One of the barn cats at the ranch where I board my horse was particularly friendly today, and climbed all over my car (iPhone photos attached), talking to me the whole time.  I think she might have been chastising me for failing to bring her any cat noms, when she’s seen me bring horse noms and treats for the ranch d*gs every week.

Anyway, it got me thinking that barn cats frequently aren’t given the respect they deserve.  Horse barns are always plagued by rats and mice, and here in South Texas, where there are rats and mice, there are also rattlesnakes.  No one wants to deal with rattlesnakes in and around the barns, so cats that keep the rodents in check are worth their weight in gold (and then some … I hate dealing with rattlesnakes, and sometimes they’re very aggressive).

Next time I go out to the ranch, I’ll definitely bring some special noms for the barn cats.

I am sorry to say that I don’t know the lovely cat’s name (we have not been properly introduced, despite having boarded my horse at this ranch for 4 months now).  There wasn’t anyone around to ask today either, since it wasn’t feeding time for the horses (and all the caretakers were indoors, since 42F and windy is freakin’ cold for most South Texans).

The feed store where I buy horse noms also has a wide selection of cat treats, so I’ll buy some special ones for my ranch visit on Wednesday!

Then, on March 4, Barn Cat got a name:

A drizzly, warm, and oppressive day here, with a cold front on the way, and every mammal at the ranch is crabby, except for the barn cat.  I still don’t know her name, but I call her “La Reina” for now (not very creative, I know).  She was very appreciative of the treats (Blue Buffalo Kitty Yums, Savory Seafood flavor), and in fact climbed into my car several times and tried to come home with me.  She is unusually friendly for a barn cat, and apparently loves to be petted and held, judging from the purring.

I gave her the noms on top of my car at first (and you can see what 14 years of Texas sun does to the paint job on a Honda Accord, even when it’s parked in the shade or a garage as much as possible).  Then, seeing that the ranch d*gs were otherwise occupied pestering the farrier, I put some noms on the wooden tie rail under the tack barn overhang, which is a more rustic Texan setting for photos.

I included the out-of-focus photo because it’s just funny.

The one was titled “Moar noms plz”:

Saturday, March 7:

The barn cat now follows me out to the paddock/barn where my horse lives (there are several such barns and paddocks at the boarding ranch, plus a number of pastures).  She sits and watches while I clean out my horse’s run, or while I groom my horse.  At one end of the run there’s a feeding barn (shared by 4 other runs/horses), so the horses that share a paddock can be separated for feeding, and so that they have some shelter from inclement weather.  I’ve attached a photo of the cat in the paddock, and another inside the feeding barn, eating crunchy chicken-flavoured noms.  Horses and cats generally get along quite well.

There’s at least one other cat living in the tack barn, but I’ve just heard it, and not yet seen it.  “La Reina” is still climbing into my car and trying to come home with me.  Two of my dogs would love for this to happen – they had feline friends while they were fostered as puppies.

And, because I am a bad person, and because La Reina kept climbing into Barn Owl’s car to go home with him/her, I suggested that he ask for or try to buy the cat. The response:

It’s definitely tempting to leave La Reina in my car and drive home with her.  However, the horse caretakers and their families live in houses at the ranch, and it’s very possible that one of them considers the barn cat to be a pet, or a valued co-worker.  Her friendliness is consistent with that.

A friend of mine once tried to take home a barn cat from the busy polo barn where I kept my first Thoroughbred.  She named the cat Chicken Bones, because that’s what the horse caretakers were feeding it (!)  Anyway, the caretakers were angry with her for even suggesting such a thing, and she had to settle for sneaking food and treats to the cat, playing with it and petting it whenever possible, and giving it some basic preventative meds.  The politics of barn cats is tricky, and people can get very possessive of them.

Anyway, it’s nice to have La Reina’s company while I’m doing horse chores, as long as the weather is decent and we don’t both get soaked or buffeted by the north wind.

Yes, I suppose that’s sensible, though I still think a barn cat would be better off in a loving home, especially if the cat keeps climbing into the car to go home with a prospective owner! I would find it hard to resist.

The philosopher Peter Singer is a thoughtful man, and isn’t given to shooting from the hip. So when he criticizes the U.S. government for failing to call Islamic extremism something that’s truly based on religion, we’d best listen up. In a piece at Project Syndicate called “Countering Islamic extremism,” Singer argues that, for several reasons, we can’t deal effectively with the problem of Islamic militancy unless we recognize its religious roots. (His quotes are indented below.)

1. It makes politicians look dumb.

The first problem is political. The conservative US Senator Ted Cruz, who may be about to announce his candidacy for the Republican presidential nomination, has said, “You cannot defeat an enemy if you refuse to acknowledge what it is.” That line could win votes. Indeed, it is never a good idea for a politician to appear to be denying what we can all see before our eyes.

2. It won’t make Muslims less extreme or less ostracized to use euphemisms like “violent extemism.”

Moreover, because it is obvious to everyone that most violent extremism is being carried out in the name of Islam, avoiding the word is unlikely to prevent attacks on Muslims in response to this violence.

3. It puts the onus on those knowledgable about Islam to convince the more radical ones that there’s a more benign form of the faith. 

At the Washington summit, Obama said that “all of us have a responsibility to refute the notion that groups like ISIL somehow represent Islam, because that is a falsehood that embraces the terrorist narrative.” At least this statement, unlike the White House Fact Sheet, acknowledges that groups like the Islamic state claim to be Islamic. Otherwise, what would be the relevance of this statement to “countering violent extremism”?

Nonetheless, Obama’s assertion that “all of us” have this responsibility needs to be more narrowly directed. If I tried to get into a debate with any moderately well-educated Islamic State supporter about whether that organization is true to the teachings of Islam, I would lose the argument. I am not sufficiently expert in the Islamic tradition to be confident that extremists are misinterpreting it, and few of us are. The responsibility to which Obama was referring rests with those who are much more learned in Islam than “all of us.”

So here’s Singer’s main reason to call a spade a spade:

By now, the problem with trying to counter those who seek new recruits for “violent extremism” without focusing on this extremism’s Islamic basis should be clear. Those considering joining an extremist Islamic group should be told: You believe every other religion to be false, but adherents of many other religions believe just as firmly that your faith is false. You cannot really know who is right, and you could all be wrong. Either way, you do not have a sufficiently well-grounded justification for killing people, or for sacrificing your own life.

Granted, some people are not open to reasoning of any kind, and so will not be swayed by such an argument. But others may be. Why rule it out in advance by denying that much extremist violence is religiously motivated?

In other words, Singer’s suggesting that extremist Muslims should be subjected to John Loftus’s “Outsider Test for Faith” procedure, which basically argues what Singer said above:  people get their faith from their upbringing and geographic surroundings, not through a reasoned examination of all faiths from which they pick their own. And since every believer is dubious of all other faiths except his or her own, thje most rational approach is to subject your own faith to the same scrutiny you apply to others. That, of course, ultimately leads to atheism—or, in Singer’s view, perhaps to a more moderate form of Islam.

I’m a bit dubious about Singer’s claim, as how many jihadists are really going to be persuaded by moderate Muslims who tell them that there are perfectly grounded but less extremist forms of Islam? And of course virtually none will be persuaded to abandon their faith completely, which is the logical outcome of concluding that “your faith is false”? As we know from Graeme Wood’s analysis of ISIS, its adherents are absolutely, positively convinced that not only are they following the precise dictates of the Qur’an, but that other Muslims are simply wrong. The end result of Singer’s argument would seem to be a claim that all of Islam is false. And, as we know, that’s simply apostasy, seen by many “moderate” Muslims as a capital crime.

h/t: rodney

A new paper in The American Naturalist by Carl Rothfels and his colleagues (reference and free download below) shows that fern species that diverged in the very distant past can still form hybrids. That’s an interesting result, but I’m not sure about the authors’ conclusion that this revises our notion about how fast species can form in some groups, and I’m absolutely sure that the way creationists have distorted the paper’s findings is bogus. But let’s look first at the science.

The authors found a single fern in the French Pyrenees that looked as if it were intermediate in appearance between two distantly related genera of ferns, Cystopteris and Gymnocarpium. These genera were so diverged that they had been placed in different families. Suspecting that this individual (which was sterile) was indeed a hybrid between species in those long-diverged genera, they subjected it to DNA and chromosome analysis. (The hybrid individual was give the name “xCystocarpium roskanianum,” with the “x” denoting the likelihood that it resulted from a cross.)

Sequencing a single nuclear gene (gapCp “short”) in the parents, the hybrid, and many species in both putative hybrid genera, the authors wanted to see whether the hybrid had a mixture of genes from these putative parents, as we’d expect if the hybrid were indeed a hybrid. They also dated the branches of the tree using five genes that had been sequenced previously. The gene sequences were further used to construct a phylogeny, or evolutionary tree, of the two groups, so they could determine how long ago they diverged.

Finally, Rothfels et al. made meiotic chromosome squashes of the putative hybrid and of species in the parental genera, which showed how the chromosomes of the hybrid paired up during meiosis (the process of gamete formation). That could also show if the chromosomes of the putative hybrid appeared to be a mixture of chromosomes from the two parental groups, and if anything went wrong in the hybrids to make them sterile.

The results:

• The hybrid did indeed appear to have a mixture of alleles (gene forms) from the parental genera: it had four versions of the gapCp gene, two closely related to Cystopteris and the other two to Gymnocarpium. This verifies the putative hybrid as a genuine hybrid between genera. (The two Gymnocarpium alleles were themselves long diverged, indicating that one parental species was itself an “allotetraploid” produced by an ancient hybridization between two species within Gymnocarpium.) The similarity of these two gene sequences to that in a living species suggested that one parent was the cosmopolitan species G. dryopteris, which has 160 chromosomes. (Ferns have huge chromosome numbers!) The other parent was tentatively identified as a member of the European C. fragilis complex, which is a mixture of polyploids with chromosome numbers ranging from 168 to about 336 (it’s hard to count a lot of tiny chromosomes in a squashed three-dimensional cell).

• The chromosome analysis showed about 160 chromosomes in the hybrid, which is close to what one expects in a hybrid between these species (½ x 160 + ½ x 168 = 164). The exact number of chromosomes is hard to determine because of course chromosomes pair during meiosis (remember freshman biology?). Here’s a picture of prophase in the hybrid, when the chromosomes begin to pair up and are already themselves duplicated. Some of the chromosomes are paired, but others are not, which is expected if some pairing occurs between “homologous” chromosomes within one parental species’ genome but not between chromosomes from different genera.

Below you can see another picture of meiosis during metaphase, when the chromosomes move to the “metaphase plate” to divide into the daughter cells. You can see that some chromosomes are properly aligned here, but others are floating around in the cytoplasm. That means that there will be a willy-nilly division of chromosomes to each daughter cell that forms the haploid spore (fern reproduction is complicated; see here for more details).  And the spore, which forms the ‘gametophyte’—the haploid plantlet that, producing sperm and eggs, produces a diploid plant—will not contain a full complement of genetic material. It’s as if a human male or female produced a sperm or egg that lacked several chromosomes: that individual would be sterile because any “zygote” that formed via fertilization would be inviable in the early stages. No fetus would be formed.

So although the hybrid fern was indeed a hybrid, and it was “viable,” because it grew into an adult plant, that plant was nevertheless sterile, and therefore a one-off anomaly that was not in itself a member of a new species. Further, because the two parental species were reproductively isolated, producing a viable but completely sterile hybrid, they are clearly members of different biological species and cannot exchange genes. .

• The calibrated molecular data show that two parental genera diverged roughly 58 million years ago (confidence interval between 40-76 million years). That is the oldest known divergence between any pair of species that can form hybrids. To show how long that is, whales and hippos diverged only 54 million years ago, and humans and lemurs about 74 million years ago. This observation is the equivalent, then, of getting a viable hybrid between hippos and whales, or between humans and lemurs! But there are a few cases of animals that are almost as long diverged producing hybrids. In our book Speciation, Allen Orr and I give the record for animals: a viable hybrid between the domestic chicken and the African helmeted guinea fowl, species that diverged abut 54 million years ago (the hybrid was anomalous, and there’s no record of its fertility).  So it is possible for anciently diverged groups to form viable hybrids in animals, and possibly in flowering plants.

• Finally, by looking at the genetic divergence between forms of the gapCp gene in parental species and hybrids, we can judge how long ago the hybridization even took place. The genetic differences are very small, so the hybrid must have formed fairly recently. Even though it’s a single plant, it can propagate clonally through the growth of rhizomes, so it’s at least possible that the hybrid could have been around for a very long time. It wasn’t, though.

The authors hypothesize that ferns may be uniquely able to form viable hybrids in nature between long diverged species because of a feature of their reproductive system: sperm and eggs join simply through meeting in a film of water on the gametophyte, so there’s no need for the complicated forms of sexual behavior in animals, or the use of pollinators in many flowering plants. Those forms of fertilization raise the possibility of other forms of reproductive isolation that couldn’t evolve in ferns—for example, a difference in mating pheromones in animals or of pollinators in plants. This, say the authors, may slow down the rate of species formation in ferns because “genetic incompatibilities may form more slowly.” In other words, if some of the features that cause reproductive isolation in other species can’t evolve in ferns, then ferns may speciate more slowly.

The problem is that while the hybrid fern is viable, it’s also completely sterile, so there are at least enough incompatibilities (perhaps in chromosome number) to make the parents full biological species. Thus, we don’t yet have enough evidence to show that the process of species formation is slower in ferns than in other species. Perhaps the evolution of “prezygotic isolation” (reproductive barriers arising before fertilization, like ecological or sexual isolation) is slower in ferns than in other species, but we don’t yet know how much of a contributor such isolation is to speciation, and we certainly don’t have enough data to draw general conclusions about the rate of species formation from a single hybrid.

Nevertheless, the paper is a good one, documenting with high confidence the formation of a viable hybrid between anciently diverged species, and producing a Guinness-style record for ability to form viable hybrids. (It’s a pity that Guinness doesn’t confer records like this!)

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Over at the Baptist Press (the news site of the creationist Southern Baptist Convention), Discovery Institute hack Casey Luskin used this paper to argue that the ferns violate the theory of evolution. The article is called “New fern discovery a ‘problem’ for evolutionists,”  Needless to say, there’s not a problem. The entire paper of Rothfels et al. fails to mention any problem with evolutionary theory. What they found, after all, was simply a surprising ability to form viable hybrids between long diverged species. But that doesn’t at all “fail to affirm the evolutionary paradigm,” as Luskin claims, for evolutionary theory says nothing about how long species can be separated and still form viable hybrids. And remember, these are still distinct parental species—the hybrids are viable but (to use a phrase from drosophilist Duane Jeffrey) are “as sterile as crowbars.”

Here’s another criticism by Luskin:

The researchers concluded the fern’s discovery implies the diversity of species that exists today may not be wholly accounted for by adaptation, but may also be the product of varied rates of the speciation clock, the rate at which a type of organism develops reproductive incompatibility with other related species.

This is completely false. The authors simply suggest that the “speciation” clock may run more slowly in ferns than in other species, though I suggest we need more data before concluding that. But even if it did, that wouldn’t constitute a violation of the “evolutionary paradigm”, since we expect some groups to speciate at different rates. Orr and I talk about this in our book. If speciation is, by and large, a byproduct of adaptation, and different groups adapt at different rates (again, completely expected), then of course different groups will form species at different rates. In the last chapter of Speciation, we deal with this exact issue, analyzing what selective forces may lead to different rates of speciation.

Nowhere do Rothfels et al. suggest that speciation may not be accounted for by adaptation. What they do suggest is that the adaptations of different groups (i.e., the reproductive system of ferns versus other taxa), may make them speciate at different rates. This may be a form of “species selection,” in which the diversity of groups, a higher-level property, depends on their lower-level properties. Orr and I discuss this issue in our last chapter, but it’s certainly no flaw in Darwinism, for it’s possible for natural selection to operate on different levels of the biological hierarchy.

Finally, Fazale Rana, a “biochemist” at Reasons to Believe (Hugh Ross’s old-earth creationist organization) says that the new paper “attests to creationism in two ways”:

• “First, ‘it represents a problem for evolutionists because it shows there are things being discovered that fail to affirm the evolutionary paradigm,’ Rana said. ‘You wouldn’t expect that hybridization to take place. It’s the work of a creator used to create a novel organism.'”

As I said, there is no a priori expectation on how fast hybridization can disappear over time, so it’s not a problem for evolutionists.

• “Second, a species that can adapt to the environment and give rise to a sister species demonstrates God’s design in giving living things the ability to respond to changes in the environment.”

We already have a way for species to respond to changes in the environment without the need for a god. It’s called “natural selection.” Rana appears mired in the pre-1859 era—the last time that rational people saw design as prima facie evidence for God.

h/t: Bob F.