A evolutionary interlude for the holiday

November 24, 2016 • 12:30 pm

Note that cats are barely intelligently designed, since most, including members of the breed, are much closer to their wild ancestors than are various dog breeds. Remember the sad specimen at bottom was artificially selected from an ancestor depicted at the top.

3pajphd

h/t: John S.

The Bubble: A safe space for all traumatized progressives

November 24, 2016 • 11:00 am

I’m sure that Lorne Michaels and the cast of Saturday Night Live are all liberals. Nevertheless, they were self-confident enough to make fun of the mentality of those liberals who wept and wailed when Trump was elected, saying that he was either “not our President” or vowing to leave the U.S. (I don’t think anyone has left over this yet.) Here’s a sketch they did after the election, laying out the world that many of us long for now. The details of this sketch are perfect, down to the Ta-Nehisi Coates book.

As one commenter on the YouTube video said, “This is Portland, Oregon. I know, I live here.”

h/t: Charleen

Jesus Christ declared the King of Poland (Mary is already Queen)

November 24, 2016 • 10:00 am

I am not making this up. According to Christian Today, and verified by my Polish friend Malgorzata, the Polish government just accepted Jesus Christ as the country’s king:

Jesus has been declared King of Poland in a ceremony attended by the country’s president Andrzej Duda.

The ceremony was held at the Church of Divine Mercy in Krakow on Saturday and the liturgy was repeated in churches across the country the following day.

According to the Conference of Polish Bishops, it was timed to coincide with the end of the Catholic Church’s Jubilee Year of Mercy and 1050th anniversary of Polish Christianity.

The ceremony included the prayer: “In our hearts, rule us, Christ! In our families, rule us, Christ! … In our schools and universities, rule us, Christ! … Through the Polish nation, rule us, Christ! … We pledge to defend your holy worship and preach Thy royal glory, Christ our King, we promise!”

It continued: “We entrust the Polish people and Polish leaders to you. Make them exercise their power fairly and in accordance with your laws. … rule us, Christ! Reign in our homeland and reign in every nation – for the greater glory of the Most Holy Trinity and the salvation of mankind.”

Good God! This of course came from a revelation experienced by a Polish nurse Rosalia Zelkova, who, early in the 20th century, heard voices that told her that Jesus demanded, as a condition for the salvation of Poland in the upcoming war, that he be recognized as the King of Poland. What an arrogant S.O.B. Jesus was!

Right-wing legislators in Poland tried this trick in 2006 but failed, opposed by the Church itself. Now that the Catholic Church has huge power in Poland with the new government’s assent, there was no problem with this declaration.

When I wrote Malgorzata asking if this could be true, she responded:

The story about Jesus becoming the King of Poland is absolutely true. Half of the Polish government was in attendance. This was the reason Andrzej wrote a huge article the other day about “Islam envy” of Polish clergy. The situation here is more absurd than it ever was since the fall of Communism, and we are quickly becoming a theocracy.
But wait! It gets better (or worse)! For a Queen of Poland has already been in power for a long time, and guess who it is? Malgorzata writes:
But do you know that we already have a Queen of Poland and it is none other than Mary, Jesus’s mother? She was taken as a Queen of Poland on April 1, 1656 by the then king, Jan Kazimierz. Three hundred years later, on August 26, 1956 , the Polish Church hierarchy, in the presence of about 1 million believers, repeated the pledge to her as Polish Queen. So now we have both a Queen and a King ruling together. Here is what Polish Wikipedia says about it (unfortunately, there’s no English version):
fc66afad614071641f4a75d7c1be0ede-670x1005
Polish royalty

h/t: Ginger K.

Readers’ wildlife photographs

November 24, 2016 • 9:00 am

We have a readers’ wildlife appropriate for Thanksgiving today (see the first photo). These four pictures were sent by reader Garry VanGelderen from Ontario, Canada. And readers: be sure to keep those photos coming in!

Garry’s notes are indented:

Wild turkeys, Meleagris gallopavo (Penetanguishene, ON):

100_2336

Snapping turtle (Chelidra serpentina) at Wye Marsh Conservation Area (Midland, ON):

980468_10200630826191329_1035103267_o

Snow bunting, Plectrophenax nivalis, male (Penetanguishene, ON):

dscn0486

American black bear (Ursus americana) on John Island (North Channel, Lake Huron):

dscn0748-1

Happy Thanksgiving (and a fossil turducken)

November 24, 2016 • 8:15 am

Today’s Bloom County cartoon, courtesy of reader Stash Krod (click to enlarge):

15123403_1369518379745578_6059188051242656840_o

Reader John W. sent this salacious Thanksgiving cartoon (if you don’t know what a “turducken” is, go here):

img_20161123_135711-1

And, for some biology on this day, we have an item reported in September by Discover Magazine and National Geographic: a “preshistoric turducken”.  Yes, it’s a three-in-one fossil find discovered in Germany’s Messel Pit, a remarkable cache of fossils from the Eocene, deposited around 47 million years ago. (Messel is also a UNESCO World Heritage site.) Like a turducken, it shows three species inside each other, though unlike a turducken, the fossils are sequential members of a food chain.  Here’s the fossil (the interpretation is below):

screen-shot-2016-09-07-at-12-04-53-pm

The white arrow above indicates the tip of the lizard’s snout resting inside the snake.

And this is what happened (from National Geographic):

Forty-eight million years ago, an iguana relative living in what’s now Germany scarfed down an insect with a shimmering exoskeleton. Soon thereafter the lizard’s luck changed—when a juvenile snake gulped it down headfirst.

We know this happened because the snake had the spectacularly bad luck to end up in a death trap: the nearby Messel Pit, a volcanic lake with toxic deep waters and a possible knack for belching out asphyxiating clouds of carbon dioxide.

It’s unclear if the lake poisoned or suffocated the snake, fates that more often befell the area’s aquatic and flying creatures. Most likely, it somehow died near the lake and was washed in. But no more than two days after eating the lizard, the snake lay dead on the lake floor, entombed in sediments that impeccably preserved it, its meal, and its meal’s meal.

And that’s a very good thing. That fossil, recently described in Palaeobiodiversity and Palaeoenvironments, is only the second of its kind ever found, revealing three levels of an ancient food chain nested one inside the other in paleontology’s version of Russian nesting dolls—or its culinary equivalent, a turducken.

“It’s probably the kind of fossil that I will go the rest of my professional life without ever encountering again, such is the rarity of these things,” says Krister Smith, the paleontologist at Germany’s Senckenberg Institute who led the analysis and a National Geographic/Waitt Grant recipient. “It was pure astonishment.”

Here’s the reveal (illustration from Kreister R. Smith): the snake is in white, the lizard, Geiseltaliellus maarius, is in orange, and the insect inside the lizard’s gut is in turquoise:

screen-shot-2016-09-07-at-12-05-00-pm

This isn’t the first fossil showing three levels of a food chain. A 2008 paper in the Proceedings of the Royal Society reports a fossil shark that ingested an amphibian that itself ingested a fish. Thus, unlike the one above, all are vertebrates. Here’s that one, about 300 million years old, which is a little harder to suss out. The caption comes from the Royal Society paper:

f1-medium
(from paper): Figure 1 Triodus sessilis with ingested prey items. (a) Photograph of a specimen from the Lower Rotliegend of Lebach, southwest Germany (UHC-P 0682). (b) Line drawing of digested temnospondyl larvae. Left: an almost complete specimen of Cheliderpeton latirostre with the remains of ingested juvenile acanthodian. Right: skull of Archegosaurus decheni. as, acanthodian scales; br, branchial apparatus; cla, clavicle; ?clei, cleithrum; fem, femur; gs, gastral scalation; fs, acanthodian fin spines; hum, humerus; icl, interclavicle; il, ilium; man, mandible; mc, Meckel’s cartilage; mca, metacarpalia; mta, metatarsalia; na, neural arch; or, orbit; pas, parasphenoid; pf, pectoral fin; pg, pectoral girdle; phal, phalanges; pq, palatoquadrate; ps, xenacanthid placoid scales; r, ribs; rad, radius; sk, skull; sta, stapes; ul, ulna.

The scenario:

f2-large

If you’re one of those having a turducken today, give us a shout in the comments. I’ve never had one!

h/t: Grania

Thursday: Hili dialogue

November 24, 2016 • 6:30 am

Good morning! It’s Thursday, November 24 (I presume you know the year), which means that it’s Thanksgiving in the U.S. But for some reason it’s been declared National Sardines Day!

But, more important, it’s Evolution Day, an international day to remember the publication of a the book laying out what was, as Dan Dennett said, “The most important idea anyone ever had.” One can make a good case that he’s right. It was on this day in 1859 that Darwin’s Big Book was published, and I’ll put the whole name up so you can remember it. I always call it The Origin, but its full name is On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.  Do you think you can remember that? Here’s the first page of the first edition, an edition now worth hundreds of thousands of dollars:

800px-origin_of_species_title_page

Exactly 18 years later, Black Beauty was published by Anna Sewell:

blackbeautycoverfirsted1877

On November 24, 1963, Lee Harvey Oswald, the killer of John F. Kennedy, was himself killed by Jack Ruby in the basement of the Dallas, Texas police headquarters. Many of us saw that live on television.

Notables born on this day include Laurence Sterne and Junipero Serra (both 1713), William F. Buckley, Jr. (1925), Pete Best (1941), and Ted Bundy (1946). Those who died on this day include, besides Lee Harvey Oswald, George Raft (1980), Freddie Mercury (1991), John Rawls (2002), and pitcher Warren Spahn (2003). Meanwhile in Dobrzyn, Hili is looking everywhere for noms. Good thing she doesn’t have a credit card!

Hili: Not everything can be found on the Net.
A: And what were you looking for?
Hili: Something tasty.
p1050116
In Polish:
Hili: Nie wszystko daje się znaleźć w sieci.
Ja: A czego szukałaś?
Hili: Czegoś smacznego.

Here’s a photo sent by Robin Cornwell showing her niece Quincey and Quincye’s cat Joe, both wearing tee shirts that show the other one. Robin says, “She carries that cat everywhere and he seems to like it.” Joe is five months old, and apparently has gotten used to being dressed.

imagejpeg_0

Reader Taskin sends a photo of “Gus in a thoughtful moment…”

img_6257

And a slur on biology from reader jsp:

15193628_10210224103346735_963752456860773018_n

Schools bring out the therapy dogs and Play-Doh to help students distraught over Trump’s victory

November 23, 2016 • 1:45 pm

Before the election I was disturbed by the many Facebook posts pointing out, over and over again, Donald Trump’s latest misstep, peccadillo, or odious statement. It’s not that I thought that this stuff shouldn’t be discussed on Facebook, but it totally dominated the feed, was repetitive, sometimes nearly hysterical, and above all, displaced the kitten posts!

But now it’s far worse, and my liberal friends rage against the rising of the Right in Facebook post after post after post. Not a kitten to be seen! I can hardly bear to look at Facebook.

Even worse: according to news.com.au, American school and college kids have been so traumatized by Trump’s victory that schools are deploying the full armamentarium of Safe Space Toys, including therapy dogs and Play-Doh.

At the University of Kansas, tutors reminded its 18 and 19-year-olds that therapy dogs were available.

And the girls at an exclusive private school in New York City last week were so stricken the teachers brought in the therapy dogs to soothe them.

. . . Students at the University of Michigan have been offered colouring books to calm them. [JAC: This unwise plan was canceled as cooler heads prevailed.]

Cornell University, an Ivy League college in New York state, held a campus-wide “cry-in,” [JAC: see here] with seniors handing out blankets, tissues and hot chocolate.

Tufts University in Massachusetts staged arts and crafts sessions for its devastated students and campuses throughout the country cancelled classes because students asked or professors were too distraught to teach.

Apparently schools in Australia, though far from Trump-Land, had similar sessions:

And in Australia, where we are all meant to be tougher, it was primary schoolers rather than adults who were feeling the heat of post-election disappointment.

Children as young as five have been chanting death threats as the backlash of the Trump presidency was felt across Sydney’s inner west.

The After School Klub at Newtown Public School confirmed it held a special art therapy lesson after students chanted “we hate Trump”, the Inner West Courier reported.

The After School Klub supervisor Bek Ames said her students were visibly upset following the election on Thursday.

“When I came in the kids were upset and chanting ‘we hate Trump’ and these are kindergarten kids who are five and six years old,” she said.

“Some of the kids were saying we should kill Trump and Trump should kill himself.

“I have never seen anything like this before — when we had the (Australian) election some of them talked about it but most didn’t know what was going on.”

While Ms Ames responded appropriately to the clearly disturbed children in her after school class, it is fair to ask from where did they get this trauma.

Yep, their parents, who started trumpeting on social media last Wednesday morning the advent of a new world order and wailing when they didn’t get it.

Oy vey! We need to get a grip. Trump is the President-Elect, we’re in for a very tough four years, but can we stop the wailing on Facebook and figure out what we should do next? That, of course, will take a bit of time as Trump lines up his Cabinet and decides which of his campaign promises he’ll continue to discard. When Al Gore lost to George W. Bush in 2000, I don’t recall the dogs, Play-Doh, or cry ins? What has happened to us? (I admit that Trump looks a lot worse than G.W.B.)

barbie-pooping-dog-play-doh-stop-motion-baby-doll-eating-from-toilet-animation-videos-compilation
Dog and Play-Doh

 

Once again: misguided calls for a thorough revamping of evolutionary biology

November 23, 2016 • 12:31 pm

On November 7-9 there was a special meeting of London’s Royal Society on “New Trends in Evolutionary Biology: Biological, Philosophical, and Social Science Perspectives.” I believe it was organized by Denis Noble, a physiologist who believes that modern views about evolution are ripe for a thorough revision.  Many of the speakers at the meeting are part of the “Third Way of Evolution” group, in which various mechanisms, supposedly ignored by the rest of us hidebound neo-Darwinists, are said to play major roles in evolution (the other two “ways” are creationism and Neo-Darwinism).

I’ve criticized Noble and the views of his colleagues before (see here and here, for instance). Here I’ll briefly reprise the themes of this new conference, and why I think that, while the mechanisms discussed are of interest, they pose no danger to the existing evolutionary paradigm; nor is there enough data to show that these mechanisms are common in nature—or even operate at all.

First, though, it’s worth noting that of the 26 presenters at the meeting, 10 were funded by Templeton’s “extended evolutionary synthesis” grant—an 8 million dollar grant over three years. Further, a representative of the Templeton Foundation was present at the meeting, presumably making sure his stable of prized thoroughbreds were running well. The grant and the meeting seem to me to represent one aim of Templeton: to show the weakness of the current evolutionary paradigm. Why they want to do this is beyond me, but it’s clear that the researchers funded by the grant are enthusiasts who have an agenda, one that partly includes self-promotion.

A good summary of the meeting, by the estimable Carl Zimmer, appears in Quanta Magazine as a longish piece, “Scientists seek to update evolution.” I won’t go through the issues raised, except to say they include the following four claims; and the critical take on these is not Zimmer’s but mine:

Epigenetics: This is the new “Lamarckian” view that environmentally-induced changes in the DNA, often affecting the methylation of DNA bases, could be an important contributor to evolution. The problem with this is that these changes are not permanent, and are often effaced after one or two generations. The record, I think, now stands at 31 generations before the environmentally-induced changes are wiped clean. But this provides no permanent basis for permanent adaptive change, which is the huge problem with the epigenetics “paradigm.” Further, when real adaptations can be genetically mapped in organisms, they always reside in the DNA sequence itself and not in the temporary alterations of DNA bases produced by the environment. Further, because environmentally induced epigenetic changes are temporary, they can’t participate in evolution by genetic drift, either.

Now there are adaptive epigenetic changes that are coded in the DNA itself: genes that code for instructions like, “Methylate bases at positions X, Y, and Z.” But those instructions evolved by conventional natural selection, and are not the types of epigenetic changes touted by promoters of the New Paradigm.

Development. Zimmer says some speakers emphaszied that development can constrain evolution: only certain evolutionary changes are possible given the evolved developmental system of organisms. (Haldane once used the example that humans couldn’t evolve into angels because they had neither the limb buds for wings nor the moral precursors!). But this is nothing new, and has been discussed for decades in the Modern Synthesis.

Plasticity.  As is well known, organisms can change their appearance, behavior, and physiology depending on their environment. Some of this is simply a “shock response” with no adaptive value, while other forms of plasticity are evolved adaptations that reside in the DNA (cats grow longer fur when it’s cold, rotifers develop predator-deterring spines when put in water with fish “odor”, etc.). But the New Paradigmists say that nonadaptive plasticity can actually initiate an adaptive evolutionary change. It’s not really clear how this would happen, and in fact we have no good examples of it happening. We have, on the other hand, plenty of examples of adaptive plasticity that evolved by conventional natural selection: organisms regularly exposed to different environments can, over time, evolve switchable genetic programs (as in cat fur length) to respond to a new environment.

Niche construction. This is the argument that an organism, by adapting to its current environment, actually changes the selective pressures that impinge on it, thus opening up further evolutionary pathways. The classic example, as Zimmer notes, is the beaver: by adapting to build a pond by cutting down trees and making dams, the beaver now occupies a new habitat, which also includes its lodge. That could present new ways for the beaver to evolve as it now lives in a pond-ish environment.

But this is not new, either, and fits well within the Modern Synthesis.  As Ernst Mayr once pointed out, many new adaptations evolve not by a change in the external environment itself, but by the organism behaviorally entering a new environment when that environment offers adaptive advantages. By making forays on land, for instance, lobe-finned fish suddenly were able to access a bunch of new food types previously unavailable. And of course once you’re moving about on land, selection will favor all kinds of new adaptations, like shelled eggs and big lungs that handle air. Similarly, warm-blooded animals, by evolving homeothermy, acquire a thin layer of warm air around their bodies, providing a good niche for ectoparasites, to which the animal must now adapt. I am in fact surprised that niche construction is seen as something radically new, since it follows ineluctably from adaptation itself.

While most of the participants in the Royal Society meeting espoused these kinds of revisions, you can see that they’re neither new nor nor have much EVIDENCE supporting them as strong challenges to the existing evolutionary paradigm.

After Carl Zimmer summarizes some of these matters, he mentions the pushback that people had against the idea that evolution is in trouble. I’ll just give one excerpt from his piece, involving a claim by Dennis Noble that organisms have an ability to detect stress and then rapidly rearrange their genomes to respond adaptively to that stress:

To illustrate this new view, Noble discussed an assortment of recent experiments. One of them was published last year by a team at the University of Reading. They did an experiment on bacteria that swim by spinning their long tails.

First, the scientists cut a gene out of the bacteria’s DNA that’s essential for building tails. The researchers then dropped these tailless bacteria into a petri dish with a meager supply of food. Before long, the bacteria ate all the food in their immediate surroundings. If they couldn’t move, they died. In less than four days in these dire conditions, the bacteria were swimming again. On close inspection, the team found they were growing new tails.

That didn’t sound right to Shuker [David Shuker of the University of St Andrews], and he was determined to challenge Noble after the applause died down.

“Could you comment at all on the mechanism underlying that discovery?” Shuker asked.

Noble stammered in reply. “The mechanism in general terms, I can, yes…” he said, and then started talking about networks and regulation and a desperate search for a solution to a crisis. “You’d have to go back to the original paper,” he then said.

While Noble was struggling to respond, Shuker went back to the paper on an iPad. And now he read the abstract in a booming voice.

“‘Our results demonstrate that natural selection can rapidly rewire regulatory networks,’” Shuker said. He put down the iPad. “So it’s a perfect, beautiful example of rapid neo-Darwinian evolution,” he declared.

This exemplifies the problem:  enthusiasts for the Third Way blather on about new mechanisms, and write dataless paper after dataless paper about them, but when the mechanisms are examined closely they’re found to be not so revolutionary after all.

Why, then, are people suddenly touting a revision of evolutionary theory? (This isn’t all new; Steve Gould tried it with punctuated equilibrium, proposing a mechanism for episodic evolutionary change that has now been discarded.)  One reason is, of course, that Templeton is funding this project big time. Where the money goes, so goes the research. The other was suggested at the meeting by my friend Doug Futuyma, not only an evolutionist but someone with  a deep knowledge of the history of evolutionary thought. As Zimmer reports:

“We must recognize that the core principles of the Modern Synthesis are strong and well-supported,” Futuyma declared. Not only that, he added, but the kinds of biology being discussed at the Royal Society weren’t actually all that new. The architects of the Modern Synthesis were already talking about them over 50 years ago. And there’s been a lot of research guided by the Modern Synthesis to make sense of them.

Take plasticity. The genetic variations in an animal or a plant govern the range of forms into which organism can develop. Mutations can alter that range. And mathematical models of natural selection show how it can favor some kinds of plasticity over others.

If the Extended Evolutionary Synthesis was so superfluous, then why was it gaining enough attention to warrant a meeting at the Royal Society? Futuyma suggested that its appeal was emotional rather than scientific. It made life an active force rather than the passive vehicle of mutations.

“I think what we find emotionally or aesthetically more appealing is not the basis for science,” Futuyma said.

Still, he went out of his way to say that the kind of research described at the meeting could lead to some interesting insights about evolution. But those insights would only arise with some hard work that leads to hard data. “There have been enough essays and position papers,” he said.

Doug is right–new insights could be in the offing. But, like him, I’d say, “Where’s the beef?” (The “beef” constitutes data and evidence.)

Doug has written a paper that summarizes and rebuts many of the supposedly serious challenges to modern evolutionary biology, and you can get it free by going to this link. The screen provides three items that can be read on SpringerLink for free; the second is Doug’s chapter.  Just go to “Download Sample Pages 2 PDF” at the bottom of the page, and you’ll get Doug’s whole paper for free. If you’re an evolutionist, this is a must-read paper, but I’d suggest that evolution-friendly readers have a look as well. The whole paper is worth reading, but if you want to just get Doug’s take on challenges to modern evolutionary theory, read section 4, from pages 53-70.

Finally, Suzan Mazur, a journalist who has long touted a total scrapping of modern evolutionary theory, wrote a piece about the conference at PuffHo (wouldn’t you know?) called “Pterosaurs hijack Royal Society Evo meeting.” It’s a bizarre piece, all over the map, but Mazur seems to have given up her crusade against modern evolutionary biology, now appearing to be on another (and better) crusade against Templeton’s funding of this kind of nonsense.

Bottom line: Modern evolutionary theory is not in trouble–far from it. Maybe sometime a New Paradigm will come around, but this isn’t it. The noise we heard from London, outside of a few papers by people like Futuyma, is the noise of Templeton’s prize horses jockeying for money and fame.