I came across these paragraphs, excerpted from an essay about possible conflicts between science and a literalistic interpretation of the Bible. Your job is to guess (no Googling!) whether the author was:

a. a sociologist

b. a liberal, non-literalist theologican

c. a creationist

d. an atheist scientist

e. a non-theological religious scholar

f. none of the above

NO GOOGLING!

The Bible seems to teach that there was a global flood in the days of Noah.  This was the universal teaching of the Fathers of the church.  Though not directly linked to the issue of the age of the earth, one’s position on the historical nature of the Flood and its extent are still important.  The response one gives to this question will indicate important core religious ideas.

The sorts of issues that flow from the idea of a global flood are critical to a religious believer.  What will control the biblical exegesis of the Christian? Will they forever be engaged in an exegesis of the moment? Later in this essay we will suggest an answer to these questions.  For now, it is sufficient to make one simple point.  Every Christian from the founding of the church until the advent of modern science believed Noah was a real person.  The Catholic and Orthodox Churches venerate Noah as a saint with the other patriarchs.

Modern naturalistic science has found no room for a flood, global or local.  Many Christians, even those otherwise quite conservative, suggest the Noah story is a myth.  It contains important theological truth, but no history.  The church was wrong. Noah never existed.

This is a serious move for the church to make.  Do the considered opinions of scientists now have the last say in important religious matters that touch on history? To a secular person, Noah’s disappearance looks very convenient. If a Bible story contains details that are contrary to science, then the Bible story is a “myth.” If the Bible story is fortunate enough to be unverifiable, like that of Abraham, it is allowed to function as history.

UPDATE:  Answer goes up at 11 am CST Sunday, Feb. 21

But he couldn’t save the garbage. . .

Another fearless mogge:

And then there’s this. . . .

h/t: Dan!

It’s always a treat to read Jason Rosenhouse, especially when he’s reviewing books or writing about creationism.  His latest post on EvolutionBlog deals with the topic of a recent post:  Kenton Sparks’s contention, on BioLogos, that the Bible isn’t a science textbook but rather a compendium of metaphorical tales that were never intended by God (or whomever wrote the book) to be taken literally.

Rosenhouse notes that of course the Bible wasn’t written to serve as a science textbook, but that, nevertheless, its stories were meant not as metaphors, but as genuine accounts of the origin and structure of the world:

Let us get one thing out of the way right up front. Creationists do not believe the Bible is a science book. They believe, along with most Christians, that the purpose of the Bible is to instruct us about our need for, and the availability of, salvation. When the 66 books of the Bible are published in one volume, the result is a long, dense book almost none of which deals with anything relevant to science. The creationists are perfectly aware of these facts.

Nor do they believe that the early chapters of Genesis were intended primarily to teach us science. In their view the function of these chapters, as with the rest of the Bible, was to give us information relevant to understanding our predicament as sinful human beings.

However, they do believe the Bible is inerrant on any subject it addresses, and if that means accepting what it says during its very rare excursions into science then so be it. Thus, the point of Chapter One of Genesis is to establish that God produced a very good creation, one that was later sullied by human sin. It was also intended to rebut both polytheism and pantheism by establishing that one God was directly responsible for creating everything in nature. That creation took place in six days, followed by a day of rest, was meant to establish a pattern for us to emulate in keeping the Sabbath. Note that none of these purposes relate to science.

But in presenting these basic truths of the human condition, the Bible expresses itself in ways that have scientific consequences. We might even find it interesting and suggestive that the Bible, which mostly avoids scientific questions, begins with so much material relevant to science. Perhaps the conclusion is that God considered these particular scientific truths to be so important that they could not be omitted without compromising the story. At any rate, it makes little sense to say we will accept the spiritual truths of the Bible as a direct revelation from God, but will simply discard the parts that conflict with modern science.

And his zinger:

When you explain something to a small child you routinely simplify the situation. You omit details and context, and express yourself in language the child will understand. It is rare, and almost never appropriate, to lie outright to the child about what is going on. Surely God could have presented the essential spiritual truths without embedding them within a fictitious story. Accommodating His presentation to the level of His audience calls for simplification, not fabrication.

Jason’s peroration:

The simple fact is that the Creationists would have felt right at home in nearly every portion of the Christian world right up until the nineteenth century. That the Bible was as reliable on scientific questions as it is on everything else was Christian conventional wisdom until relatively recently. The Catholic Church that tormented Galileo certainly thought the Bible was reliable on those scientific questions it addressed, for example. The common view, certainly supported by Augustine and Calvin, was that science was the servant of religion, and needed to be kept in its place. I find it unlikely that they would have appreciated the complete role reversal typical of modernity.

What Darwin Got Wrong, the new book by Jerry Fodor and Massimo Piattelli-Palmarini (not to be confused with Massimo Pigliucci), came out two days ago.   Its thesis is that while evolution may be true, natural selection plays at best a minor role in evolutionary transformation.  Selection, say F&P-P, can be rejected on two grounds:  it is empirically untenable and philosophically unsupportable.  Both of its authors are respected academics (Fodor is a philosopher, Piattelli-Palmerini a cognitive scientist) and neither is a creationist—or even religious—so we can expect this misguided critique of evolution to be warmly received and touted by creationists of all stripes. In other words, it will damage evolutionary biology, although I don’t think Fodor is worried about this in the slightest.

Because of this, I’ll be highlighting some of the reviews before my own piece, a long one, comes out in a while.  The first is by the philosopher Michael Ruse in the Feb. 14 Boston Globe. I’ve had, and suspect I’ll continue to have, my differences with Ruse.  We don’t see eye to eye about accommodationism, or about faith, or about anything concerning the intersection of science and religion.  But damn if he didn’t produce a good review of What Darwin Got Wrong.  From the outset it hits the nail on the head:

“What Darwin Got Wrong’’ is an intensely irritating book. Jerry Fodor, a well-known philosopher, with coauthor Massimo Piattelli-Palmarini, a cognitive scientist, has written a whole book trashing Darwinian evolutionary theory – the theory that makes natural selection the main force of change in organisms through the ages.

You would think that somewhere in the pages there would be one – just one – discussion of the work that evolutionists are doing today to give a sense of how the field itself has evolved. Peter and Rosemary Grant on Darwin’s finches for example; Edward O. Wilson and Bert Hölldobler on ant social structures perhaps; David Reznick on Trinidadian guppies perchance? But no such luck. A whole book putting in the boot and absolutely no serious understanding of where the boot is aimed. . .

Read it; it’s a deft, albeit brief, dissection of F&P-P’s specious arguments. (The review, in fact, is titled “The Origin of the Specious”, presumably referring to F&P-P’s motivations, discussed in the last paragraph of the piece.)

On the other hand, I can’t say much good about philosopher Mary Midgley’s review in the Feb. 6 Guardian.  Midgley, who is infamous for reviewing The Selfish Gene while completely failing to understand its premise, still fails to grasp modern biology.  Look at this postmodern analysis, claiming that all we’ve recently learned about biology and inheritance militates against Darwinism (the use of “privilege” as a verb immediately tips you off that you’re in academic La-La land):

Its authors do not, of course, deny that this kind of classical natural selection happens. But they argue strongly that there is now no reason to privilege it over a crowd of other possible causes. Not only are most mutations known to be destructive but the material of inheritance itself has turned out to be far more complex, and to provide a much wider repertoire of untapped possibilities, than used to be thought. To an impressive extent, organisms provide the materials for changes in their own future.

Surprise!  Most mutations are bad!  Lord, we didn’t know that before, did we?  It’s unclear what she means by “organisms providing the materials for changes in their own future.” In one sense that’s trivially true—organisms are the repository of mutation, which is the raw material for evolution.  But I suspect that Midgley, bamboozled by F&P-P’s long and arcane discussion of stuff like genetic assimilation, epigenetics, and modularity, simply doesn’t know what she’s talking about.

She then invokes the self-organization of individuals by physical and chemical laws as an explanation of evolutionary change.  (We’re going to hear a lot more of this; trust me.):

Besides this – perhaps even more interestingly – the laws of physics and chemistry themselves take a hand in the developmental process. Matter itself behaves in characteristic ways which are distinctly non-random. Many natural patterns, such as the arrangement of buds on a stem, accord with the series of Fibonacci numbers, and Fibonacci spirals are also observed in spiral nebulae.

I’m going to hurl if I hear this stuff about Fibonacci spirals in plants one more time.  I’d be more impressed if Professor Midgley could tell me how “self organization,” without the intervention of natural selection, produced the bodies of whales (who evolved from terrestrial artiodactyls) or the camouflage of stick insects.

Finally, she buys F&P-P’s call for a multiplicity of mechanisms causing evolution:

If we now ask what will take its place, their answer is that this question does not arise. There is not – and does not have to be – any single, central mechanism of evolution. There are many such mechanisms, which all need to be investigated on their own terms.

True, there are processes besides selection that can cause genetic change—meiotic drive and genetic drift are two of them—but no process other than natural selection can yield those remarkable features of organisms—the apparent “design” of plants and animals—that used to be explained by God.

I’ll start paying attention to these radical revisions of Darwinism, including attacks on natural selection, when they tell me how non-Darwinian processes can yield the appearance of design.  I’ll exit the flock of “hidebound Darwinists” (a term Steve Gould once applied to me) when I hear how modularity, epigenesis, self-organization, or evo-devo constitute self-contained explanations for the elephant’s trunk.

Yesterday I reported on a paper by Hawass et al. in the Journal of the American Medical Association claiming that the death of King Tut may have been due to a combination of inbreeding and malaria.  A piece by Declan Butler in yesterday’s Nature News, however, reports several experts questioning this conclusion, and it’s only fair that I give space to the counterclaims. Here are the issues:

Is this the first demonstration of malaria in ancient Egypt?  According to Butler’s experts, mummies older than Tut’s have previously shown evidence of infection by Plasmodium falciparum malaria. Butler adds that genetic evidence—presumably of the age-of-origin of anti-malarial alleles like sickle-cell hemoglobin—suggests that malaria was a problem well before Tut’s time.

Did Tut have bone disease? Butler’s experts say there are other explanations for Tut’s malformed feet, including malaria itself or even the embalming process: “burning or crushing [of the feet] by embalming salts or bitumen.”

But what about the canes in his tomb? Gino Forniciari, director of paleopathology at the University of Pisa says that canes were commonly used in ancient Egypt as “a symbol of power.”  Well, maybe, but did the tombs of other kings have 130 canes, too?

So what killed him? I noted yesterday that it’s a bit dicey to claim that either malaria, bone disease, or their combination was the actual cause of Tut’s death. Albert Zink, one of the authors of the Tut paper, agrees.  But he does argue that the bone necrosis occurred before Tut’s death, as there was evidence of healing before death.

Is the genetics o.k.? There’s some dissent here.  Declan notes that “most researchers agree that the details [about Tut’s family tree] do not allow for a full assessment.” One red flag is this: “Eric Willerslev, an expert in ancient DNA at The University of Copenhagen and co-author on a paper published last week in Nature reporting the oldest human genome sequences so far, says he’s not convinced by the fingerprinting data.”  That’s worrisome, because few reputable scientists would go public with such a claim unless the data were pretty unconvincing.  The onus is on Hawass et al. to provide all of their data.

The upshot: as most of us know already,  you can’t always trust published papers, even those appearing in reputable journals, to be free from flaws or, especially, exaggeration.  Although some say it’s not the job of science journalists to find and highlight problems with an already-published paper, I strongly disagree.  Any science journalist who is more than a hack should interpret new findings for her reader, and that means not only describing the results in language a layperson can understand, but also explaining why a study is important.  And to do that, you need to take on board more than the author’s claims or their hype; you need to canvass other experts in the field for their reaction to the paper.

That’s precisely what Declan Butler did.  A side benefit of all this is that is shows the public when there is still active controversy about an issue.

I’ll try as often as I can to draw attention to problems with or dissent about published work, but I have a day job and can’t always do this.  But do see the comment by Occam on yesterday’s post (#10).  He also finds problems with the Hawass et al. paper.

______________

Butler, D.  2010.  King Tut’s death explained? Nature | doi:10.1038/news.2010.75

Malaria.

Or inbreeding.

Or both. That’s the tentative conclusion of a new paper in the Journal of the American Medical Association.  (Lead author Zahi Hawass, Secretary General of the Egyptian Supreme Council of Antiquities, is a colorful and controversial figure who was profiled in The New Yorker last November; subscription required to see full article. One wonders what he did to justify first authorship.)

The paper with its 17 authors is a laborious genetic, phenotypic, and archaeological study of 16 mummies from ancient Egypt, with particular emphasis on the boy-king Tutankhamun, who died, aged 19, around 1324 B.C.  DNA was extracted from bones and analyzed to construct pedigrees; the mummies were X-rayed to look for aberrant morphology; and samples were PCRed to look for DNA of microorganisms that could have caused fatal infections.  Hawass is no stranger to publicity, and it’s clear that finding out what killed King Tut, probably the most famous of all ancient Egyptian kings, would garner considerable attention.  It has. But the study is still a good one, a felicitous combination of forensic archaeology, pathology, and genetics.

Here’s what it found:

1. Analysis of both Y-chromosomal and nuclear DNA produced a five-generation pedigree for Tut, his ancestors, and perhaps two of his children (some of the relationships had previously been inferred from archaeological data).  His great-grand parents were identified as Yuya and Thuya, and his parents, Akhentan and a mummy known as KV35YL, were classified as brother and sister based on genetic data.  If these data are right, Tut was pretty inbred.

2.  Ancient Egyptian art depicts Tut, and some of his male relatives, as having a feminized appearance, sometimes with enlarged breasts. This has led to speculation that royals of that era had various genetic conditions that could produce feminized appearance, including Marfan syndrome (once supposed to have afflicted Abe Lincoln) and gynecomastia (abnormally enlarged breasts in males).  None of these diagnoses were supported by the morphological studies, so the peculiar depiction of the rulers in ancient Egyptian art is taken as a stylistic device.

3.  Nevertheless, Tut and his relatives were really screwed up. Table 3 gives a list of pathologies found in the royalty, and hardly one of them is free from something bad, including rotting teeth, heart disease, cancer, arteriosclerosis, “traumatic events to the face”, and so on.  Here’s what was wrong with Tut himself:

cleft palate

clubfoot

mild curvature of the spine

foot abnormalities (missing bones)

bone disease, leading to bone bone loss in the foot

Now some of these (particularly the abnormalities in Tut’s relatives) were likely due to the absence of medical care, but I suspect (as do the authors) that this preponderance of abnormalities reflects the well-known tendency of Egyptian royalty to intermarry, leading to inbreeding and all the attendant problems that come with genetic homozygosity.  Based on the bone problems, it’s likely that Tut limped, a diagnosis supported by the presence of 130 canes in his tomb (some of which showed wear) and the depiction in Egyptian art of Tut sitting during ceremonies when other Egyptian kings would have been standing.

4. Oh, and there was one more thing wrong with Tut: he had malaria.  Not just malaria, but the deadliest form of the disease, falciparum malaria.  Now there’s no independent evidence that malaria existed in ancient Egypt, but its presence there seems likely, given its present distribution and the swampy areas around the Nile.  But the DNA tells the tale. PCR amplification of genes in the malaria parasite (a sporozoan), clearly shows that Tut had it, and so did both of his great-grandparents:

Fig. 1 (Fig. 6A in the paper): Evidence for malarial infection of Tut and relative. From the paper: A. Polymerase chain reaction amplification of a 196–base pair (bp) apical membrane antigen 1 (AMA1) fragment of Plasmodium falciparum in Egyptian mummies. DNA marker indicates molecular size marker phiX/ 174 HaeIII. Successful amplification is indicated by “ .” [JAC note: Thuya and Yuya were Tut’s great-grandparents].

We’ll never really know what did young Tut in, but the authors speculate that it was the combination of malaria and inbreeding:

He might be envisioned as a young but frail king who needed canes to walk because of the bone-necrotic and sometimes painful Köhler disease II, plus oligodactyly (hypophalangism) in the right foot and clubfoot on the left. A sudden leg fracture²³ possibly introduced by a fall might have resulted in a life-threatening condition when a malaria infection occurred. Seeds, fruits, and leaves found in the tomb, and possibly used as medical treatment, support this diagnosis (eAppendix, eFigures 3D and 3E).^24-25,53-57

This seems reasonable, although Hawass, with his usual penchant for publicity, is going around telling reporters, with no reservations, that malaria definitely killed the young king.  Well, maybe, but falciparum malaria isn’t always fatal.  Two of of Tut’s great-grandparents had it, and, as the authors note, they died in their 50s, and the infection might have been chronic, or suppressed by their immune systems.

________________

Z. Hawass et al. 2010.  Ancestry and pathology in King Tutankhamun’s family. JAMA 303:638-647.

. . . and by humans, not God.  Today’s New York Times reports that a physics experiment conducted at Brookhaven National Laboratory, and involving the collision of nuclei to create states mimicking those present in the early universe, has succeeded in creating local conditions that violate the laws of physics.  The law, in this case, was parity: the principle that other physical laws, and the behavior of particles, are independent of a distinction between left and right.  Apparently a violation of parity was seen in the quarks produced by those nuclear collisions, quarks that behaved asymmetrically.  (Those collisions also created a temperature of 4 trillion degrees Centigrade!).

I’m not a physicist and can’t vouch for the importance of this result, but I suspect that Sean Carroll will soon be explaining it over at Cosmic Variance.

________

Update:  Sean Carroll did his homework and put up a post on this.  In the end, the result doesn’t seem nearly as earth-shaking as the Times made out, but is that a surprise?