Greta Christina goes after Andrew Brown’s snivelling defense of the Catholic Church.

Russell Blackford continues the Guardian’s series on evolution and morality.

Fess Parker, my boyhood hero, dies at 85.

Fig. 1.  “Be sure you’re right first, then go ahead.”

One of the letters in today’s Durango Herald (Colorado)

Christian texts right to dump Darwin

by Paul Bynum

It is amazing how the evolutionists react when their messiah, Charles Darwin, is ignored or otherwise abused. The very fact that he is not given top billing in Christian-based biology textbooks for the home-schooling market sends them in an absolute thither [sic]. In an Associated Press story (“Top home-school texts dismiss Darwin,” Herald, March 7), Jerry Coyne, an evolutionary professor at the University of Chicago, went so far as to say, “I feel strongly about this. These books are promulgating lies to kids.”

Lies? I believe that opinion may depend on which side of the creation coin you come down on.

On the humanistic, God-denying, evolutionary side, you can tell children they are nothing more than animals that appeared by mere chance through a prolonged process that began in a great big explosion that over millions and millions of years now allows them to wonder and care how they got here and what it might matter in the eons to come. If they are just animals, why not act the part? Why not blow away the other animal that stole your peanut butter sandwich at lunch?

On the creation side of the coin, children are told they are created in the image of a loving God that cares for each and every one of them. Their Christian home-schooling parents do, indeed, want to give their children religious and moral instruction that teaches them they are more than just another animal in the evolutionary food chain. In order to give this type of education to their children, textbooks are needed that are from a godly, biblical-based point of view. Not a Charles Darwin, God-denying view point.

So why should the evolutionists blow a gasket when textbooks are released giving a different point of view? They want God totally out of any educational process and bring Christian home schooling under the state-controlled school system, thereby eliminating free choice of your child’s future.

Paul Bynum, Durango

This letter encapsulates one of the faithful’s commonest objections to evolution: it does away with God-given morality, thereby giving us license to act like beasts.  Accommodationists would have us believe that if Mr. Bynum and his ilk were politely informed that many religious people have no problem accepting evolution, they’d suddenly abjure their views and embrace Darwinism.  The morality argument would vanish!

And if you believe that, then I have a a Ray Comfort edition of The Origin to sell you.

(Bynum and his Durago buddy Gary Anderson were involved in a bit of P. Z. Myers-bashing four years ago.)

Imagine being forced to go to work every day and, as part of the job, profess something that you absolutely don’t believe.  More than that: at least once a week you have to publicly profess it, and also counsel other people on the explicit premise that you share the beliefs you reject.  In other words, you’re forced to live a lie.

Such is the position of clergy who don’t believe in God.  Yes, there are some of them, and they’re the subject of a new study by Daniel Dennett and Linda LaScola from Tufts University, “Preachers who are not believers.” You can find that 28-page study at the Washingon Post‘s “On Faith” section (click the link on that page to download the pdf).  I recommend reading it if you have time.

Dennett and LaScola managed to find and interview five Protestant “nonbelievers.” Given the liberality of today’s clergy, and the resistance of many nonbelieving preachers to participate in the study, this may be only the tip of the iceberg.  Although some interviewees accept a numinous notion that might be termed “God,” none of them believe in the theistic God limned by the faith they profess.  Here’s the testimony of “Jack,” a Southern Baptist preacher:

“OK, this God created me. It’s a perfect God that knows everything; can do anything. And somehow it got messed up, and it’s my fault. So he had to send his son to die for me to fix it. And he does. And now I’m supposed to beat myself to death the rest of my life over it. It makes no sense to me. Don’t you think a God could come up with a better plan than that?”

“What kind of personality; what kind of being is this that had to create these other beings to worship and tell him how wonderful he is? That makes no sense, if this God is all-knowing and all-wise and all-wonderful. I can’t comprehend that that’s what kind of person God is.”

“Every church I’ve been in preached that the Jonah in the Whale story is literally true. And I’ve never believed that. You mean to tell me a human was in the belly of that whale? For three days? And then the whale spit him out on the shoreline? And, of course, their convenient logic is, ‘Well, God can do anything.’”

“Well, I think most Christians have to be in a state of denial to read the Bible and believe it. Because there are so many contradicting stories. You’re encouraged to be violent on one page, and you’re encouraged to give sacrificial love on another page. You’re encouraged to bash a baby’s head on one page, and there’s other pages that say, you know, give your brother your fair share of everything you have if they ask for it.”

“But if God was going to reveal himself to us, don’t you think it would be in a way that we wouldn’t question? …I mean, if I was wanting to have…people teach about the Bible…I would probably make sure they knew I existed. …I mean, I wouldn’t send them mysterious notes, encrypted in a way that it took a linguist to figure out.”

I can’t help but note that “Jack” was influenced by an classic argument for atheism:  if God wants us to know his presence, why is He always hidden?  Isn’t it more parsimonious to posit the absence of God rather than a God who, for reasons that elude us, is always just around the corner? Theologians, of course, have lots of arguments why the absence of God is precisely the evidence that God exists.

Surprisingly, two of the clergy lost their faith, in part, by reading new atheist books by Sam Harris and Christopher Hitchens.  Even Bill Maher’s movie, Religulous, influenced one of them. So much for the notion that new atheism makes no converts.  “Adam” speaks:

“I tell you, the book that just grabbed my mind and just twisted it around, was Christopher Hitchens’ God is Not Great. It was shocking, some of that stuff – the throws and jabs against faith and stuff. I would think, ‘He’s crazy.’ But then I’d say, ‘No. Step back and read it for what it is.’

The preachers’ testimony makes a sad but enlightening read.  The road to eroded faith is tortuous, but often involved exposure to Biblical scholarship at the seminary or graduate school.  Faced with the notion that the Bible is a human construct, and not the inerrant word of God, several of these preachers began to question everything.

Why do these preachers stay in the faith and on the job? Three reasons, mostly.  One is financial: what else could they do with their training if they left the ministry? Often they have neither equity (living in church-owned houses) nor pensions.  Another, and perhaps more important, reason is that an admission of unbelief  would shock and disappoint their friends and family.  This is a very powerful motive, for facing the truth would rip asunder your network of social and family support.  We’ve encountered this before in the admission of Karl Giberson,  still a professed believer, head of BioLogos, and someone who may be teetering on the edge of apostasy:

As a purely practical matter, I have compelling reasons to believe in God. My parents are deeply committed Christians and would be devastated, were I to reject my faith. My wife and children believe in God, and we attend church together regularly. Most of my friends are believers. I have a job I love at a Christian college that would be forced to dismiss me if I were to reject the faith that underpins the mission of the college. Abandoning belief in God would be disruptive, sending my life completely off the rails.

Finally, many of these preachers like their work, especially the part of the job that involves helping troubled people. Jack again:

“And that’s what people told me my best skills were – dealing with people. …I can be with somebody and genuinely have empathy with them, and concern and love and help them get through a difficult situation. And every time that I did it, those people thought that I was wonderful. And they would just bend over backwards to tell me ‘Thank you.’ That was one of my strengths. …Being with somebody when their husband died. And just holding their hand, or putting my arm around them. But I never said ‘Now, he’s in heaven. Aren’t you glad for him?’”

There’s absolutely no doubt that faith, and religious institutions, have provided important help for those in need or in trouble.  Some religions do this more than others.  Sikhs, for example, seem to have a well-developed system of intra-faith welfare.  Such help doesn’t, of course, prove the existence of God or support any of the fact claims of faith, nor does it offset all the harms that faith has wrought on humanity.  But isn’t it a shame that there aren’t secular communities where those with altruistic instincts can “minister” without hypocrisy or fear?

_________________________________________

The On Faith page features commentary on the Dennett and LaScola article by seventeen other people, including ex-Bishop John Shelby Spong, writer Rebecca Goldstein, theologian Martin Marty, and—God help us—Deepak Chopra. I haven’t yet read these.  There are also (surprisingly few) comments by readers.

The Huffington Post’s new “Religion” section is a mixed bag.  It is full of their usual woo, but also has a fair dollop of articles on atheism.  Tuesday’s column by Eric Michael Johnson, a journalist and graduate student in history, asserts in its title that “The Unseen and Unknowable Has No Place in Science.”

Johnson was raised as a Lutheran, but jettisoned his faith when he realized that, unlike science, it was fully prepared to accept things for which there was no evidence.  A snippet:

Faith, as Gary Whittenberger wrote in Skeptic magazine, has multiple common uses.

“Faith” may refer to a religion or worldview, as in “My faith is Islam.” It may refer to an attitude of trust or confidence, as in “I have faith in my physician.” Or it may refer to believing propositions without evidence or out of proportion to the available evidence.

It is this latter use of faith that is incompatible with science. His Divine Grace A.C. Bhaktivedanta Swami Prabhupada, founder of the International Society for Krishna Consciousness (which has 170 Hare Krishna centers in Europe and North America alone), was up front that he denied the evidence for evolution. Why? He didn’t argue that the methods employed may have biased the results and that he would reserve judgment until the studies were replicated. He didn’t dispute the sample size in a given study or suggest a separate interpretation of the observable facts. He completely disregarded the entire pursuit of such knowledge because it contradicted his faith in a prime mover. His faith told him that he was correct, regardless of what the facts might be. There is a word for that, when you prefer your own private fantasy to the real world. I think Richard Dawkins used it as part of the title to one of his more popular books.

Yes, religion is incompatible with science. This doesn’t mean, of course, that religious people are incapable of doing science. Far from it. There are certain questions that don’t probe too deeply into the foundations of a person’s faith and they have no problem employing their reason to its fullest in those cases. But when reason starts to get uncomfortably close (as it has for Francis Collins, Deepak Chopra and Michael Behe) well, that’s when the desperate appeal to fuzzy thinking becomes apparent. Because the assumption of God is so obvious to them (and I’m sure they feel it powerfully) the evidence suggesting that evolution follows natural mechanisms and has no need of a supernatural intelligence must therefore be wrong. They’ll bend over backwards trying to rationalize irrationality.

In this week’s Nature, philosopher/biologist Massimo Pigliucci reviews What Darwin Got Wrong, the book-length attack on natural selection penned by Jerry Fodor and (the unrelated) Massimo Piattelli-Palmarini:

By misusing philosophical distinctions and misinterpreting the literature on natural selection, Fodor and Piattelli-Palmarini make a mess of what could have been an important contribution. The authors are correct in two of their assessments. Namely that: mainstream evolutionary biology has become complacent with the nearly 70-year-old Modern Synthesis, which reconciled the original theory of natural selection with Mendelian and population genetics; and that the field needs to extend the conceptual arsenal of evolutionary theory. But in claiming that there are fundamental flaws in an edifice that has withstood a century and a half of critical examination, Fodor and Piattelli-Palmarini err horribly. . .

. . . Fodor and Piattelli-Palmarini offer only sterile and wrongheaded criticism. Fortunately, other philosophers of science and theoretical biologists are coming together to clarify and build on the conceptual foundations of science and explore issues of its practice; this is a better way to bridge the two cultures.

The “important contribution” that F&P-P fail to make, apparently, is the contribution that Pigliucci himself is bent on making, for that “extension” of neo-Darwinism is laid out in a soon-to-appear book, Evolution: The Extended Synthesis, edited by Pigliucci and Gerd Müller.

And Fodor and Piattelli-Palmarini?  Well, they’ll claim that Pigliucci is just another philosopher who has failed to grasp their point.

My own review of What Darwin Got Wrong will appear in four weeks.

Since 1996 it’s been known that, according to mitochondrial-DNA-based phylogenies, polar bears (Ursus maritimus) are actually nested within brown bears (Ursus arctos) rather than being a separate lineage.  In other words, the mtDNA of some populations of brown bears—in particular, those from the Admiralty, Baranof, and Chichagof (ABC) islands of southwest Alaska—is more closely related to the mtDNA of polar bears than to the mtDNA of other brown bears.

This makes brown bears “paraphyletic” with respect to polar bears.  That is, the brown bear species U. arctos does not include all of the descendants of its most recent common ancestor, since some of these descendants are placed within polar bears.

This conclusion was just confirmed by complete mtDNA sequencing of the bears. A new study in PNAS by Lindqvist et al. used “fossil DNA” from a subfossil polar bear jaw to look at the evolution of polar bears vis-à-vis their relatives.  The jaw, from Norway, was estimated at about 130,000-110,000 years old, and was sufficiently well preserved that a complete polar bear mtDNA genome could be extracted and sequenced.

This sequence was compared to mtDNA sequences from two living individual polar bears and four living brown bears.  The phylogeny based on this sequence is given below.  The main result is that this jawbone came from a polar bear living about the time (estimated at 152,000 years ago) when the ancestors of modern polar bears diverged from those of brown bears.  The authors also did stable carbon-isotope analysis of a tooth from the subfossil’s jaw, and found that the isotope values for carbon-13 were close to that of modern polar bears, suggesting to the authors that the individual engaged in “marine feeding,” i.e., ate seals.

The figure below also confirms the results of earlier phylogenies, using smaller segments of mtDNA, showing that brown bears—at least these three brown bears—from the ABC islands are more closely related to polar bears than to brown bears from other places.  Again, brown bears seem to be paraphyletic.

Fig. 1 (Fig. 3 of Lindqvist et al.)  A. Maximum clade probability tree of bear mtDNA using BEAST anaysis. B.  Phylogenetic network of complete mtDNA genomes. Note that brown bears from the “Adm” (Admiralty) and “Baranof” populations are more closely related to polar bears (including the subfossil specimen shown in red) than to other brown bears.

The authors conclude:

The stable isotope data, phylogenetic analysis, and the geological and molecular age estimates of the Poolepynten specimen indicate that ancient polar bears adapted extremely rapidly both morphologically and physiologically to their current and unique ecology within only 10–30 ky following their split from a brown bear precursor and, subsequently, within the course of ~100 ky, spread to the full perimeter of the polar basin. As such, the polar bear is an excellent example of evolutionary opportunism within a widespread mammalian lineage (33). Moreover, the extreme proximity of the Poolepynten specimen to the polar bear ancestor provides a unique case of a morphologically and molecularly validated fossil link between living mammal species.

Now this is pretty interesting, but I don’t find it terribly exciting.  I think its acceptance in PNAS is based more on the novelty of using subfossil DNA than on any new and pentrating insight into bear evolution.  But I want to discuss the “paraphyly” of brown bears highlighted here and in previous work.

If this DNA-based tree really reflected the species tree, then the ancestry of the groups shows true “species paraphyly“: that is, some living populations of brown bears are more closely related to living polar bears than to other living populations of brown bears.  And if that were the case, then hardcore cladists, who employ a species concept based only on “monophyly,” would not recognize the two species “brown bears” and “polar bears.”  They would have to lump them together into a single species of bear.  We would no longer have polar bears.

Of course, cladists aren’t rushing to do this, even though the paraphyly has been known for 14 years.  Why not? Well, a lot of cladists aren’t interested in “alpha taxonomy,” the practice of naming species. But anyone who’d lump polar with brown bears would also be derided.  That’s because, regardless of the genetic ancestry of these groups, the two species now seem to be independent evolutionary units, presumably isolated from each other by reproductive isolating barriers such as habitat and mate preference.

But if this is true “species paraphyly,” how could it have come about?  How could one or a few populations of species X be more genetically related to members of species Y than to members of its own named species? Well, it’s possible that the ancestor of all polar bears came from only one geographic population of brown bears (that population represented by the ABC  localities), and so the ancestry of polar bears reflects this origin.  If gene flow were sufficiently restricted among all populations of brown bears, then the species phylogeny (which, after all, is only a formalization of evolutionary history) could reflect this localized origin.

This probably happens quite commonly, as it cannot be all that rare for a widespread species to bud off a new descendant from only one or a few of its populations. (Migration of a few individuals to an island or a distant new habitat, for example, must involve such a process.) Usually, however, gene flow among members of that big, interbreeding species would soon efface this history.

But all this presupposes that the mtDNA phyogeny gives us the true species phylogeny—the evolutionary history of the populations themselves rather than just that of  mtDNA segments.  Does the “gene tree” of mtDNA—which, since all the DNA in a mitochondrion is physically linked, behaves as if it were a single gene—reflect the “species tree” of bears?

It may not.  We’ve known for a while that hybridization between species can occasionally move DNA between them, even after they’re formed, if reproductive barriers aren’t complete. And, for reasons we don’t understand, mitochondrial DNA (or chloroplast DNA) seems to move between species more easily than does nuclear DNA. If the ABC populations of brown bears exchanged, some time in the past, mitochondria with polar bears, though rare hybridization (and this is known to occur between the species), then sequencing mtDNA might tell us, erroneously, that for all genes, ABC populations are more closely related to polar bears than to other brown bears. And, importantly, such hybridization, which might have occurred after the polar and brown bear lineages diverged, would give us an erroneous idea of when the lineages diverged.

Such hybridization isn’t rare. There are lots of cases—Allen Orr and I list many of them in the appendix of our book Speciation (Sinauer, 2004)—in which mitochondrial-DNA based trees give a false diagnosis of paraphyly, while nuclear DNA, consisting of lots of independent genes and not just one, shows a nonparaphyletic tree.  This is true for oak trees, birds, fruit flies, and many other species. Sometimes, as in the Drosophila species I work on, movement of mtDNA between different species makes them seem genetically identical, while independent nuclear genes show well-demarcated species. Hybridization between species can make it very risky to use just one gene to reconstruct their history.

Yet somehow people continue to accept mtDNA trees as equivalent to species trees.  To be sure, Lindqvist et al. formally recognize that hybridization between polar and brown bears could produce an illusory species paraphyly, although they, like earlier authors, don’t give the possibility much weight (the PNAS paper gives the caveat,”Although mtDNA capture cannot be excluded to have happened between ABC bears and polar bears, these estimates nevertheless affirm with strong support a very recent divergence of polar bears from brown bears.”)  But it’s time for biologists to stop calling species paraphyletic when what they mean is that genes (e.g., mtDNA) are paraphyletic.

To determine if brown bears are really paraphyletic with respect to polar bears, and thus whether cladists would designate (brown + polar) bears as a single (very variable!) species, we’d have to look at a lot more genes—and genes from the nucleus.  If the consensus phylogeny from all these genes still shows the paraphyly, then systematists can worry about nomenclature. (But even if there were true species paraphyly, I’d still vote on retaining the two named species of bears, since I adhere to the “biological species concept” that is based not on phylogenies but the presence of reproductive barriers.)

For now, brown and polar bears are phylogenetically safe. But I wish that systematists would worry more about the problem of equating gene trees with species trees, and would stop relying solely on mitochondrial DNA when they can also use nuclear DNA. The more genes the better!

_____________

Lindqvist, C. et al. 2010.  Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc. Nat. Acad. Sci. USA 107:5053-5057,

Shields, G. F., D. Adams, G. Garner, M. Labelle, J. Pietsch, M. Ramsay, C. Schwartz, K. Titus, and S. Williamson. 2000. Phylogeography of mitochondrial DNA variation in brown bears and polar bears. Molecular Phylogenetics and Evolution 15:319-326.

Talbot, S. L., and G. F. Shields. 1996. Phylogeography of brown bears (Ursus arctos) of Alaska and paraphyly within the Ursidae. Molecular Phylogenetics and Evolution 5:477-494.

I haven’t been able to find the archived recording of my own short appearance on yesterday’s Thom Hartmann show, but if you go here, and click on the clip labeled “100316 home school disadvantage”  (currently on top of the list), you’ll be able to listen to Michael McHugh. (The clip is about nine minutes long and you can read the listeners’ comments here.) McHugh heads a young-earth creationist organization, CLASS, that sells home-school materials on biology to parents.

Note that while desperately trying to defend his (and his company’s) notion that the earth is 6,000 years old, McHugh makes a couple of wonky arguments.  The first is that there are “no neutral facts.”  That is, every fact militates either for or against a certain worldview.  McHugh’s suggestion for how to educate your kids involves choosing which worldview suits them best, and then selecting the “facts” that fit this worldview.  I am not making this up: he says it explicitly.

Finally, forced into a corner by Hartmann, who basically takes him apart, McHugh resorts to the old defense that religious views of science must be correct because scientists as eminent as Newton were religious.

If you listen to McHugh, you’ll see what kind of “biology” hundreds of thousands of American kids learn at home.  It’s beyond belief that, in the name of “education,” McHugh and other Christian home-school outfits profit from peddling lies to children.

I was just on the Thom Hartmann show (briefly), appearing after Michael McHugh, head of a Christian (and creationist) homeschooling outfit.  Thom was on the side of truth, and evolution, but he also took calls on the topic, and you know what that means.  McHugh had pushed a young-earth view, insisting that the earth is 6,000 years old, and Hartmann said that didn’t compute—that the earth was billions of years old.  So one gentleman called in offering the following:

I have a solution to your time theory: what if the earth is billions of years old but God didn’t create time until 6,000 years ago?

There should be audio/video links, which I’ll post when I get them.