butler’s ideas, because it is difficult to figure out what they are. Butler is a very smart person. In public discussions, she proves that she can speak clearly and has a quick grasp of what is said to her. Her written style, however, is ponderous and obscure. It is dense with allusions to other theorists, drawn from a wide range of different theoretical traditions. In addition to Foucault, and to a more recent focus on Freud, Butler’s work relies heavily on the thought of Louis Althusser, the French lesbian theorist Monique Wittig, the American anthropologist Gayle Rubin, Jacques Lacan, J.L. Austin, and the American philosopher of language Saul Kripke. These figures do not all agree with one another, to say the least; so an initial problem in reading Butler is that one is bewildered to find her arguments buttressed by appeal to so many contradictory concepts and doctrines, usually without any account of how the apparent contradictions will be resolved.

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A further problem lies in Butler’s casual mode of allusion. The ideas of these thinkers are never described in enough detail to include the uninitiated (if you are not familiar with the Althusserian concept of “interpellation,” you are lost for chapters) or to explain to the initiated how, precisely, the difficult ideas are being understood. Of course, much academic writing is allusive in some way: it presupposes prior knowledge of certain doctrines and positions. But in both the continental and the Anglo-American philosophical traditions, academic writers for a specialist audience standardly acknowledge that the figures they mention are complicated, and the object of many different interpretations. They therefore typically assume the responsibility of advancing a definite interpretation among the contested ones, and of showing by argument why they have interpreted the figure as they have, and why their own interpretation is better than others.

This is a very long article, and dissects many of Butlers’ views, concentrating on her idea that sex is not a biological reality but a social construct mirroring the power of those who make the constructs. If you want to see what a fraud Butler is, read the article, which ends this way:

Finally there is despair at the heart of the cheerful Butlerian enterprise. The big hope, the hope for a world of real justice, where laws and institutions protect the equality and the dignity of all citizens, has been banished, even perhaps mocked as sexually tedious. Judith Butler’s hip quietism is a comprehensible response to the difficulty of realizing justice in America. But it is a bad response. It collaborates with evil. Feminism demands more and women deserve better.

*I didn’t realize until today that Chicago’s Field Museum has its own specimen of Archaeopteryx, a transitional form between dinosaurs and birds, and one of the world’s most famous fossils (there are 12 body specimens and some bits and bobs). It was perhaps the earliest transitional form discovered (1861, only two years after publication of The Origin), though its status as evidence for transitions between major forms wasn’t touted until later.

Here’s Wikipedia’s dope on the Chicago specimen, which is the subject of a brand-new paper (below):

The existence of a fourteenth specimen (the Chicago specimen) was first informally announced in 2024 by the Field Museum in Chicago, US. One of two specimens in an institution outside Europe, the specimen was originally identified in a private collection in Switzerland, and had been acquired by these collectors in 1990, prior to Germany’s 2015 ban on exporting Archaeopteryx specimens. The specimen was acquired by the Field Museum in 2022, and went on public display in 2024 following two years of preparation.  In 2025, the paleornithologist Jingmai O’Connor and colleagues officially published a study describing this fourteenth Archaeopteryx specimen.

From Reuters:

The new study, examining the Chicago fossil using UV light to make out soft tissues and CT scans to discern minute details still embedded in the rock, shows that 164 years later there is more to learn about this celebrated creature that took flight 150 million years ago during the Jurassic Period.

The researchers identified anatomical traits indicating that while Archaeopteryx was capable of flight, it probably spent a lot of time on the ground and may have been able to climb trees.
The scientists identified for the first time in an Archaeopteryx fossil the presence of specialized feathers called tertials on both wings. These innermost flight feathers of the wing are attached to the elongated humerus bone in the upper arm. Birds evolved from small feathered dinosaurs, which lacked tertials. The discovery of them in Archaeopteryx, according to the researchers, suggests that tertials, present in many birds today, evolved specifically for flight.

Feathered dinosaurs lacking tertials would have had a gap between the feathered surface of their upper arms and the body.

“To generate lift, the aerodynamic surface must be continuous with the body. So in order for flight using feathered wings to evolve, dinosaurs had to fill this gap – as we see in Archaeopteryx,” said Field Museum paleontologist Jingmai O’Connor, lead author of the study published on Wednesday in the journal Nature, opens new tab.

“Although we have studied Archaeopteryx for over 160 years, so much basic information is still controversial. Is it a bird? Could it fly? The presence of tertials supports the interpretation that the answer to both these questions is ‘yes,'” O’Connor added.

It’s still not clear that tertial feathers are a strong indicator of flight, though they do provide lift. But that can also be used for gliding, or hopping up in the air to get prey. I have to get down to the Field Museum to see this specimen; I think it’s one of the few in the world—and the only one in America—that you can see with your own eyes.

Here’s the paper in Nature (I won’t summarize it):

And a short video that shows the specimen, which took two years to prepare:

Meanwhile in Dobrzyn, the cats are enjoying the good weather (she’s down by the Vistula River):

Hili: I have a dream.
A: What dream?
Hili: That May would last all year round.
In Polish:
Hili: Mam marzenie.
Ja: Jakie?
Hili: Żeby maj był przez cały rok.

*******************

From Another Science Humor Group:

From Animal Antics:

From Things With Faces, a goofy ice cream bar:

Masih is quiet as she’s still recovering from surgery. Have a tweet reposted by JKR; the original Torygraph article is archived here. And get a load of this excerpt:

The NHS is treating nursery-age children who believe they are transgender after watering down its own guidance, The Telegraph can reveal.

The health service was previously set to introduce a minimum age of seven for children to be seen by its specialist gender clinics, claiming anything less was “just too young”.

The limit was removed after the proposals were put out to consultation, with new guidance due to be published showing that children of any age are eligible.

However, a source close to the consultation process said NHS England had “caved to the pressure” of trans activists to remove the limits.

The children are not given powerful drugs such as puberty blockers at the clinics, but are offered counselling and therapy along with their family.

The tweet:

From Luana: another post I can’t embed (what’s going on with “X”?). But here’s a screenshot AI is doing grading now!

More mockery from Simon:

— George Conway 👊🇺🇸🔥 (@gtconway.bsky.social) 2025-05-14T20:03:54.847Z

From Jay; a prank AND a marriage proposal!

Two from my site (I’m having trouble embedding):

From the Auschwitz Memorial, one I reposted:

This Dutch Jewish girl was gassed to death upon arriving at Auschwitz. She was nine (I think they got the birthdate wrong; should be 16 May.

— Jerry Coyne (@evolutionistrue.bsky.social) 2025-05-16T09:53:19.042Z

Two posts from Dr. Cobb. I never saw anything in baseball like this one:

THAT BALL WENT THROUGH HIS GLOVE

— Codify Baseball (@codifybaseball.bsky.social) 2025-05-14T13:36:22.392Z

And a baby rattler:

Carefully avoided an adorable baby rattlesnake on the trail at the Santa Rosa Plateau today. #iNaturalist #herps

— Flower Prof (@flowerprof.bsky.social) 2025-04-12T01:17:08.232Z

 

Green sea turtle noms jellyfish

May 15, 2025 • 1:38 pm

It doesn’t get stung for some reason! However, one site says this:

The green sea turtle is the largest hard-shelled sea turtle. They are unique among sea turtles in that they are herbivores, eating mostly seagrasses and algae.

I guess it wanted a change.

The species, Chelonia mydas, is endangered and has undergone a steep decline in population size.  It is protected everywhere.

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:

@dentistry.everyday

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

♬ original sound – Dentistry everyday

Readers’ wildlife photos

May 15, 2025 • 8:15 am

Today we have some lovely insect photos by regular Mark Sturtevant. Mark’s ID’s and captions are indented, and you can enlarge his photos by clicking on them.

Here are more pictures of insects taken two summers ago from area parks near where I live in eastern Michigan.

First up is a slightly embarrassing accomplishment, which is a decent picture of one of our Sulphur butterflies. Sulphurs are an exceedingly common group with several local species, but for some reason they are extremely wary around me. Anyway, this one was unwary, and I think it is the Orange Sulphur (Colias eurytheme):

Next up is our largest butterfly, the Eastern Giant Swallowtail (Heraclides cresphontes). They are often challenging since they tend to keep their “engines running” (meaning their wings are almost always in motion) when rapidly foraging from flower to flower, but this one paused very briefly:

One of my favorite insects is shown next. This is Anotia uhleri, or what I call the “Flat Derbid”, although this Derbid planthopper has no common name. They can be found in forests sitting on the undersides of leaves. The orange thingies sticking out of the head are stumpy antennae:

Here is a Leaf-footed Bug nymph (Acanthocephala terminalis):

I was finding quite a few of these Lacewing egg clusters along a forest trail. Lacewings lay eggs on the ends of long stalks for protection. Having the eggs tied together in a bundle suggests that these are one of our larger Green Lacewing species, Leucochrysa insularis. This species tends to stay in forests, sitting under leaves by day, and like the Derbid above they lay their wings flat.

An occasional visitor to the porchlight at home are Mosquitos of Unusual Size, and one is shown in the next picture. I was eventually able to identify this giant mosquito as the Gallnipper, Psorophora ciliata. This one is a female. Although she will require a blood meal to reproduce, and they are described as being rather aggressive in pursuit of humans, a relatively good thing about them is that the larvae are predatory on other mosquito larvae. I have pictures coming up later that compares one of these beasts to a regular mosquito, but for now the attached picture can give some idea:

The next three pictures show a surprise, but the story starts out unremarkably. The beetles foraging on flower pollen are Brown Blister Beetles, Zonitis vittigera. Blister Beetles are a large family, and are so-named because they are chemically protected by exuding an irritating fluid if annoyed. It is relevant to point out that they have interesting biology in that they grow up as parasites on other insects, usually on bees. The mobile first instar larvae are called triungulin larvae, and they start their journey by clambering up onto flowers and wait for a bee to visit. Once the flower is visited by their intended target, they hitch a ride to the nest where they move in and eat the bee provisions and even bee larvae:

I almost did not bother processing the 2nd picture because it had motion-blur, though the composition was nice. But do you see the tiny things on the thorax of the beetle? The 3rd picture provides a blow-up. Those little things are Blister Beetle triungulin larvae! Possibly not this species, though. So, what is going on? I have sent these pictures on to a Blister Beetle Facebook group and to iNaturalist to ask for opinions. There is no answer yet, but possibly the larvae attach to any insect visitor. Although non-bee visitors would be temporary dead-ends, one can imagine that this would at least disperse them to other flowers:

Finally, here are pictures of our most common Sand Wasp, which is the Four-banded Stink Bug Wasp (Bicyrtes quadrifasciatus). Females of these highly energetic wasps will provision a burrow with paralyzed stink bugs, and these are used to raise the next generation of wasps. In the first picture you can see the spray of sand being flung out as she excavates her burrow:

Thursday: Hili dialogue

May 15, 2025 • 6:45 am

Welcome to Thursday, May 15, 2025, and International Conscientious Objectors Day. I was one of these, and applied for I-O status in 1970. My draft number in 1971 was 3!. I vowed to go to jail rather than fight in Vietnam, which I saw as a useless and unjust war in which the U.S. was not defending itself.  Fortunately, I got a 2-S (CO) status without evan an examination (I had a history of antiwar work). So, I did my CO work in a NYC hospital for 13 months until I found I had been “drafted” illegally (they drafted COs from the class of 1971 but no soldiers, which violated the draft law). With the help of the ACLU, I initiated a class action suit (Coyne et al. v Nixon et al,) and we won in NY federal court. We were released (the class was, as I recall, about 2500 COs all told), but of course not compensated, as we were allowed to earn no more than a GI ( about $6000 per year) but had to pay for our own food and housing.  Then I was free to go to graduate school, but that is another story, and a long one. . . .

It’s also Bring Flowers to Someone Day, National Apértif Day (always a dry sherry), National Chocolate Chip Day, and Peace Officers Memorial Day.

Readers are welcome to mark notable events, births, or deaths on this day by consulting the May 15 Wikipedia page.

Da Nooz:

*Republicans are getting antsy about Trump accepting an expensive plane from the terrorist-supporting state of Qatar to use as Air Force One for the next four years.

Republican lawmakers on Tuesday expressed national-security concerns over the proposed $400 million plane that the Qatari royal family wants to give to the U.S. for use as Air Force One, offering rare GOP resistance to a venture backed by President Trump.

Many of the Republicans who expressed doubts serve on congressional committees that oversee the nation’s armed services and intelligence agencies. They said that the White House would be subject to a battery of questions regarding security if the transfer goes forward. They noted that scrubbing the plane for foreign surveillance technology would be a costly and laborious process and questioned whether the Qatari plane would have necessary capabilities—like being able to refuel midair—or carry the advanced technology needed for an airborne command center.

Several suggested that President Trump and the White House might rethink the offer.

Senate Majority Leader John Thune (R., S.D.) stressed Tuesday afternoon that nothing was official yet and predicted there would be “plenty of scrutiny” around the arrangement should it move forward. “There are lots of issues around that that I think will attract very serious questions if and when it happens,” Thune said.

Senate Majority Leader John Thune (R., S.D.) stressed Tuesday afternoon that nothing was official yet and predicted there would be “plenty of scrutiny” around the arrangement should it move forward. “There are lots of issues around that that I think will attract very serious questions if and when it happens,” Thune said.

Trump also has faced some criticism over the deal from conservative commentators: Ben Shapiro characterized the idea as “skeezy,” and influencer Laura Loomer took aim at Qatar via social media saying “we cannot accept a $400 million ‘gift’ from jihadists in suits.”

The objections voiced by GOP lawmakers also are noteworthy given that Trump is currently on an overseas trip to the Middle East. He is set to be in Qatar for a state visit on Wednesday, and the blowback at home about the gift threatens to overshadow the trip.

And it looks as if the plane will sort of belong to Trump after his term is over, as it reverts to the Trump Presidential Library. What will happen then? Will it no longer fly? Will it be used to ferry documents and books back and forth? No, this is very bad optics, and you know it’s bad when even Republicans criticize it. And to prevent eavesdropping, they’d have to take the whole damn plane apart to see if the Qataris have put listening devices in it. It’s not like they’re even a friendly state, though they pretend to be.

*Here’s Section 1 of the Fourteenth Amendment to the Constitution. Pretty clear, no?

All persons born or naturalized in the United States, and subject to the jurisdiction thereof, are citizens of the United States and of the State wherein they reside. No State shall make or enforce any law which shall abridge the privileges or immunities of citizens of the United States; nor shall any State deprive any person of life, liberty, or property, without due process of law; nor deny to any person within its jurisdiction the equal protection of the laws.

That looks like Trump’s “birthright ban” for children of immigrants is palpably unconstitutional. But yet. . . . .

Shortly after the Supreme Court announced in April that it would consider the nationwide freeze on President Trump’s executive order ending birthright citizenship, he gleefully spoke to reporters in the Oval Office.

Mr. Trump said that he was “so happy” the justices would take up the citizenship issue because it had been “so misunderstood.” The 14th Amendment, he said — long held to grant citizenship to anyone born in the United States — is actually “about slavery.”

“That’s not about tourists coming in and touching a piece of sand and then all of the sudden there’s citizenship,” Mr. Trump said, adding, “That is all about slavery.”

For more than a century, most scholars and the courts have agreed that though the 14th Amendment was added to the Constitution after the Civil War, it was not, in fact, all about slavery. Instead, courts have held that the amendment extended citizenship not just to the children of former slaves but also to babies born within the borders of the United States.

. . . The story of how the theory [that it was about slavery] moved from the far edges of academia to the Oval Office and, on Thursday, to the Supreme Court, offers insight into how Mr. Trump has popularized legal theories once considered unthinkable to justify his immigration policies.

“They have been pushing it for decades,” said John Yoo, a law professor at the University of California, Berkeley, School of Law and a top lawyer in the George W. Bush administration. “It was thought to be a wacky idea that only political philosophers would buy. They’ve finally got a president who agrees.”

The White House did not respond to requests for comment.

So far, courts have agreed. Judges in Washington State, Massachusetts and Maryland quickly instituted nationwide pauses on Mr. Trump’s policy.

Attorney General Andrea Campbell of Massachusetts spoke out in February against Mr. Trump’s executive order seeking to end birthright citizenship. Massachusetts joined Maryland and Washington State in instituting nationwide pauses on the policy.Credit…David L. Ryan/The Boston Globe, via Getty Images

In oral arguments this week, the justices will primarily consider whether federal judges have the power to order these temporary pauses, known as nationwide injunctions. But the question of birthright citizenship will form the backdrop.

If the Supreme Court can’t rule on the Constitution like this, but merely throws the case back to federal judges, it’s a total abnegation of their task: to rule on the constitutionality of law. Individual states can’t make conflicting criteria for citizenship. Trump was wrong, and I’m betting he loses this one.

*The IDF has been trying to get Muhammad Sinwar, the younger brother of now-extinct Yahya Sinwar, who was the military head of Hamas. Muhammad is a top Hamas official, if not the top Hamas official, and has eluded numerous attempts to kill him:

Like his elder brother, Muhammad Sinwar has long been wanted by the Israeli authorities. He is said to have been targeted in six assassination attempts by 2021.

In 2014, the Israeli military believed that it had killed the younger Mr. Sinwar, only to discover that he had survived. In late 2023, the Israeli military said on social media that it had searched his office in a raid on a Hamas military post and training compound in Gaza, “where military doctrine documents were located.”

But both Sinwar brothers continued to elude Israel, until Yahya, then the political leader of Hamas, was killed by the Israeli military in October.

In a 2022 interview with Al Jazeera, it was reported that Muhammad was so elusive that he would not be recognized by most people in Gaza, and had even missed his father’s funeral to maintain secrecy about his whereabouts.

He is believed to have spent much of the war underground in an effort to escape Israeli airstrikes. But in recent months, he had been seen aboveground in Khan Younis, including at Nasser Hospital, according to a Middle Eastern intelligence official.

The Jerusalem Post and BBC both report that the IDF struck a meeting in a hospital in Khan Younis, a meeting reportedly involving top Hamas officials.

The IDF on Tuesday attempted to assassinate Hamas leader Mohammed Sinwar in a strike on the European Hospital in Khan Yunis in Gaza, sources told The Jerusalem Post. 

The military may have used a bunker buster bomb in their attempted attack against Sinwar, defense sources told the Post.

Following the initial attack, the IDF reportedly struck the area where Sinwar was allegedly located a second time, with the objective of preventing the evacuation of casualties, Israeli public broadcaster KAN reported.

Israel reportedly did not update the US prior to the assassination attempt, a source familiar with the details told Ynet. According to the report, the strike was the result of a “sudden opportunity,” leading to no time to inform the Americans or consider the timing of US President Donald Trump’s speech in Riyadh, Saudi Arabia.

“We will not allow the Hamas terrorist organization to use hospitals and humanitarian facilities in Gaza as shelters and terrorist headquarters,” Defense Minister Israel Katz said. “We will pursue them and their leaders and strike them everywhere.”

It’s not yet clear if they got Sinwar, and it’s won’t be believable until the IDF reports it (they haven’t).  And even if they did, it’s not at all sure that Hamas will be appreciably weakened with his death, for if he does go to the Virgins in the Sky, another leader may step forward to replace him. But it’s now seems clear that Hamas is losing, and will be clearer when the IDF conducts its promised intensified warfare after Trump leaves the Middle East.

*It’s hard to find any news that’s not about Trump, but here’s some, and good news. Deaths due to overdoses fell very sharply last year, the sharpest decline ever.

There were 30,000 fewer U.S. drug overdose deaths in 2024 than the year before — the largest one-year decline ever recorded.

An estimated 80,000 people died from overdoses last year, according to provisional Centers for Disease Control and Prevention data released Wednesday. That’s down 27% from the 110,000 in 2023.

The CDC has been collecting comparable data for 45 years. The previous largest one-year drop was 4% in 2018, according to the agency’s National Center for Health Statistics.

All but two states saw declines last year, with Nevada and South Dakota experiencing small increases. Some of the biggest drops were in Ohio, West Virginia and other states that have been hard-hit in the nation’s decades-long overdose epidemic.

Experts say more research needs to be done to understand what drove the reduction, but they mention several possible factors. Among the most cited:

— Increased availability of the overdose-reversing drug naloxone.

— Expanded addiction treatment.

— Shifts in how people use drugs.

— The growing impact of billions of dollars in opioid lawsuit settlement money.

— The number of at-risk Americans is shrinking, after waves of deaths in older adults and a shift in teens and younger adults away from the drugs that cause most deaths.

Still, overdose deaths are still higher than they were during the pandemic, and death rates have fluctuated before. Still, we now have Naloxone, which every first responder should be carrying:

Experts note that there have been past moments when U.S. overdose deaths seemed to have plateaued or even started to go down, only to rise again. That happened in 2018.

But there are reasons to be optimistic.

Naloxone has become more widely available, in part because of the introduction of over-the-counter versions that don’t require prescriptions.

Meanwhile, drug manufacturers, distributors, pharmacy chains and other businesses have settled lawsuits with state and local governments over the painkillers that were a main driver of overdose deaths in the past. The deals over the last decade or so have promised about $50 billion over time, with most of it required to be used to fight addiction.

If you want to see how serious the opioid crisis is, how addictive they are, and how some pharma companies tried to make them more addictive, read Empire of Pain: The Secret History of the Sackler Dynasty by Patrick Radden Keefe: It’s really about one family’s nefarious deeds pushing opioids, but I found it a fantastic read. And the Sacklers still didn’t suffer much for all they did.

*Finally, Matthew brought my attention to a Guardian article about a duck being caught by a Swiss speed camera, and it was likely a repeat offender. Yes, ducks can fly quickly, and this was a mallard drake.

A radar image of a speed offender caught in central Switzerland last month has revealed that the culprit was not only a duck but probably a repeat offender, local authorities have said.

Police in the town of Köniz, near Bern, were astounded when they went through radar images snapped on 13 April to discover that a mallard was among those caught in the speed trap, the municipality said on its Facebook page at the weekend.

The duck was caught going 52km/h (32mph) in a 30-km/h zone, the post said.

That’s reckless flying!

The story, first reported by the Berner Zeitung newspaper on Monday, got even stranger.

It turned out that a similar-looking duck was captured flying in the same spot at exactly the same speed, on exactly the same date seven years earlier, the Facebook post said.

The municipality said it had considered whether the whole thing might not be a belated April Fool’s joke or a “fake” picture.

But the police inspectorate said it was impossible to doctor images or manipulate the radar system.

The computers are calibrated and tested each year by Switzerland’s federal institute of metrology, and the photos taken are sealed, the municipality said.

Lock him up!  Here’s the photo, credited to: Gemeinde Köniz/Facebook:

Meanwhile in Dobrzyn, the boys have a botanical exchange:

Hili: The grass grows quickly after rain.
A: I don’t blame it.
In Polish:
Hili: Trawa po deszczu szybko rośnie.
Ja: Ja jej się nie dziwię.
And a picture of Szaron.

*******************

From Now That’s Wild:

From Meow:

From Jesus of the Day:

Masih is still recovering from her operation, but here’s a tweet retweeted by JKR. I can’t embed it but you can go to it by clicking on the screenshot, and you can read the letter here. The BBC is accused of being homophobic!

Simon says this is “hilarious if true”, but I simply can’t believe it.  Readers–help!

You can’t make this up

— Adam Parkhomenko (@adamparkhomenko.bsky.social) 2025-05-13T16:18:26.272Z

From Malcolm: I can’t embed this but you can see the original by clicking on the screenshot. (Note that “only” should be before “once”.)

Shermer gives all the excuses why this is okay:

From my feed.  Turkey loves its cats, and this vending machine apparently dispenses cat food when it hears a meow. Now seagulls are trying to game the system.

From the Auschwitz Memorial, one that I reposted:

A Polish dressmaker died in the camps barely a month after arriving. She was 22.

— Jerry Coyne (@evolutionistrue.bsky.social) 2025-05-15T09:56:14.034Z

Two posts from Dr. Cobb, who is recovering from both a chest infection and respiratory virus. But he’s getting better! First, a little crab stole some food from the big one. Sound up to hear the Spanish:

Libidoclaea granaria 🦀 from @schmidtocean.bsky.social dive 741 #ChileMargin2024 #MarineLife

— Lisa (@tuexplorer1.bsky.social) 2025-05-14T03:12:03.111Z

Matthew says this about the tweet, which starts a thread: “I briefly felt well enough last night to pen this Wodehousian thread (inspired by listening to a lot of BBC Jeeves dramatisations, which is only vaguely droll if you know the Jeeves books and also UK WW2 literature 

What did Bertie Wooster get up to in WW2? He was 24 when he employed Jeeves (20 years older?) who later said he had “dabbled to a certain extent” in WW1. That must have been in 1920ish. In 1939 he would have been in his early 40s, slightly liverish, but still a game old bird. 1/n

— Matthew Cobb (@matthewcobb.bsky.social) 2025-05-13T20:46:14.308Z

A new member of the archaea without metabolism: is it alive?

May 14, 2025 • 10:15 am

This post reports a new form of life that is clearly a member of the archaea, with characteristics of that group, but also lacking a vital feature of other archaea as well as other bacteria and all eukaryotes: metabolism: the pathways (mostly involving enzymatic proteins) that keep an organism going and reproducing by converting nutrients into energy. Its lack of genes for metabolism makes it resemble a virus, what hijacks its nutrients from the cells it infects. But viruses can’t completely self-replicate like this new critter, for viruses also partly hijack the DNA/RNA replication system of their hosts.

The new creature, whose appearance is unknown since it was identified from DNA alone, must get its metabolites through association with other species. Finally, the new creature does have something that viruses lack—a complete system for replicating its genome: ribosomes, DNA, genes for transfer RNAs, and so on. In other words, in important ways it’s different from viruses, but also different from other archaea as well as bacteria and eukaryotes (organisms with “true cells” that have their DNA in the nucleus and have membrane-covered organelles like mitochondria and chloroplasts).  The DNA of this creature is in a single circular chromosome like that of bacteria and archaea. Its unique features appears to make it a member of a new domain of life.

The question is this: is this new organism even alive? Viruses are regarded by many biologists as “not alive” because they can’t grow, they have no metabolism to sustain themselves, and are completely dependent for reproduction on the replication machinery of other organisms (bacteria or eukaryotes) they parasitize.

Well, read about this new organism below, discovered by sequencing DNA inside of a singe eukaryotic cell tell me if you think it’s “alive.”

But I’m getting ahead of myself. Let’s review:

There are three domains of life: the bacteria, the archaea (discovered only in 1977 by Woese and Fox), and the eukaryotes (everything else, all having membrane bound nuclei and organelles). Together, the bacteria and archaea are called “prokaryotes” (i.e., single celled microorganisms), and everything else besides viruses comprise the “eukaryotes.”

The phylogeny (family tree) of these domains is shown below.  It was realized only recently that all organisms with true cells (e.g., us) descended from archaea, as shown below. That means three things. First, we are more closely related to the archaea (which often live in weird places like hot springs or hyper-salty water) than we are to bacteria. Eukaryotes did not evolve from bacteria.

Second, eukaryotes like us could be thought of as archaea, since we are nested within that group. In the same way, we could be thought of as fish, and birds as reptiles.

Finally, archaea are considered paraphyletic: the group does not contain all the descendants of its common ancestor. The eukaryotes are not considered archaea, but ARE descendants of the common ancestor of archaea; they just branched off later into a new domain of life.

Now this family tree was constucted from DNA sequence similarity, but archaea also share certain traits with eukaryotes that bacteria don’t have, including “shared metabolic pathways, similar enzymes involved in transcription and translation, and DNA replication mechanisms.” That is what a query to Google tells me. Remember, this area is far from my own biological expertise, so if you see an error, let me know!

This tree is from Sadava et al. 2020. Life. The science of biology. 12th edition. Oxford Univ. Press)

Here is a comparison of the traits of the groups (there are overlaps),from Wikipedia.

Note that all three groups have metabolism (pathways to produce energy and grow), and cell walls, but eukaryotes have a special cell wall with two layers of lipids and a layer of protein. Viruses, not shown in this comparison, have only a protein capsule around them. (Bacteria and archaea have more complicated cell walls.)

Viruses do not metabolize and are widely regarded as “nonliving particles”.  Bacteria and most archaea have metabolism.

The paper describing the new finding is apparently not yet published, but you can find it at bioRχiv by clicking the title below or downlading the pdf here.

How did they find this thing? In a weird way. The researchers took a single individual of the dinoflagellate Citharistes regius and amplified and sequenced all the DNA it contained. Besides the DNA of the dinoflagellate, it also found DNA from three other types of organisms: cyanobacteria (photosynthetic bacteria once called “blue-green algae”), two species of gamma proteobacteria (a well-known group) and then the weird species under consideration, which they call Candidatus Sukunaarchaeum mirabile. This apparently means it’s a candidate species that hasn’t been formally described.  We’ll call it CSM in this post. We don’t know what it looks like or what its ecology and behavior is, except we know it must be parasitic, commensal, or symbiotic with some other species. It cannot live on its own because it can’t metabolize.

Here is its genome shown in the paper. This is all we know of the organism’s biology:

(From the paper) Figure 1. The genome map of Sukunaarchaeum. From outermost to innermost circle, the positions of protein-coding genes and rRNA genes on the +/- strands, tRNA genes, GC content, and GC skew are shown. Color codes for the outermost and 2nd outermost circle: Blue, genes of unknown function; light blue, genes of known function; yellow, rRNA genes.

 

It is in the Archaea as the DNA certainly shows its affinity. But, as shown below, its lineage originated very soon after the archaea branched off from their common ancestor with bacteria.

It has a very small genome: 238,000 base pairs, though that is not the smallest genome known of any organism in the three domains of life (note I’m using “life” here, though this thing may be more virus-like and hence “not alive”).

The chomosome is circular, presumably because sequencing it, one arrives back at the beginning again.

It has 222 genes, most of which are devoted to the machinery for making copies of itself. These include transfer RNAs and ribosomal RNAs, which are not found in viruses, all of which hijack that stuff from the cells they infect.

It has NO genes for metabolism (no genes for it), so CSM must grow and divide using resources from cells that it hijacks. Other bacteria and archaea (and of course eukaryotes) have the genes for metabolic processes, making CSM more virus-like. But, as I said, it differs from viruses by having a complete set of “self-replication core machinery” and genes that are like those in archaea.

189 of its 222 genes make proteins. All but five of these are devoted to self-replication. Several are very large and strongly suggest that they constitute part of the cell wall (they call it “membrane”), though the researchers are not sure about this.

Here’s a summary of the organism. Note that its unique character, lacking metabolism, makes it distinct from other domains of archaean life.

 

And a figure from the paper  (just look at “a” on the left side) showing where it fits in the family tree of prokaryotes. It branches off from the rest of the archaea early, and then evolves very fast, as you can see by the long branch of its lineage, probably reflecting strong natural selection on the lineage.

(From paper) Figure 2. Phylogenetic placement of Sukunaarchaeum within the Archaeal domain. a, Maximum likelihood (ML) phylogenetic tree based on a concatenated alignment of 70 conserved archaeal marker proteins. The tree was inferred under the LG+C60+F+I+R10 model, based on a dataset of 150 taxa and 18,286 sites. The scale bar represents the estimated number of substitutions per site.

To summarize:

CSM is an Archaea as seen from its DNA sequence.  Of this there is no doubt.

But unlike other Archaea or even bacteria, it has NO metabolic machinery. In this way it’s similar to a virus.

But it is dissimilar to viruses because it has the complete machinery for self-replicating its genome, which viruses lack.

Ergo, it must be associated in some way with other organisms to be able to replicate.

We have no idea what it looks like, though it almost certainly is a cell rather than a virus.

Here’s how the authors highlight CSM’s uniqueness:

The discovery of Sukunaarchaeum not only expands the known boundaries of archaeal diversity but also challenges fundamental concepts of cellular life. The extreme metabolic simplification raises fundamental questions about the minimal requirements for cellular life. Sukunaarchaeum, focused almost entirely on genetic self-perpetuation, represents a compelling example of how far metabolic reduction can proceed within a cellular framework. Its minimal genome, absolute host dependence necessitated by profound metaboliceduction, rapid evolution, and significant investment in large, membrane-associated proteins potentially mediating host interaction constitute a unique combination of characteristics that are collectively reminiscent of viruses. Nonetheless, Sukunaarchaeum remains fundamentally cellular – a key distinction from viruses, which typically lack their own core replication machinery genes and rely on host systems. It possesses ribosomes and the core transcriptional and translational apparatus inherited from cellular ancestors. Thus, while clearly cellular, its extreme metabolic dependence and specialization for self-replication are virus-like in nature, suggesting that Sukunaarchaeum may represent the closest cellular entity discovered to date that approaches a viral strategy of existence.

The authors found this organism by sequencing a single eukaryotic cell; CSM was likely inside this cell, like a virus in a human cell, but we don’t know if CSM damages its host(s) in any way. It is likely that many more organisms like this exist but aren’t known because people don’t do DNA sequencing of entire single-celled eukaryotes very often. Dinoflagellates are aquatic organisms, but there may be more stuff like CSM found by sequencing DNA in the soil.

I’ll add that this organism might give us an idea of how viruses originated because, if it loses some of its core replication machinery and genes for making membranes, it would become a virus. It is unlikely to be a virus that might develop into an archaean, as it already is an archaean with a membrane, but would have to evolve a tremendous amount of new metabolic machinery to be able to fuel itself, and that metabolic machinery would have to be genetically similar to the metabolic machinery of already-existing archaea.  That would be an unheard-of event of convergent evolution, thus very unlikely.  This thing, so far, is sui generis.

Finally, IS IT ALIVE? That, as you might guess, depends on your definition of “life”.

If you count the ability to self-replicate on its own, CSM is alive. In that sense viruses are not alive, and most of us think they’re not. (Bur remember that it needs to be assocated with another species to self-replicate.)

But if you count the ability to sustain itself by metabolizing and fueling its own replication, then it is NOT alive.

You pays your money, you takes your choice.