Why Evolution is True Feed

Here’s an amazing video sent to me by reader Bryan Lepore. I didn’t quite understand what it showed, and he explained:

I think it is simply this:

1. Create a soap bubble from a soap solution that is sitting in a speaker/woofer.

2. Shine a light on the bubble. Here, you can see a ring of dots—that is simply a strip of LEDs in a ring. I have a light strip like this, and it produces unexpected results compared to an incandescent light.

3. Activate the speaker with different frequencies. This vibrates the bubble and the reflected image of the LED light strip.

… does that make sense?

Yep, sure does.

Did you spot the two kleptoparasitic flies from the picture by Gregory I put up this morning?  Here’s the original below it, and then the reveal:

If you found the wasp, you’ll know they were nearby.  Did anybody get both of them?

The argument continues about whether the virus causing covid originated in a wet market in Wuhan or as an accidental release from The Wuhan institute of Virology.  While several U.S. government agencies have agreed that the evidence is tilted towards a lab-leak origin, in my view the evidence is not dispositive on either side.

Matt Ridley, however, has been a hard-core advocate of the lab-leak theory, and even co-wrote a book with Alina Chan that, at the time, presented both sides and, as Ridley says below, he “remained unsure what happened at that stage.”

No longer. Since 2021, Ridley has promoted the lab-leak theory, which he does in a Torygraph article shown below (click on headline below to get the archived version). Apparently Ridley teamed up with another collaborator, P. Anton van der Merwe, and wrote a scientific paper laying out his evidence for a lab-leak origin of covid. I’ve put the paper’s title below, but you can read it at the same Torygraph site. The scientific argument was published in the newspaper rather than in a scientific journal because the journal rejected it. (No explanation is given.)

In the intro before he shows the paper (surely a first for the Torygraph), Ridley explains how this came about:

In 2024 I was approached by a single member of the editorial board of a respected biological journal with a request that I team up with a British biologist with relevant expertise and compose an academic paper setting out the case for the lab leak hypothesis: he hoped the journal would consider it. With the help of Anton van der Merwe of Oxford University, and advice from Alina Chan, I drafted such a paper. The paper was rejected; I suspect that it was another case of not wanting to rock the scientific boat. Now I am posting this paper online for all to read. It was composed several months ago so one or two small new items may be missing, but nothing in it has proved wrong. It is written not in my normal style but in dry, scientific prose, with each statement backed up by a source, in the shape of nearly 100 end-note references, so that readers can check for themselves that we have represented the sources faithfully. It deserves to be available to people to read. So the paper was commissioned, but the reviewers’ comments that led to rejection aren’t shown. Here’s the paper itself:

Here is some of the evidence Ridley and van der Merwe adduce:

• Attempts to find evidence for a wet-market leak have been unsuccessful. The cases found around the wet market could simply reflect sampling bias, as the Chinese concentrated on looking for infected people in that area.
• The Chinese have not been forthcoming with their data, and in fact locked one site with a catalogue of the sequenced but unpublished viruses they were working on
• If a person got infected with a bat virus from Yunnan (one theory), that person would have infected others on his/her journey to Wuhan, but there is no such trail of infection
• The Wuhan institute was doing “gain of function” experiments to increase the infectivity of SARS viruses (not the progenitor of the covid virus), but these did involve making viruses more transmissible.
• There were plans to put “furin cleavage sites” into SARS viruses, sites that make it easier for the viruses spike protein to get into cells. The virus causing covid has such a site—12 nucleotides long— which Ridley and van der Merwe insist was inserted into the virus progenitor by humans. As Ridley notes:

When the pandemic began in January 2020, Shi Zhengli of the WIV published two articles, one co-authored with Shibo Jiang, yet in both of them failed to mention the furin cleavage site, by far the most remarkable feature of the new virus’s genome. This may have been an oversight, but by contrast, it was the furin cleavage site that immediately alarmed several western virologists on first seeing the genome of the virus and led to the drafting of the Proximal Origin paper. Messages released during a congressional investigation reveal that the authors of the paper were not themselves convinced that a laboratory origin could be ruled out, either during or after the writing of the paper

• The containment of viruses at Wuhan for the SARS experiments was Level 2, which American scientists think was far too lax for such potentially dangerous experiments (this itself, of course, is not great evidence for a lab leak).

Here’s Ridley and van der Merwe’s conclusion:

In only one city in the world were sarbecoviruses subject to gain-of-function experiments on a large scale involving human airway cells and humanised mice at inappropriate safety levels: Wuhan. At only one time in history was research to create novel sarbecoviruses with enhanced infectivity through furin cleavage under consideration: 2018 onwards. The surprising failure to find better evidence for a natural spillover, and the lack of transparency from the Chinese scientists, is therefore best explained by positing a laboratory accident involving a live virus experiment as the cause of the Covid pandemic and attempts to cover it up.

This is a Bayesian conclusion, arguing that the total weight of the evidence supports a lab-leak prior. And it sure sounds conclusive, but I’m wondering why the paper was rejected (they don’t say what journal they submitted it to).

Further, a number of virologists I respect either adhere to the alternative wet-market theory or remain agnostic.  When I asked a colleague some questions about this, he/she said this:

All the **data** (including new stuff) points to a natural origin. It might have been a leak, but all the evidence that has been obtained points in the direction of a spillover in the wet market. Not everyone who disagrees with the prevailing view of something is Galileo.

And then I asked “What about the furin cleaveage site?” This was something that Nobel laureate David Baltimore considered almost conclusive evidence for the lab-leak theory, but walked it back a bit:

The virologist David Baltimore commented that “these features make a powerful challenge to the idea of a natural origin for SARS2,” later clarifying that “you can’t distinguish between the two origins from just looking at the sequence” (Caltech Weekly 2021).

My colleague commented about the furin cleavage site: “It is common in closely related [corona]viruses.” also citing a paper saying, “This is a good summary of the issues.”

That article, in the Journal of Virology from 2023, concludes that the wet-market hypothesis is more likely, though is somewhat agnostic:

Scientific conclusions are based on likelihood given the scientific data, and conclusions can change as new data are obtained. Based on the scientific data collected in the last 3 years by virologists worldwide, hypotheses 1 and 2 are unlikely. Hypotheses 3 and 4 cannot be ruled out by existing evidence. Since hypotheses 1 and 2 support the lab leak theory and hypotheses 3 and 4 are consistent with a zoonotic origin, the lab leak- and zoonotic-origin explanations are not equally probable, and the available evidence favors the latter. Further insight into CoVs in animals at the animal-human interface requires additional surveillance of circulating virus sequences from animals. There is ample precedent for the seeding of pandemics and more geographically limited outbreaks from nonhuman species. Common-cold CoVs, SARS-CoV, Ebola virus, HIV, influenza A virus, mpox virus, and others all have zoonotic origins (31–33). SARS-CoV-2 is the ninth documented coronavirus to enter the human population. The best existing scientific evidence supports a direct zoonotic origin. As new evidence continues to emerge from scientific studies or other investigations, our understanding of the origin of SARS-CoV-2 will continue to evolve. Nevertheless, it is possible that its origin may never be known with certainty.

I’ll add that Ridley is, as he says below, an adherent to a less stringent form of climate change than many scientists. He calls himself  a “climate-change” lukewarmer (see comment #2 below). Of course, he could be wrong about that yet right about covid. Nevertheless, I remain agnostic about how the virus got into our species. We may never know how this occurred, but investigating its origin is still worthwhile. In the article cited above, David Baltimore explains why:

Why is it important to know where the virus originated?

Well, I think we want to know the pathway of generating highly infectious new viruses that could cause pandemics because we want to protect ourselves against this happening again. If it happened by natural means, it means that we have to increase our surveillance of the natural environment. We have to try to find the hosts that provide an ability for the virus to change its sequence, to become more infectious. This would mean we need to keep surveillance on markets, on zoos, on places where viruses could jump from one species to another.

But if SARS-CoV-2 came about by an artificial means, it means we’ve got to put better defenses around laboratories. I’m not suggesting that it was deliberately released if it came from a laboratory, but we have to realize that whatever a laboratory does might get out of the laboratory and create havoc. It means that work of this sort should only go on in what are called biosafety level 4 laboratories.

UPDATE 1:  Author van der Merwe wants me to add another point, which I will, despite his rude last line:

I would add one more point, concerning why this issue matters.

Even the possibility that the COVID-19 was the result of a lab leaks mandates that close attention is paid to preventing another research related pandemic in future. At present scientists largely self-regulate when it comes to deciding what gain of function experiments to do, even if such experiment could generate a pandemic organism. Many of the scientists arguing most strongly for natural origins have a clear conflict of interest as they oppose tightening of restrictions on these sorts of experiment.

Refusing to tighten regulations until a lab leak is proven, is equivalent to refusing to reduce CO2 emissions until it is proven beyond doubt that these greenhouse gas emissions will result in catastrophic effects.

It is ‘pandemic-risk denialism’.
Are you siding with these people?

UPDATE 2.  Ridley also wrote me, as expected. and wants me to change my article. I have modified my comment on climate change to reflect his claim that he is a “lukewarmer.”  But his last point I already dealt with in my comment from Baltimore in the original post.

1. The (anonymous) virologist colleague that you consulted has misled you in a rather shocking way. He told you that furin cleavage sites are  “common in closely related [corona]viruses.” This is simply untrue: the only coronaviruses that count as “closely related” by a reasonable definition of that term are other sarbecoviruses. None of the over 800 sarbecoviruses yet found have a FCS. Not one. Other less closely related coronaviruses do have one, as we state in our article, where we say “MERS has one”. But to call other coronaviruses, such a as merbecoviruses “closely related” to SARS-CoV-2 is like calling birds or reptiles “closely related” to a mammal. You would not argue that finding the first mammal to grow feathers was unsurprising because “closely related tetrapods have feathers”. And if it was found near a lab that had engineered feather genes into other animals, I would be surprised if you did not find it suspicious. Note that an FCS is selected against in bats, where sarbecoviruses cause enteric infections, as we state.

2. Your colleague says “all” the data points towards the market. That’s just an empty slogan: what data? Not a single infected animal has been found, the very minimum expected in every other zoonotic outbreak. We set out the data on both sides of the argument in our paper and lots point to the lab. None of the data is proof but that does not make it “un-data”.

3. You wonder what the editor said to justify rejection. He said that there is no evidence of gain of function research at the WIV. That’s simply laughable. There’s tons of published evidence of exactly that, proudly published in journals by the WIV scientists.

4. You call me a climate denialist. This is false, lazy (easy to check) and defamatory. I have covered climate change in print for more than 40 years. I have repeatedly stated exactly why I think climate change is real and man-made. I just don’t yet see good arguments for it being net very dangerous. That’s not “denialism”. I am a lukewarmer.

5. Several commenters argue that it does not really matter how it started. This is gobsmacking. Knowing how this pandemic began is vital for preventing the next one: next to no effort is being made to enhance lab safety currently, or to prevent terrorists gaining access to virology expertise. In addition, a lab leak could explain why the virus was so highly infectious from the start of the outbreak. I have yet to hear anybody argue after an airliner crashes that it does not matter what caused it.

I suggest your readers read the whole paper.

h/t: Christopher for the Torygraph archive.

Reader Gregory sent us what may be the hardest “spot-the” photo ever.  There are two flies in this photo, but I’ll let Gregory describe the scene:

While kayak camping on the Kansas River this weekend, we were entertained by the energetic searching of a spider wasp (Hymenoptera: Pompilidae) seeking a spider to paralyze and oviposit on. However, following the spider were small flies, which turn out to be satellite flies, a subfamily of Sarcophagidae (flesh flies). The larvae of the flies are kleptoparasites and feed on prey captured by solitary wasps like the spider wasp. So the adult female flies were following the spider wasp to lay their eggs on the paralyzed spider and use it for their young. There are two flies in the photo.

Good luck. If you find them, just say so in the comments but don’t tell people where they are! As I said, this will take some searching, so I suggest you enlarge the photo.   The reveal will be at 11 a.m. Chicago time.

Math professor and Hero of Intellectual Freedom Abby Thompson of UC Davis has sent us some tidepool photos, along with a few birds. Her captions are indented, and you can enlarge the photos by clicking on them.

The first picture is of a pair of foolish birds from my back porch, followed by some Northern California tidepool pictures from late April and May.   The tides the last week of May were among the lowest of the year, occurring at a very unfortunate time of day (near dawn) for those who prefer a leisurely morning, like me.    As usual I got help from people on inaturalist for some of the IDs.

I don’t understand how mourning doves ever manage to reproduce. Here’s a pair pondering building a nest on the extremely wobbly fan hanging from the trellis over our porch. I’ve also seen them trying to nest on the peak of the roof and on a very narrow garden railing.  They give new meaning to the word birdbrain.    I strung up a nice, spacious, secure basket for them right near the fan, which they totally ignored.   They eventually gave up on the fan; they’ve probably found a nice spot smack in the middle of a parking lot somewhere.

On to the tidepools:

Thorlaksonius subcarinatus: This is a species of amphipod, which (I feel like I keep saying this) is tiny, just a bright orange speck. Amphipods are like isopods (the roly-polys in your garden) except they’re flattened vertically instead of horizontally.  The Thorlaksonius part is for sure, the species seems likely correct:

Liparis florae (tidepool snailfish).  About 2” long.  The second picture is a close-up of its weird eye:

Rostanga pulchra (nudibranch). This species eats a bright orange sponge, on which it becomes practically invisible:

(Family) Sabellidae (feather duster worm) It’s not possible even to determine genus from this photo:

Phidiana hiltoni (nudibranch):

I took a picture of the brown-and-white-striped worm (Tubulanus sexlineatus) and only noticed afterward that the photo includes both a nudibranch (Coryphella trilineata) to the right of the worm and a sea spider (Pycnogonum stearnsi) to the left. Tidepools are crowded places:

A little jellyfish, Polyorchis haplus (I think). This one was stranded on the sand, but when plopped into a small pool it started zipping around. The red spots are eyespots:

Acanthodoris nanaimoensis (nudibranch). I don’t see this species very often, and it’s a knock-out:

 

Camera info:  Mostly Olympus TG-7 in microscope mode, pictures taken from above the water.

As I say repeatedly, I find it very difficult to listen to long videos (and long podcasts without visuals are even worse). But I happened to click on the one below, part of the biweekly Glenn Show dialogue between Glenn Loury and John McWhorter, and found it quite worthwhile, even though it’s a bit more than an hour long (Loury gives an advertisement between 11:12 and 13:14). It’s interesting because of the topics: wokeness, race, and their intersection, and McWhorter (with whom I’m on a panel in three weeks) is particularly interesting.

The first thing we learn is that Loury has left (actually been fired from) the rightish-wing Manhattan Institute. He explains why in his website post “I was fired by the Manhattan Institute. Here’s why.”:

 In short, I think they disapproved of my opposition to the Gaza War, my criticisms of Israel’s prosecution of that war, and my praise of Ta-Nehisi Coates’s meditations on the West Bank settlements.

Well, I knew that Loury was a stringent critic of Israel, but praising Ta-Nehisi Coates’s “meditations” on the West Bank, meditations that followed just 10 days visit in the Middle East and did not even mention Palestinian terrorism, isn’t something to praise.  At any rate, since Loury retired from Brown, he’s contemplating his next move, and hints that the University of Austin (UATX) has been courting him.

That leads to a brief discussion of whether schools like UATX are the wave of the future: schools that can teach humanities courses without them being polluted by extreme “social justice” mentality. Both men ponder whether universities like that are the wave of the future, and whether regular universities will devolve into “STEM academies”.  That, in turn, leads to a discussion, mostly by McWhorter, about music theory and how that, one of his areas of expertise, has been polluted by wokeness.

The biggest segment of the discussion involves McWhorter’s recent visit to Washington’s National Museum of African American History and Culture, and his thoughts about it (read his long NYT op-ed piece, which is very good, here). McWhorter characterizes it as not a dolorous place but a “happy place,” and one that gives a balanced view of black history—a view in which black people are more than simple oppressed people who serve to remind the rest of us of their guilt. It portrays as well, he avers, the dignity and positive accomplishment of African Americans. (McWhorter compares the dolorous view of black history with the narrative pushed by Nikole Hannah-Jones of the 1619 Project.)  His description makes me want to visit that museum more than ever (I haven’t yet been but will, and I must also visit the United States Holocaust Memorial Museum).

Finally, they discuss the question of whether they were wrong to be so hard on DEI, given that some aspects of it (e.g., a call for equality) are positive. Here McWhorter is at his most eloquent, saying that, given the overreach of DEI, it was imperative for both of them to have criticized it. As McWhorter notes, the extreme construal of DEI did not “fight for the dignity of black people” and, he says, in the face of that extremist ideology, their silence would not have been appropriate. Loury agrees.  At this point McWhorter brings up Claudine Gay, ex-President of Harvard, claiming that she was hired simply because she was a black woman, which was “wrong and objectifying.” (Only McWhorter could get away from saying something like that.) The elevation of Gay, says McWhorter, was the sort of thing they were pushing back against when they opposed DEI.

This is worth a listen, and I’ve put the video below.

It’s time for a Sunday Duck Report. Esther’s brood hatched on May 6, and so today they are 26 days old, coming on to four weeks. As we’ll see at the bottom, in the last week or so they’ve started growing their feathers.

Here are some videos and pictures of the brood, most taken around May 20 when they were two weeks old.

The brood (still six):

A swimming duckling. They are starting to look like big ducks, though they still have their baby down:

A diving duckling. It’s learning a skill that will help it not only forage, but also escape predators:

They get fed two or three times a day and are coming quite close to us. (I whistle for them, a call that they recognize as “feeding time,” but all I really have to do is show up at the pond with my bag ‘o duck food, and they coming swimming towards me rapidly.)

By the way, they get a good diet: Mazuri duck chow, which is a complete diet. Esther and big ducks get big pellets (I get this in 50 lb. bags), while the babies get the same thing, but in smaller pellets since their bills are too small to engulf the big ones (this “waterfowl starter chow” I get in 25-lb bags).  As a special treat, they get freeze-dried mealworms, which are high in fats and protein. This is their favorite food, but it’s a dessert, not the main course.

They love to enter the plastic tubs that used to be used as supports for the “plant cages”. I think of it as a duck spa:

Here are two ducklings, their swollen craws making it obvious that they just ate. They store some of the foot they eat in their esophagus.

About a week ago, the ducklings and Esther climbed up the southern “ramp” on the east side of the pond, where they’d sun themselve and then, going further into the brush, would all rest together. Here they are approaching the ramp that leads to their resting spot.  Esther always leads the way, but sometimes the brood is reluctant to land as they still want to swim and play:

More recently, since the babies have gotten large enough to jump directly out of the pond onto its edge, they like to do that together and sun themselves on the cement. Esther, of course, is always nearby.

Having a good rest:

Sometimes they pile up a few feet away from mom, but she’s always nearby. The piling up keeps them warm, as it’s been a bit chilly lately.

A video showing their postprandial resting on the edge of the pond:

A pile o’ ducklings:

Finally, in the last eight days or so the babies have been sprouting their feathers.  Feather appearance starts at the tail, in which a few tiny feathers make the tail look like a paintbrush:

. . . then the feathers start sprouting on their wings (arrow). Next stop: scruffy-looking “punk ducks” with a mixture of feathers and fluff.  Stay tuned for that!

Here’s the latest comedy/news stint from Bill Maher’s “Real Time” show, a “New Rule” segment called “Freak-end update”, referring of course to Diddy’s “Freak offs,” his drug-fueled sex orgies often involving prostitutes. Diddy is very likely to be convicted (you’ve seen the tape, right?), and it will be a huge come-down from his status as music king to living in a cell sans sex and drugs.

Maher’s new rule is this: “If you’ve being abused, you gotta leave right away.” He understands why abused women and loath to report it, and will even send affectionate messages to their abusers, but Maher adds that we must understand these dynamics and not let them soften our attitudes towards abuse. He then recounts how laws and attitudes are changing to punish abusers more seriously, and advises abused women to go to the police immediately rather than just telling a few friends or writing about it in a journal.

This is far more serious than most of Maher’s other bits, but he feels strongly about it.  Yet he still manages to eke out a few laughs.

Today we have a historical/natural history post by reader Lou Jost, who works as a naturalist and evolutionary biologist at a field station in Ecuador.

A diatom sample from the HMS Challenger expedition of 1872-76

The Challenger in 1873, painting by Swine

The HMS Challenger was a British naval ship equipped with both sail and steam power. At the urging of scientists, and riding the wave of popular curiosity about our then-poorly-known planet, the ship was converted by the Royal Society of London to become the world’s first specialized oceanographic vessel. It went on a mission from 1872 to 1876 to systematically explore the world’s oceans, especially the scientifically almost completely unknown Southern Ocean near Antarctica. This mission was the 19th century equivalent of a trip to the moon or to Mars (except that this  HMS Challenger mission had a much more interesting and diverse subject region!).

One of the navigators, Herbert Swine, made contemporaneous drawings and paintings on site, including the two HMS Challenger images I have shared here (though these were probably polished somewhat for publication). He also published his lively diaries of his time on the expedition, in two volumes, just before he died of old age. He was the last survivor of the crew.

A map of the expedition

The voyage of exploration went 80,000 miles, lasted 1250 days, and circumnavigated the globe. They made systematic chemical, temperature, and depth readings across the globe, taking biological specimens along the way. They discovered over 4000 new species, from vertebrates to phytoplankton, and lost several lives along the way. They were the first to systematically explore the mid-Atlantic Ridge, and by pure chance they also discovered the Marianas Trench,  the deepest part of the Pacific Ocean. In 1950-1951 a modern vessel, again bearing the name Challenger in a homage to the original, found the deepest part of any ocean, the “Challenger Deep”, just 50 miles from the HMS Challenger’s deepest depth record.

The Challenger at work

The immense number of samples obtained by the crew of the Challenger took 19 years to analyze and publish, in 50 volumes. Specimens were sent to many scientists of the time, and some of these still circulate today. Among the most interesting organisms they sampled are diatoms. Diatoms are single-celled organisms that make up much of the oceans’ phytoplankton, and their most notable features are the finely sculpted glass cases called “frustules” that enclose them. These glass frustules are often preserved intact for tens of millions of years, sometimes forming enormous deposits of pure frustules known as “diatomaceous earth” on the beds of ancient lakes and oceans. Some of these deposits are so big that millions of tons of diatom frustules thousands of years old are whipped up by the wind in dry parts of Africa every year, and then cross the Atlantic by air and rain down on the Amazon basin in South America.

The expedition of the HMS Challenger launched the most systematic study of the 19th century on the diatoms of the Southern Ocean. They sampled at regular intervals during their voyage, and at multiple depths, including very deep water that had never before been studied, discovering new species of diatoms such as Asteromphalus challengerensis, named after the vessel (using bad Latin unfortunately). The samples were distributed to diatomists around the world, who carefully mounted them on microscope slides using special mountants of high-refractive-index liquid, designed to make the transparent diatom frustule more visible under standard microscopic illumination. Some of these Challenger diatom slides come up for sale periodically, and I could not resist buying one that appeared in eBay.

Increasing zooms of the diatoms on the slide:

This one slide, from 1873 during an Antarctic visit, has hundreds of individuals consisting of maybe a couple of dozen species. There are also many broken diatom fragments. Among the individuals, I was lucky enough to find several examples of what appear to be the aforementioned A. challengerensis. This is a rare species which is found only in water that is within 1 degree Centigrade of freezing. The taxonomy of this species and its relatives is in flux as we learn more about how the structures change with age.

Two slides of the species A. challengerensis:

Some of the taxonomic problems of these diatoms is caused by their weird way of replication. Diatoms can’t grow like a normal organism because they are in a glass case, so instead they shrink, each half of the frustule making a new matching half that is slightly smaller than the parent half-frustule, so that the two new halves each nest inside their parent half-frustule. Then they separate. Here is a nice illustration of this:

The population thus has a large spread of different sizes, and it appears that some frustule features may change as they get smaller, causing taxonomic confusions in the case of A. challengerensis and others.  By the way, eventually the smallest ones go through a sexual reproductive phase that builds a new full-sized frustule, so that the cycle can start over. This is really weird. Later I hope to write long post about the utterly astounding, almost unbelievable biology of diatoms.

Darwin published his theory of evolution just 13 years before this expedition, and evolution was on everyone’s mind, and the commander of the ship was an “early adopter” of the theory. At the time there was still not much clarity about the predictions of the theory. It was widely believed that the cold dark oceans would preserve “living fossils” similar to the earliest forms of life on earth. The expedition did not find this to be true, and so it actually was a slight setback for evolutionary theory. They unfortunately missed the hydrothermal vents which do indeed shed light on the origins of life.

I wrote at the beginning of this post that the HMS Challenger expedition was the 19th Century analogue of space exploration. So it was fitting that NASA decided to name one of the space shuttles “Challenger”, after the two scientific ships which carried that name. The photo above shows Challenger orbiting over the ocean 110 years after the original HMS Challenger sailed that same ocean. Unfortunately, as in the original Challenger expedition, people died on that space shuttle in the name of science, a reminder that exploration on the margins of what is known will always be risky, and the participants are real heroes of their age.

Today we have a guest post from reader Coel Hellier, who does this kind of stuff for a living. His text deals with the recent kerfuffle about whether a nearby planet shows an atmospheric gas indicative of life.  I particularly like the details about how scientists go about analyzing a question like this. His text is indented, and he’s added the illustrations.

Is the dimethyl sulphide in the atmosphere of exoplanet K2-18b real?

Everyone is interested in whether there is life on other planets. Thus the recent claim of a detection of a biomarker molecule in the atmosphere of an exoplanet has attracted both widespread attention and some skepticism from other scientists.

The claim is that planet K2-18b, 124 light years from Earth, shows evidence of dimethyl sulfide (DMS), a molecule that on Earth arises from biological activity. Below is an account of the claim; I try to include more science than the does mainstream media, but do so largely with pictures in the hope that the non-expert can follow the argument.

Transiting exoplanets such as K2-18b are discovered owing to the periodic dips they cause in the light of the host star:

And here is the lightcurve of K2-18b, as observed by the James Webb Space Telescope, showing the transit that led to the claim of DMS by Madhusudhan et al.:

If we know the size of the star (deduced from knowing the type of star from its spectrum), the fraction of light that is blocked then tells you the size of the planet.

But we also need to know its mass. One gets that from measuring how much the host star is tugged around by the planet’s gravity, and that is obtained from the Doppler shift of the star’s light.

The black wiggly line in the plot below is the periodic motion of the star caused by the orbiting planet. Quantifying this is made harder by lots of additional variation in the measurements (blue points with error bars), which is the result of magnetic activity on the star (“star spots”). But nevertheless, if one phases all the data on the planet’s orbital period (lower panel), then one can measure the planet’s mass (plot by Ryan Cloutier et al):

So now we have the mass and the size of the planet (and we also know its surface temperature since we know how far it is from its star, and thus how much heating it gets).  Combining that with some understanding of proto-planetary disks and planet formation. we can thus dervise models of the internal composition and structure of the planet.

The problem is that multiple different internal structures can add up to the same overall mass and radius. One has flexibility to invoke a heavy core (iron, nickel), a rocky mantle (silicates), perhaps a layer of ice (methane?), perhaps a liquid ocean (water?), and also an atmosphere.

This “degeneracy” is why Nikku Madhusudhan can argue that K2-18b is a “hycean” planet (hydrogen atmosphere over a liquid-water ocean) while others argue that it is instead a mini-Neptune, or that it has an ocean of molten magma.

But one can hope to get more information from the detection of molecules in the planet’s atmosphere, a task that is one of the main design goals of the James Webb Space Telescope [JWST]. The basic idea is straightforward: During transit, some of the starlight will shine through the thin smear of atmosphere surrounding the planet, and the different molecules absorb different wavelengths of light in a pattern characteristic of that molecule (figure by ESA):

So one observes the star both during the transit and out of transit, and then subtracts the two, and the result is a spectrum of the planet’s atmosphere.

If the planet is a large gas giant with a fluffy, extended atmosphere and is orbiting a bright star (so that a lot of photons pass through the atmosphere), the results can be readily convincing. For example, here is a spectrum of exoplanet WASP-39b with features from different molecules labelled (figure by Tonmoy Deka et al):

[I include a plot of WASP-39b partly because I was part of the discovery team for the Wide Angle Search for Planets survey, but also because it is pretty amazing that we can now obtain a spectrum like that of the atmosphere of an exoplanet that is 700 light-years away, even while the planet itself is so small and dim and distant that we cannot even see it.]

The problem with K2-18b is that the star is vastly fainter and the planet much smaller than WASP-39b. This is at the limit of what even the $10-billion JWST can do.

When you’re subtracting two very-similar spectra (the in- and out-of-transit spectra)  to look for a rather small signal, any “instrumental systematics” matter a lot. Here is the same spectrum of K2-18b, as processed by several different “data reduction pipelines”, and as you can see the differences between them (effectively, the limits of how well we understand the data processing) are similar in size to the signal (plot by Rafael Luque et al):

The next problem is that there are a lot of different molecules that one could potentially invoke (with the constraint of making the atmospheric chemistry self-consistent). For example, here are the expected spectral features from eight different possible molecules (figure by Madhusudhan):

To finally get to the point, I show is the crucial figure below. Nikku Madhusudhan and colleagues argue — based on an understanding of planet formation, and on arguments that planets like K2-18b are hycean worlds [with a liquid water ocean under a hydrogen-rich atmosphere], and from considerations of atmospheric chemistry, in addition to careful processing and modelling of the spectrum itself — that the JWST spectrum of K2-18b is best interpreted as follows (the blue line is the model, the red error bars are the data):

This interpretation involves large contributions from DMS (dimethyl sulphide) and also DMDS (dimethyl disulphide) — the plot below shows the different contributions separated — and if so that would be notable, since on Earth those compounds are products of biological activity—mainly from algae.

In contrast, Jake Taylor analysed the same spectrum and argues that he can fit it adequately with a straight line, and that the spectral features are not statistically significant. Others point out that the fitted model contains roughly as many free parameters as data points. Meanwhile, a team led by Rafael Luque reports that they can fit the spectrum without invoking DMS or DMDS, and suggest that observations of another 25 transits of K2-18b would be needed to properly settle the matter.

There are several distinct questions here: Are the details of the data processing sufficiently understood? (perhaps, but not certainly); are the relevant spectral features statistically significant? (that’s borderline);  and, if the features are indeed real, are they properly interpreted as DMS? (theorists can usually think of alternative possibilities). Perhaps a fourth question is whether there are abiotic mechanisms for producing DMS.

This is science at the cutting edge (and Madhusudhan has been among those emphasizing the lack of certainty, though the doubts have not always been in news stories), and so the only real answer to these questions is that things are currently unclear. This is a fast-moving area of astrophysics and we’ll know a lot more in a few years.

Today we feature some lovely flower pictures from Thomas Webber. Thomas’s captions and IDs are indented, and you can enlarge the photos by clicking on them. (The images are stacked but, at the photographer’s request, I’ve omitted the info for each photo.)

The theme for today’s installment is Lawn Weeds. All the plants shown here are from roadsides, vacant lots, parks, yards, and the University of Florida campus in Gainesville, at the north end of the Florida peninsula. All are mowed from time to time, and as far as I can tell they weren’t planted where I found them. I think I’ve identified all of them correctly to genus, and most to species, but I’ve added the qualifier “cf.” to the species epithets I’m less sure of. I invite corrections.

White clover, Trifolium repens. Individual flowers 8 mm long. Native to Europe and Central Asia:

Oakleaf fleabane, Erigeron quercifolius. 1 cm diameter at full size. Native:

Lyre-leaf sage, Salvia lyrata. 1.5 cm long. Native:

Marsh pennywort, Hydrocotyle cf. umbellata. Individual flowers 2 mm. Native:

Pennywort leaves (2-5 cm) make an arresting pattern when they grow together in a thick mass. This is part of a patch that covered about 25 square meters of a University of Florida lawn:

Wood sorrel, Oxalis cf. corniculata. 6 mm. Native:

Blue-eyed grass, Sisyrinchium angustifolium. 1 cm. Native:

Hawksbeard, Youngia japonica. 1.5 cm. Native to east Asia, now world-wide. The informative article linked here is devoted largely to means of exterminating this plant:

Vetch, Vicia cf. sativa. 8 mm across. Native to Europe and the Middle East, now cultivated and naturalized around the world:

Perennial peanut, Arachis glabrata. 1.5 cm across. Native to South America, cultivated and escaped in the southeastern United States:

False pimpernel, Lindernia dubia. 1 cm across lower petals. Native. These two were among over a thousand that carpeted the bottom of a small seldom-flooded retention basin:

Sunshine mimosa, Mimosa strigillosa. Flower head 3 cm tall. Native:

Peppergrass, Lepidium virginicum. Individual flowers 2 mm. Native:

I saw a picture of this thing on my Facebook page, and automatically assumed that it–or at least its color–was fake.  But here’s a real photo of the Conehead Mantis (Empusa pennata) from Wikipedia.  An excerpt from the article:

Empusa pennata, or the conehead mantis, is a species of praying mantis in genus Empusa native to the Mediterranean Region. It can be found in Portugal, Spain, southern France, Italy and on the mediterranean coasts of Morocco, Algeria, Tunisia, Libya, Turkey and Egypt.[1] Because of its cryptic nature, or also possibly because of its fragmented, low-density populations, it is rarely encountered in the wild.

They’re incredibly cryptic, as well as patient, as the video below shows:

Frank Vassen from Brussels, Belgium, CC BY 2.0 via Wikimedia Commons

. . . and the head of the male (both sexes have cones):

Raúl Baena Casado from Sevilla, España, CC BY 2.0 , via Wikimedia Commons

A short video which shows the main features. Ah, the marvels of natural selection, which, it seems, can do almost anything.

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.

The latest Jesus and Mo cartoon, called “sky,” came with the caption, “Important court case today.” It’s this, from the National Secular Society:

The prosecution of a man on trial tomorrow for burning a Quran could edge the UK “dangerously close to a prohibition on blasphemy”, the National Secular Society has warned.

Hamit Coskun will stand trial at Westminster Magistrates’ Court for protesting against Islamism outside the Turkish Consulate in February. He set fire to a Quran as part of the protest, which led to a man attacking him with a knife.

Coskun was subsequently charged with intent to cause “harassment, alarm or distress” against “the religious institution of Islam”.

And the cartoon reflects the case:

Matthew sent me this qui, involving ten pairs of photos in Brittanica Education. The object is to see whether you can tell which is generated by AI and which is real.  Click on the headline below to go to the quiz, which is fun to take. After you click on which photo you think is real, the explanation of why you should have known pops up.

Here is one pair of photos, but take the quiz yourself, which is quick.  Matthew says “I got 10/10”, but poor PCC(E) got only 9/10. Some are more obvious than others.

Have a look and then go to the quiz. Give us your score and then beef if you wish. This is the last one:

Today’s photos are by reader Ephraim Heller, and come from Tanzania (see his earlier photos from that location here). Ephriam’s links and captions are indented, and you can enlarge the photos by clicking on them.

Brief introduction: These photos were taken on safari in Tanzania in April 2025. Most are from the Serengeti National Park with a few from the Ngorongoro Conservation Area.

Today’s photos focus on antelope (hartebeest and wildebeest) and zebra.

Zebras scratching and socializing:

Zebra suckling her youngster:

Zebra baby, fur still wet from birth and wobbling on its legs:

Hartebeest mom watching over sleeping baby. According to the African Wildlife Foundation: “The hartebeest is a large, fawn-colored antelope. Their most distinctive characteristics are a steeply sloping back, long legs, and elongated snout. Despite their ungainly appearance, they are as elegant, if not more than, other antelopes. They are one of the most recent and highly evolved ungulates and are far from clumsy. In fact, they are one of the fastest antelopes and most enduring runners — capable of reaching speeds of up to 70 km/h. These qualities gave rise to their name, which means ‘tough ox.’ Their sedentary lifestyle seems to inhibit the mixing of populations and gene flow, and as a result, there are several subspecies of hartebeest.”

Wildebeest beginning their annual migration. This line of animals was miles long and they didn’t stop running during the hour that I observed them:

Dawn wildebeests:

For our final video of the day, we have a two-minute clip of a very gutsy man rescuing a big male kangaroo who was caught in a metal cable. All’s well that ends well.

Kangaroos are reputed to be dangerous, for they can kick you hard. But I found only two reported human deaths due to kangaroos. The animal most likely to kill you in Australia, according to Wikipedia’s “animal attacks in Australia” article, is snakes, with between 3 and 10 deaths per year.

More video today!  This one, of course, was suggested to me by YouTube, since I watch a lot of food videos as well as history videos. And it’s exactly the kind of video that I would have to click on, as it lists the favorite foods of every American President.

Here are the Presidents who, in my view, had the best taste (you’ll have to watch to see their favorites):

Thomas Jefferson
James Madison
James Monroe
John Tyler
James K. Polk
Abraham Lincoln
Ulysses S. Grant
Teddy Roosevelt
William Howard Taft
Woodrow Wilson
Lyndon Johnson***
Jimmy Carter

LBJ gets the kudos for liking the best dish, and, looking over the list, I see that it’s weighted with Presidents who liked Southern food. No surprise, as it’s America’s best regional cuisine.  They do mention a McDonald’s Filet O’ Fish as Trump’s favorite, but I thought he liked Big Macs better. Either way, he doesn’t make the list.

A friend who is laid up with covid, and watching New Atheist videos (Hitchens, Dawkins, Harris, etc.) for the first time, sent me a new (six-day-old) [rp=atheist video made by someone I didn’t know. That would be Darante’ LaMar Martin, a former pastor who deconverted. In this 17.3-minute video, he makes two assertions: that there is no tangible evidence supporting the miracles of the Bible and thus the foundational claims of Christianity; and the spread of Christianity was based on “imperial enforcement” by king rather than on its truth. (Later adherents would have no way on checking the truth, anyway, and we know that the sole evidence underlying the world’s most popular religion, with 2.6 billion adherents, is solely the Bible. There is no extra-Biblical evidence for a person, much less his acts, on whom the New Testament is based.

You probably have heard some of the arguments against Jesus’s miracles before (e.g., the lack of contemporaneous evidence for a Jesus Man, as well as the absence of evidence that, upon the Crucifixion, the sky darkened and dead saints emerged from their graves. But the stuff about the subsequent spread of the faith, like the story of Constantine’s conversion (or rather, cooption), was new to me. (I can’t vouch for this other stuff; perhaps readers can judge it.)

It’s not clear whether Darante‘ believes that there was a Jesus figure on whom the faith was based. He implies that there was a “spiritual figure”  named Christus, a man who didn’t have a lot of followers but was executed by the Romans because he posed a “fringe threat.”  As he says, “The Romans didn’t kill a king; they killed a failed prophet.”

About the spread of Christianity he adds this: “The story of Christianity’s rise is not a story of truth triumphing over doubt. It’s a story of power rewriting the rules of belief. Christianity didn’t spread because Jesus walked out of a tomb. It spread because Christianity coopted its rivals, aligned with empire, absorbed its enemies, and forged its own legitimacy with law, violence, and theological branding.”

You know of prominent Christians who expound their beliefs in the mainstream media.  Some, like Andrew Sullivan, irk me because while I admire their political views, I see their religious belief as a form of irrationality or even hypocrisy: they accept things without the evidence they’d demand for political assertions.  Others include Ayaan Hirsi Ali, whom I’m not too hard on because she found religion to be the only palliative for her severe, suicidal depression.

The most irksome is Ross Douthat, whose new book is Believe: Why Everyone Should Be Religious. Douthat is flogging it everywhere (the NYT gives him a big platform), and making no bones about believing in not only Jesus and the Crucifixion, but also the afterlife, Satan, assorted demons, purgatory, and angels.  While Sullivan and more liberal believers are clearly reluctant to describe the contents of their beliefs, Douthat has purchased the whole hog and proffers slices of ham to everyone.

Martin’s YouTube page, with more atheist videos, is here. (try “The ten top lies I told as a pastor.“) He has a charismatic style of speaking, and I can imagine that he was a good preacher before he saw the light.

 

We have 2-3 more groups of photos, so please send in any good ones you have.

Today’s photos are of plants, and were taken by Aussie Julia Monaghan. Her captions and IDs are indented, and you can enlarge the photos by clicking on them:

Australian Native Plants (mostly)

These photos were taken in my and my neighbour’s garden, in the Lake Macquarie area of New South Wales, one of Australia’s largest coastal salt water lakes. As Australia often has a very hot, dry climate (thought we do have flooding at the moment), plants have many different adaptations to cope with the generally harsh climate, often growing in poor soils with full sun and low water supply. I took my photos using my Samsung phone.

Hairpin Banksia flower (Banksia spinulosa). A species of small woody shrub in the Proteaceae family, native to eastern Australia. The spikes are gold or sometimes yellowish. Specimens of Banksia were first collected by naturalists Sir Joseph Banks and Daniel Solander, on the Endeavour during Lieutenant James Cook’s first voyage to the Pacific Ocean:

Hairpin Banksia bush (Banksia spinulosa). Banksia are adapted to fire, which plays an important role in seed release and germination. The plant’s reproductive structures, the woody follicles, store its seeds and only release them when exposed to the heat of a bushfire:

Hairpin Banksia (Banksia spinulosa) post pollination. As the flowers die they will develop into woody, fruiting cones:

Grevillea Mason’s Hybrid (Grevillea banksii × Grevillea bipinnatifidajubata) are a small spreading shrub that attract and feed native birds throughout sping and summer. A cultivar from a genus of over 350 flowering plants in the family Proteaceae, they are also known as  spider flowers.  This Grevillea is also named the Ned Kelly after one of Australia’s most notorious bushrangers:

Grevillea ‘Peaches and Cream’ (Grevillea bankssi × Grevillea bipinnatifida). Another Grevillea cultivar, their nectar is a reliable food source from winter to spring that feeds honeyeaters such as lorikeets and parrots. Grevilleas are generally very heat and drought tolerant:

Stiff Bottlebrush (Calistemon rigidus) attracts a variety of birds, from nectar-feeding species such as honeyeaters, to seed-eating birds such as cockatoos. Its dense foliage acts as a habitat for many different birds, as it provides thick cover and many nesting opportunities:

Purple Morning Glory (Ipomoea indica) is a climbing vine that grows quickly and smothers other plants. Considered a reportable weed, it was introduced from  Mexico or Central America as a garden plant but has become established in different ecosystems:

Coastal or Cairo Morning Glory (Ipomoea cairica) is another climbing vine introduced from Africa or Asia, that grows rapidly, smothering other plants. It has also been classified as an environmental weed:

Kangaroo Paw Bush – Pink (Anigozanthus) are a smaller cultivar of the Kangaroo Paw. They are very tolerant of drought and coastal conditions once they are established. They come in a variety of vibrant colours, including brilliant red, bright pink and bright yellows:

Kangaroo Paw Flower – Pink ( Anigozanthus). Their tufted flowers covered with velvety hairs resemble the paw of a kangaroo, hence their name:

Kangaroo Paw Flower – Yellow (Anigozanthus):

Grasstree (Xanthorrhoea australis). These are ancient trees consisting of a thick trunk made up of a dense layer of old leaves forming a protective layer around a softer core, with a tuft of newer leaves forming a crown at the top of the tree. These trees are extremely slow growing and may take many years to flower. While bushfires may burn the leaves and blacken the trunk, the plant’s living core is protected as it sits underground. In this species, fire stimulates flowering: