Jonathan Wells’s new book attacking evolution

Sixteen years ago, Jonathan Wells, now a senior fellow at the creationist Discovery Institute, published an intelligent-design creationist book Icons of Evolution: Science or Myth? Of course they were a myth to him, but the book was dreadful and a totally misguided attack on evolution. I reviewed it for Nature (free link here), and said this:

Wells’s book rests entirely on a flawed syllogism: textbooks illustrate evolution with examples; these examples are sometimes presented in incorrect or misleading ways; therefore evolution is a fiction. The second premise is not generally true, and even if it were, the conclusion would not follow. To compound the absurdity, Wells concludes that a cabal of evil scientists, “the Darwinian establishment”, uses fraud and distortion to buttress the crumbling edifice of evolution. Wells’s final chapter urges his readers to lobby the US government to eliminate research funding for evolutionary biology.

Wells also got a Ph.D. in biology from Berkeley, but to judge his objectivity about the evidence for evolution, I also added one of his publicly available statements in my review, and put it right at the beginning:

Opposition to evolution is found in many corners of the American religious landscape, including the Unification Church. Church founder Sun Myung Moon has frequently condemned darwinism for giving God no role in the history of life. In 1976, Jonathan Wells, a student in Moon’s seminary, answered his leader’s call. He writes, “Father’s [Moon’s] words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a PhD program in 1978, I welcomed the opportunity to prepare myself for battle.” The University of California supplied Wells with his weapon, a PhD in biology and, with Icons of Evolution, Wells has fired the latest salvo in the eternal religious assault on Charles Darwin.

Wells has also questioned the connections between HIV and AIDS.

In 2006 Wells, continuing his battle against truth, published his second book. It was no better than the first, and on the same topic: The Politically Incorrect Guide to Darwinism and Intelligent Design, issued, like the first, by conservative outlet Regnery Publishing.

In 2011 came his The Myth of Junk DNA, and by this time Wells had to go to the Discovery Institute Press, the equivalent of a vanity press for creationists. Sadly, the ID argument that nearly all junk DNA really does stuff—thus supporting an Intelligent Designer who put it in the genome for Reasons—has been largely quashed: there really is useless DNA, and its presence, nature, and location attest to evolution.

And now, ten years later, we have a new book, Zombie Science, also issued by the Discovery Institute Press.

The Amazon link (you can find it yourself) says this about it:

In 2000, biologist Jonathan Wells took the science world by storm with Icons of Evolution, a book showing how biology textbooks routinely promote Darwinism using bogus evidence—icons of evolution like Ernst Haeckel’s faked embryo drawings and peppered moths glued to tree trunks. Critics of the book complained that Wells had merely gathered up a handful of innocent textbook errors and blown them out of proportion. Now, in Zombie Science, Wells asks a simple question: If the icons of evolution were just innocent textbook errors, why do so many of them still persist? Science has enriched our lives and led to countless discoveries. But now, Wells argues, it’s being corrupted. Empirical science is devolving into zombie science, shuffling along unfazed by opposing evidence. Discredited icons of evolution rise from the dead while more icons—equally bogus—join their ranks. Like a B horror movie, they just keep coming! Zombies are make believe, but zombie science is real—and it threatens not just science, but our whole culture. Is there a solution? Wells is sure of it, and points the way.

Who writes these blurbs? Does anybody check them for accuracy?

And my point in the Nature review, which was that even if some textbook examples were out of date or incorrect, evolution is still true, remains. After all, ID books are wrong about every claim they make supporting Intelligent Design (ID). Further, the evidence for ID that its advocates promised was “right around the corner”, simply hasn’t emerged over a decade later. Established science has rejected Intelligent Design because there’s simply no evidence supporting it. Period.

I will be accused of having “reviewed” Wells’s book here without having read it, but this isn’t a review: it’s a notice that a scientifically rejected charlatan has published another book, and has even issued a “teaser trailer” for it. Here it is below. There’s no intellectual content there, but of course the buyers of the book aren’t looking for truth and reason; they’re looking to confirm their own religiously-based biases.

Will I read it? I don’t know, but I’m not going to pay for it. ID books are like theology books: if you haven’t read every single one, their proponents will claim that you haven’t addressed their best arguments. But I’ve read a much higher proportion of all ID books than IDers have for evolution books.  I’m sure they’re missing the best arguments! 🙂

It’s kind of pathetic that these people, whose efforts are motivated solely by religion, waste their brainpower attacking a paradigm that’s so well supported by evidence. I wonder if on some level they’ve realized they’re wasting their lives and will have no effect on science; and that that realization simply makes them redouble their efforts.

h/t: Michael

This is science, Bill Nye?

It’s no secret that I am not a big fan of Bill Nye, regarding him as a buffoon who will engage in any shenanigans that keep him in the public eye and help him retain the fame he desires—fame accrued as “The Science Guy”. I never saw the old show, and realize that many people liked it and it seemed to promote good science to kids; but his activities since I became aware of him have largely caused me embarrassment since he’s supposed to represent and burnish my own profession of science.

Well, Nye has a new show humbly called “Bill Nye Saves the World“, which apparently still has the goal of promoting science.

Here’s a new video from the show. Featuring comedian and actor Rachel Bloom singing “My vagina has its own voice,” it’s an arrant travesty:

Seriously, “butt stuff”? Now this may be social justice stuff, but it ain’t science—not even if you construe it as promoting a “spectrum of sexuality,” which is misleading because most people bunch at either end of the “spectrum.” In fact, I’m not sure what this is doing on a science show. It’s not even funny,

Nye, of course, was one of the honorary chairs of the March for Science, and this shows why I wasn’t keen on that choice. Defend this travesty if you want, but I’ll never admit it promotes anything but ideology. What’s next, Bill?:

“Do it before the paparazzi:
for the sake of Science, punch a Nazi!”

Once again, is female genital mutilation connected with Islam?

According to CBS in Detroit, Michelle Hoitenga, a state representative in Michigan, has introduced a bill (see it here) that in effect bans sharia law, although U.S. law already supercedes sharia law and the bill seems completely unnecessary and anti-Muslim.  The bill doesn’t specifically mention sharia law, but that’s clearly its aim:

A bill to limit the application and enforcement by a court, arbitrator, or administrative body of foreign laws that would impair constitutional rights; to provide for modification or voiding of certain contractual provisions or agreements that would result in a violation of constitutional rights; and to require a court, arbitrator, or administrative body to take certain actions to prevent violation of constitutional rights.

As used in this act “foreign law” means any law, legal  code, or system of a jurisdiction outside of any state or territory 5 of the United States, including, but not limited to, international  organizations and tribunals, and applied by that jurisdiction’s courts, administrative bodies, or other formal or informal tribunals. A court, arbitrator, administrative agency, or other  adjudicative, mediation, or enforcement authority shall not enforce  a foreign law if doing so would violate a right guaranteed by the 6 constitution of this state or of the United States.

A court, arbitrator, administrative agency, or other adjudicative, mediation, or enforcement authority shall not enforce a foreign law if doing so would violate a right guaranteed by the constitution of this state or of the United States.

According to Hoitenga, the bill was motivated by the recent case of female genital mutilation (FGM) practiced on several girls aged 6 to ) by a Muslim doctor in Detroit. The doctor, Jumana Nagarwala, has been duly charged with a criminal offense:

The sponsor, Republican Rep. Michele Hoitenga of Manton, said in an email to House members this week that a Detroit-area doctor recently charged with performing genital mutilation on two young girls was “essentially practicing a fundamentalist version of Sharia law,” according to MLive.com.

Again, you can argue about whether sharia law promotes FGM, or even whether sharia law is oppressive, but there’s little doubt that many branches of Islam do promote FGM or even make it mandatory, and that sharia law is oppressive where applied though it is superseded by US law in our country.

The Huffington Post, however, argues that FGM is not an Islamic practice, and also that sharia law has been grossly misunderstood; this is part of PuffHo’s Regressive Leftist campaign to glorify Islam by hiding some of its shady practices. As always, this is because Muslims are considered People of Color and therefore oppressed.

HuffPo is right on one count: the bill is superfluous, prohibiting what is already prohibited. But it errs, deliberately, in saying that sharia law is innocuous and misunderstood:

Sharia law, a favorite bogeyman of anti-Muslim extremists, is the deeply misunderstood legal or philosophical code of Islam. It’s interpreted differently by Muslims across the world using an assortment of texts, including the Quran, the Sunnah and Hadiths.

Yes, sharia law is interpreted differently in different places, but in no place is it superior to the laws of Western democracies, and in many places sharia (which in most Muslim-majority countries has become part of state law) is oppressive, unfair, and ludicrously regressive. For instance, in many places sharia makes apostasy a capital crime, prohibits drinking, makes the testimony of a woman in court worth only half of a man’s (!), considers in judicial sentencing that a woman’s life is worth half of a man’s, and allows or even requires barbaric practices like beheading or the mutilation of hands or limbs. Yet, according to the 2013 Pew Survey of beliefs in Muslim-majority lands, support for sharia is widespread (note: countries like Saudi Arabia, Yemen, and Iran weren’t surveyed), with many suggesting that it be applied to non-Muslims. Here are some data I’ve shown before from that survey:

So yes, Michigan’s anti-sharia bill is superfluous, but support for sharia among Muslims is widespread. Even in Britain, Muslim support for sharia is strong: the National Secular Society reports a Policy Exchange Survey of British Muslims that showed this:

“There are relatively large levels of support among British Muslims for the implementation of elements of Sharia law,” Policy Exchange said.

43% said they supported “the introduction of Sharia Law” and just 22% were opposed. 16% of British Muslims “strongly support” the “introduction of aspects of Sharia law into Britain”.

35% of 18-24 year olds expressed support for “aspects” of sharia and nearly half of the over-55s supported some “provisions” of sharia.

Okay, but putting that aside, is FGM an Islamic practice, or does it have something to do with the faith? The accused doctor certainly thought so! As the Detroit News reported:

A Detroit emergency room physician charged with mutilating the genitalia of two 7-year-olds from Minnesota denied cutting the girls, saying she merely performed a religious procedure that involved removing and then burying skin in the ground.

Dr. Jumana Nagarwala’s lawyer offered the explanation Monday during a dramatic 90-minute court hearing in front of a standing-room-only crowd. The hearing ended with a federal magistrate judge ordering the Northville doctor jailed without bond while awaiting trial, the first of its kind in federal courts nationwide.

Dr. Nagarwala is clearly a Muslim:

Dr. Jumana Nagarwala (Photo: Henry Ford Health System)

We all know that Reza Aslan, another apologist for Islam, has also denied that FGM has anything to do with the religion, and PuffHo echoes his sentiments:

The practice [FGM] “has not been confined to a particular culture or religion,” according to the Female Genital Mutilation National Clinical Group, a United Kingdom-based charity working with women who have suffered FGM. “FGM has neither been mentioned in the Quran nor Sunnah.”

FGM existed long before Islam and it sadly persists today as a cultural tradition that traverses religious lines. Qasim Rashid, visiting fellow at Harvard University’s Prince Alwaleed bin Talal School of Islamic Studies

FGM is practiced in many Muslim-majority countries as well as in some Christian-majority countries, according to Politifact, citing a UNICEF report. And some Muslim-majority countries, such as Yemen and Iraq, have low rates of FGM.

Qasim Rashid, visiting fellow at Harvard University’s Prince Alwaleed bin Talal School of Islamic Studies, wrote in a HuffPost blog post in 2014 that FGM predates Islam, Christianity and Judaism.

“FGM existed long before Islam and it sadly persists today as a cultural tradition that traverses religious lines,” Rashid wrote. “For example, in Ethiopia, Muslims, Christians, and Jews have all practiced FGM — though no faith endorses the act.”

And because there is no solid theological basis for FGM in Islam, Rashid said, the only people today who believe FGM is a part of Islam are “Islamophobes and extremists [who ascribe to Islam].”

Well, I can think of no better refutation of this nonsense than Heather Hastie’s post from 2014, “Reza Aslan: Lying for Islam on FGM.” Read it if you encounter people who disavow a connection between Islam and FGM, for Heather simply demolishes that claim with data. Here’s a small excerpt:

In Sunni Islam, there are four schools of jurisprudence that express an opinion on the matter. Two of them, the Hanbali and Shafi’i schools, consider FGM obligatory, while the other two, the Hanafi and Maliki schools, recommend it. In addition, there have been several fatwas issued regarding FGM over the years, the majority of which favour it. (Fatwas are not compulsory, but devout Muslims consider them morally imperative.) For example, Fatwa 60314 includes statements that express the importance of FGM within Islam and dismiss the opinions of doctors.

The belief that FGM is an expression of faith if you are a good Muslim is widespread, insidious and promoted by religious leaders. Even in those Muslim countries where it has been banned, there is push-back by religious leaders. In Egypt for example, FGM was finally banned after several failed attempts in 2008. However, it is still being carried out outside hospitals and the Muslim Brotherhood has a campaign to get the law overturned. Mariz Tadros reported in May last year that “the Muslim Brotherhood have offered to circumcise women for a nominal fee as part of their community services”.

FGM apologists like Aslan and PuffHo could find out about this stuff if they wanted, but it goes against their pro-Muslim narrative. Talk about “alternative truths”!  These are not a monopoly of the Right.

A successful cat experiment—and a failure

Last Caturday, I put up an item about some cats having a propensity to enter and sit in squares of tape on the floor. I also urged readers to try it. What do you have to lose besides a bit of tape? Anyway, three readers tried it: one failed utterly, one succeeded, but only when the cat was enticed into the tape-square with a treat (this doesn’t count!) and then one success, from reader Rhonda. Her notes and photo:

The square experiment was successful in my household with really only one of our three cats. One stood in it for just a second, and the third was much too suspicious to get inside. This is Happy, our tiny and very trusting almost 15-year-old girl.

And we have a failure from Peter N., who also sent a photo and an account:

A few years ago a friend sent me an article that said cats would gravitate toward any defined small space, just like you said in your post of April 22. I set up a loop of digital audio cable on our bed, where Gus (1999-2017) always slept during the day. The result: it’s hard to generalize about cats!

The verdict so far: the behavior certainly isn’t ubiquitous Try this at home!

Readers’ wildlife photos

Reader Tony Eales sent some lovely spider photos from Queensland, in a country where everything is poisonous! His notes are indented:

A few of my favourite spider shots. The first is a cute little orb-weaving spider Araneus rotundulus. Only a few millimetres across, it can roll up into an almost perfect ball.

JAC: Here it is in a ball; photo from Brisbane Insects: (link above):

The next, Argiope ocyaloides, is another orb weaver. These specialise in weaving webs in the deep furrows in the bark of eucalyptus trees like the Ironbark.

Next are a couple of the bizarre Argyrodes species with their weird humped and reflective-skinned abdomens.

Russian Tent Spiders, Crytophora hirta, in the morning dew. These small orb-weavers can fill parts of coastal scrub and in the morning light it just looks magical.

One of the classic Huntsmans. The ones that come inside are well known for freaking out tourists and some squeamish locals. They are a large and extremely fast spider prone to sitting stock still them taking off at half an eye-blink speed. I’ve never heard of one biting. They’re very peaceful but terrifying. This large species, Holconia immanis, is only ever found under peeling bark of large Eucalyptus trees, not indoors. When you’re peeling back a piece of bark to see what’s worth photographing and something impossibly fast but about the size of a mouse shoots up your sleeve…it’ll be this guy:

This cute little jumping spider, Omoedus orbiculatus, lives on tree trunks eating ants.

A muppet headed Variable Lynx SpiderOxyopes variabilis. As the name suggests, they come in all shapes and patterns, but I’ve never seen one with such a comically swollen head before.

Last, a member of a really interesting family: the Thomisids (Crab and Flower Spiders). There are species from a few genera which are social to semi-social forming collective snare webs. This is the first and only social spider I’ve seen in the wild but I’ll be keeping my eye out for more. Xysticus bimaculatus, the Sub-social Crab Spider:

Monday: Hili dialogue

I am late this morning because–mirabile dictu–I have overslept! Till 6:15! Oy! Anyway, I’m told that it’s Monday, April 24, 2017, and it’s National Pigs-in-a-Blanket Day. Do other lands like Britain have these things? If not, here are les porcs dans des couvertures:

I haven’t had one of these dough-encased hot dogs in decades. It’s also World Day for Laboratory Animals, and I’m glad that all my lab animals were fruit flies, which I always killed humanely, etherizing them to death–instant unconsciousness.

On this day in 1800, the U.S. Library of Congress was established by President John Adams,  and 16 years later the Easter Rising began in Dublin. On this day in 1953, Winston Churchill was knighted by Queen Elizabeth II (do read Winnie’s biography by William Manchester), and in 1990 the Hubble Space was launched from the space shuttle Discovery.  It’s still working, and could work for 20 more years! What a piece of work is Homo sapiens!

Notables born on this day include Anthony Trollope (1815), Shirley MacLaine (1934; she and her brother Warren Beatty attended my high school in Arlington, Virginia), and Barbra Streisand (1942; she’s 75 today). Those who died on this day include Willa Cather (1947), Bud Abbott (1974), and Estée Lauder (2004). Meanwhile in Dobrzyn, Hili is strutting her stuff, not at all humble, but it is a lovely photo:

Hili: Sometimes it amazes me.
A: What amazes you?
Hili: How perfect I am.
In Polish:
Hili: Czasem mnie zdumiewa.
Ja: Co cię zdumiewa?
Hili: Jaka jestem doskonała.
Lagniappe: Look at this caracal kitten (courtesy of Grania):

 

 

A great last-second goal by Messi

Barcelona vs. Real Madrid—Ronaldo vs Messi—fighting for the La Liga title. It looked like a tie (which would give Madrid the title) until the last ten seconds of injury time. Then Messi, battered in the game and possibly having lost teeth to an elbow, came through, scoring a seemingly effortless left-footed goal to give Barca a 3-2 victory and keeping his team in the running.

The commentary from the Independent:

Barring a complete collapse Real Madrid had won La Liga. Only a miracle could stop them.

That miracle was Lionel Messi, surviving 95 minutes’ worth of battering and beasting to curl home a left-footed strike in the dying seconds. It was a goal to settle any title race, but whether it proves to be such a strike will only become clear down the line – right after those bruises heal and the teeth are replaced.

And a video link (I’ve found a better one) and commentary from reader Michael:

Here is a video of Messi’s vital [literally] 2nd goal.  Messi is left unmarked & has lots of space to strike with his left.
 
I watched this game down the pub – the place went mental when Messi scored his 2nd goal with 10 SECONDS LEFT of injury time to keep Barca in the title. Messi is one tough hombre – I think some of his teeth were loosened [or lost] at one point, but he isn’t slowed.
The video may not show on this post, but will on YouTube here. (These videos tend to be taken down because capitalism.) Note that despite what the announcer says, this does NOT “defy the laws of physics.” And I wish they’d stop calling Messi a “little man”!

As soccer commentator Seamus Malone told me, Messi appears to be the greatest soccer player of all time. This was also Messi’s 500th goal for Barca.

What a world!: UN elects Saudi Arabia to its Commission on the Status of Women

Here’s a case where the fox has been chosen to guard the henhouse. The website for the UN’s Commission on the Status of Women outlines its mission:

The Commission on the Status of Women (CSW) is the principal global intergovernmental body exclusively dedicated to the promotion of gender equality and the empowerment of women. A functional commission of the Economic and Social Council (ECOSOC), it was established by Council resolution 11(II) of 21 June 1946.

The CSW is instrumental in promoting women’s rights, documenting the reality of women’s lives throughout the world, and shaping global standards on gender equality and the empowerment of women.

One would think, then, that the member states of this organization would be those with a track record of promoting gender equality.

Wrong. According to several sources, including UN Watch (the link keeps disappearing!), the UN has just elected (wait for it) Saudi Arabia as a member of that commission. In fact, the vote, made by the UN’s Economic and Social Council was by secret ballot (why?), and 15 EU countries voted for the Saudi membership (see below):

Saudi Arabia is a country where women can’t drive, must appear fully covered in public, cannot go out unless accompanied by a male guardian, need permission from a guardian to travel, marry, or do business, and weren’t allowed to either vote or run for election until just two years ago. It’s a horrible place to be a woman if you have any aspirations toward equality.

Further, according to the World Economic Forum’s Gender Gap Rating, Saudi Arabia ranks 134 out of 145 countries assessed—right at the bottom. Here are the top nations:

. . . and the bottom (note the predominance of Muslim-majority countries):

Iceland, showing the indices used:

 

Saudi Arabia, whose low score is due largely to reduced “economic empowerment and opportunity” and “political empowerment”:

We don’t know who voted for Saudi, but, according to this tweet from a UN Watch official, lots of EU countries gave an “aye”:

And a response from a Saudi woman (clearly living elsewhere!):

Others have said this, and I agree: the United Nations has become a joke.

h/t: Lesley

Why do cave fish evolve to become blind?

As you almost certainly know, animals from many groups have colonized caves, and more often than not they evolve to lose or reduce their eyes in the Stygian environment. But why? It’s hard to tell, for losing eyes takes thousands of generations, and we’re not around long enough to do experiments. I seem to recall an experiment in which Drosophila workers kept flies in the dark for years and observed no reduction of eye size, but they didn’t test their vision (this can now be done). At any rate, that experiment wasn’t long enough.

A new paper in The American Biology Teacher by Mike U. Smith, a Professor of Medical Education at Mercer University School of Medicine (Macon, Georgia), goes over the various theories for eye loss, with the piece aimed at biology teachers, suggesting how this subject should be taught and how to avoid misconceptions. (Reference below; access is free.) Smith gives three theories, but I think he gets it a bit wrong, and I wanted to give my take. I’ll ignore the stuff about teaching, as I want to concentrate on the biology.

First,  an example: Smith’s is the classic case of Astyanax mexicanusthe Mexican tetra or “blind cave fish” found in caves in the southwest U.S. and northern Mexico.  It is in fact considered the same species as its surface-dwelling form. Here are photos of each form and the range of the blind fish (from the paper). There are 26 known populations of the blind variant, representing at least five independent cases of evolutionary eye loss. Breeding experiments show that the cave and surface forms are interfertile, and that the loss of eyes in the cave form involves several genes, not just one:

 

The cave form eats mostly the bacteria film on the water that results from the breakdown of bat and cricket feces. The eyes are still there as vestigial remnants below the surface of the skin, but begin development as normal eyes and then regress as the fish grows up. (That itself is evidence for evolution.) Fish from at least one cave have an ability to detect light, but others have no such ability; this probably reflects different evolutionary stages of eye loss (or perhaps differential light levels in the caves). The fish find their way around via vibrations detected in their lateral lines. As Smith notes, “In fact, scientists capture these fish simply by putting a net in the water and vibrating it.”

Here are Smith’s three ideas for the evolution of eye loss. His words are indented (my emphasis). I maintain that two of the hypotheses are conflated, one is largely incorrect, and he’s neglecting another hypothesis.

According to the first hypothesis, eye loss is indeed caused by direct natural selection because there is an advantage to being eyeless in the dark. Studies have shown that maintaining eye tissue, especially the retina, and the related neural tissue comes at a high metabolic cost (Moran et al., 2015; Protas et al., 2007). Therefore, cavefish without eyes are at an advantage in this environment where energy sources (food) are scarce, because blind fish do not waste energy on these useless structures.

This is a reasonable hypothesis, and one my students used to always think of first when I asked them. It applies to the disappearance of any non-used structure, like the tiny nubbins that are the vestigial “wings” of the kiwi. The “not wasting energy”, of course, implies that that energy be directed towards other structures or functions that enhance reproduction, for that’s implicit in saying that reduces eyes give cave fish an advantage via natural selection.

A second hypothesis employs the phenomenon of pleiotropy, that is, cases in which multiple phenotypic effects are caused by the same mutation in a single gene. There is, for example, evidence that one of the genes responsible for eye loss in cavefish also increases the number of taste buds on the ventral surface of the head, which helps cavefish find food more effectively (Gross, 2012). Natural selection for this increase in taste buds would, therefore, also promote blindness.

I would argue that this second hypothesis isn’t substantively different from the first. After all, if resources are redirected from inactivated eye genes to other structures or functions that enhance reproduction, those other features would reflect pleiotropic effects of the mutations that reduced the eyes. I don’t see a material difference between a). An eye-reducing gene increasing the number of taste buds (the “pleiotropic” theory) or b). An eye-reducing mutation making more nourishment available for other structures by reducing the energy requirement for building an eye. In both cases, the mutation reducing eye formation has beneficial effects on other aspects of development. Those are both instances of “pleiotropy”.

The third hypothesis is based on neutral mutation and genetic drift. All too often textbooks use the terms “evolution” and “natural selection” interchangeably, ignoring the importance of genetic drift. Genetic drift is “the process of change in the genetic composition of a population due to chance or random events rather than to natural selection, resulting in changes in allele frequencies over time” (Biology Online, 2008). Genetic drift differs from natural selection because observed changes in allele frequency are completely at random, not the result of natural selection for a trait. Genetic drift can have a relatively larger impact on smaller populations such as a typical population of cavefish. According to the neutral mutation and genetic drift hypothesis, therefore, normal mutation processes in a small population of cavefish sometimes produce neutral mutations (mutations that lead to phenotypic changes that natural selection does not act on), and in the absence of natural selection, totally random events can sometimes result in the increased frequency of such mutations over time. Such changes could include eye degeneration.

This discussion is confusing. Even if the eye-reducing genes were neutral, and didn’t give eyeless fish a reproductive advantage, genetic drift (the random fluctuation of eyeless and eyed forms couldn’t by itself contribute to pervasive eye loss in caves, for the caves contain only fish without eyes. Drift would produce a “random” effect: varying mixtures of eyed and eyeless fishes in different caves. We don’t see that.

Now drift may play a slight role in eye loss (slightly deleterious mutations are more likely to persist in small populations), but I think what Smith is neglecting here is a non-random phenomenon: directional mutation. By that I don’t mean that somehow there is an increased frequency in the caves of mutations that inactivate eyes compared to the surface populations—that would be a Lamarckian or teleological process—but that random mutation applies to both cave and surface populations.  In surface populations those mutations that reduce or inactivate the eyes are weeded out by selection, and these mutations are more numerous than those creating better eyes. Remember that in the genes for eye formation, as in all genes, a random hit in a complex and evolved DNA sequence is more likely to damage the gene than improve its effect on reproduction.

Therefore, with a rain of mutations affecting eyes in both populations, and in general degenerating the eyes, the more numerous “bad” mutations will be selected out of the surface populations, but, with no selection against them in the cave populations, will tend to accumulate—perhaps aided by natural selection (hypotheses 1 and 2 above). Look at it this way: if you have a fleet of cars that are never driven, and people randomly adjust the engines of those cars without knowing anything about them, all the non-used cars will eventually lose their ability to run. That’s because a random adjustment of an engine is more likely to hurt it than to improve its function.  The engines are the eyes of cave fish, and the adjustments are mutations. The adjustments accumulate because the cars don’t need to run. I think this is a more plausible explanation than simple genetic drift, which seems implausible anyway because eye-reducing mutations aren’t likely to be “neutral”, for reasons given above but also because of what I say just in my fourth hypothesis below.

Smith says this:

. . . studies of the sequences of other genes related to the cavefish eye show high frequencies of substitutions in both coding and noncoding regions, which would support the genetic drift hypothesis (Retaux & Casane, 2013).

But that seems to be wrong for several reasons.  First a high frequency of substitutions in coding regions can be due to any of the forms of natural selection discussed above. Second, non-coding regions (parts of the DNA that do not code for proteins) can sometimes affect gene expression and regulation. More important, I couldn’t find any data in the Retaux and Casane paper suggesting an increased frequency of truly neutral non-coding mutations in these cavefish. (I may have missed it, but it doesn’t seem to be there.) What I see is this paragraph (note: this is for evolutionary geneticists)

The reports cited above only concern the evolution of the coding sequences. However, phenotypic evolution (including the loss of structures) can also occur through changes in non-coding, cis-regulatory sequences. Famous examples include the loss of the pelvic spine in freshwater sticklebacks through deletion of a Pitx1 enhancer [98, 99], or gain or loss of pigmentation patterns in Drosophilae through co-option or mutation of regulatory elements in the pigmentation gene yellow [100]. Although the exact mechanism is unknown, this happened for crystallin αA in cave Astyanax [55, 101]. This chaperone and anti-apoptotic crystallin whose coding sequence is almost identical in surface fish and cavefish (one amino-acid difference only) is strongly downregulated in the cavefish lens during development and was suggested as a potential major player in the onset of cavefish lens apoptosis. In the naked mole rat Heterocephalus glaber, gamma-crystallins are turned off after birth [46]. In the mole rat Spalax ehrenbergi, the αB-crystallin promoter and intergenic regions have selectively lost lens activity after 13.5 days of embryogenesis [102, 103]. These examples show that changes in regulatory sequences also occurred in cave and other underground animals.

Note that there are no data here on “high frequencies of substitutions in noncoding regions” of cavefish eyes. We see a change in gene regulation without accompanying changes in the sequence of the regulated genes, but that’s probably due to “coding” changes in other regulatory genes or substitutions in regulatory regions that are not “neutral” because they affect eye formation. (Note that Smith emphasizes “neutral” mutations in his third hypothesis.) These regulatory regions are thus subject to natural selection, and are not “neutral” changes acted on solely by genetic drift, even if they’re noncoding. We would in fact expect that selection would produce that observation: more substitutions accumulating in regulatory regions in cave fish than in surface fish! No need for drift here.

Coyne’s fourth hypothesis (not really mine but neglected by Smith). Eyes are delicate organs, easily damaged and prone to infection. If you reduce the eyes when you don’t need them, you’re less prone to this kind of environmental damage, and so the genes reducing the eyes make their bearers more likely to live and reproduce. Yes, this is a form of eye loss promoted by selection, but is conceptually different from hypotheses 1 and 2 above. I wish Smith had mentioned this idea as well.

At the end, Smith says that all his suggested processes might act together:

So, what’s the right answer? What genetic evidence is there to support each of these hypotheses? As with so much in science, the answer is probably that these explanations are not mutually exclusive; it is likely that all three partially explain cavefish blindness. To understand that statement, we must have some further background on A. mexicanus genetics.

Well, the explanations may not be mutually exclusive, but to say that it’s “likely” that all three explain cavefish blindness is unwarranted. One or two of the hypotheses may explain most of the eye loss. Just because there are several possibilities doesn’t mean they’ve all acted in concert.

While I’m trying to correct or put my own gloss on Smith’s paper, I’m not trying to say it’s a bad paper. It isn’t: it brings up a useful topic to discuss in evolution classes, and suggests a wealth of hypotheses and experiments. It also has very useful suggestions on what misconceptions students might have about this issue, and how to correct them. I just think the ideas could have been formulated and expressed more carefully. While we don’t know the precise evolutionary reason for eye loss in tetras, the fact that it has occurred several times independently, as well as in other species inhabiting caves, suggests that selection rather than drift has played the major role.

___________

Smith, M. U. 2017. How does evolution explain blindness in cavefish? 

Readers’ wildlife photos and video, and more on New Zealand

Several days before I left New Zealand, Gayle Ferguson was kind enough to drive me to the Muriwai Gannet Colony near Auckland. I’d never seen a gannet before, and didn’t know what to expect, but it turned out to be a fantastic experience. Here’s where it is–near Auckland (colony is starred):

We brought Bob the Kitten with us, as he required feeding every few hours. He stayed in his carrier in the car while we were at the Colony (a little over an hour), as it was cool and there was no danger. His carrier was also covered with a blanket to prevent kitten-napping by jealous people.  But while we were driving, Bob was in my lap the whole time:

We stopped at a seaside cafe for lunch, and I couldn’t resist ordering my Last Pie in New Zealand: a steak-and-Guinness pie (one of my favorites), served with a salad. On the side I had a banana milkshake:

First things first—Gayle fed Bob at the cafe before having her cake:

Of course, feeding a tiny and very cute kitten in public attracts attention, especially from kids. Here two young girls got the privilege of stroking and holding Bob. Children are nearly always very gentle with kittens.

To see the colony, one climbs to the top of a cliff overlooking the sea. On the way up we saw this bird. Anyone know what it is? (I don’t.)

A bit about the colony from its site:

Muriwai’s gannet colony is a one hour drive from the centre of Auckland. Next to the car park, a short walking track leads to a viewing platform right above the main colony area. Out to sea, the colony continues on two vertical-sided islands. About 1,200 pairs of gannets nest here from August to March each year.

The nests are just centimetres apart. It’s an air traffic controller’s nightmare, but somehow the birds have it under control. Those coming in to land must glide over the squawking raised beaks of their neighbours – so getting it wrong can be painful. These two-and-a-half kilogram birds have a wingspan of two metres, and their mastery of the onshore updrafts is impressive to say the least.

Each pair lays one egg [breeding occurs in September through November, with one egg laid] and the parents take turns on the nest. The chicks hatch naked, but within a week they’re covered with fluffy down. As they mature, they grow juvenile feathers and begin to exercise their wings in preparation for the one-shot jump off the cliff.

Once airborne, the young gannets leave the colony and cross the Tasman Sea to Australia. A few years later, surviving birds return to secure a nest site at the colony.

The views from the colony are very impressive. Muriwai Beach extends 60 kilometres to the north – a line of black sand between the thundering surf and the sand hills. Far below, enthusiastic surfers look like seals on the large ocean swells.

The colony occupies three sites: two cliffside sites on bare ground, and the top of a rocky peak just offshore. It is a raucous site. The chicks had mostly grown up and left (see below), but hundreds of adults remained in situ:

A precarious place to nest!

The species at hand: the Australasian gannet (“tākapu”), Morus serrator. It’s a large bird, and can weigh up to 2.3 kg. There are about 46,000 of these birds in New Zealand.

The species breeds on islands and the coast of New Zealand, Victoria and Tasmania; around 90% of the adult population lives in New Zealand. Normally they nest on islands off the coast, where fish are plentiful, but increasing populations have led to their colonizing coastal areas of the mainland.

I’m told that they prefer nesting areas like this because the coastal winds helps them take off and helps them land safely and on point.

Gannets are socially monogamous (who knows if they engage in “sneaking fucking”?), and remain as pairs for several seasons—or a lifetime. I have no idea how a male and female find each other year after year, but I suspect it has to do with recognizing each other’s calls.

What a handsome bird!

There were a few teenage chicks at the site. They fledge in March and April, so these may have been slow developers. As New Zealand Birds Online notes:

Fledglings from New Zealand fly directly to Australia, and typically do not return to their home colonies until their third year. Some New Zealand breeders migrate to Australian and Tasmanian waters to winter between breeding seasons. Australasian gannets often breed with the same partner over consecutive seasons. Some birds retain the same mate for the rest of their lives, but divorces do occur. [Anthropomorphism!]

Here’s an Attenborough video of gannets diving; these are probably not Australasian gannets, but that species also fishes this way:

The birds have adaptations for surviving these high-speed dives. Oceana notes this:

Gannets are champions among the “plunge-divers.” The largest species, the Northern gannet (Morus bassanus), can plummet into the ocean from as high as 130 feet (40 meters) in the air, hitting the water at around 55 miles (88 kilometers) per hour. This species uses a combination of speed and wing-beats to dive as deep as 115 feet (35 meters).

Unlike the sudden (and painful) deceleration of a human belly-flopper, the diving posture of a Cape gannet (Morus capensis) is so streamlined that the bird only slows down a little — or not at all — when it plunges into the sea.

For humans and birds alike, hitting the ocean at high speed can mean two nostrils uncomfortably stuffed with saltwater. To get around this issue, gannets breathe through thin slits located where the upper jaw meets the head. These slits are covered by a flap of hard tissue that closes when the bird dives.

A high-diving lifestyle also comes with the additional risks of sore muscles or even a broken neck. So gannets come equipped with “airbags,” extensions of their respiratory system that cushion their bodies when they hit the water.

Here’s an even better video from Smithsonian:

Notice the even spacing of the birds; this becomes rigorously enforced during the breeding season when they fiercely defend their nest mounds, and those mounds are spaced just beyond the reach of a sitting gannet. The spacing, I was also told, is about “the diameter of a large pizza.”

Their blue eye rings are distinctive:

Some crazy fishermen were braving the dangerous swells to tend their lines. One misstep would lead to their death, as there’s really nowhere to climb out, and the waves are fierce:

Here’s a small video I took of the colony; you can hear their diverse calls here (on the right at the link):