News flash: creationists distort science

March 21, 2011 • 5:14 am

This time it’s personal, because the creationists are dissing fly research!

Yesterday I described a new paper by Wiegmann et al. on the family tree of flies (Diptera); the reference and free link are at the bottom. It’s a good piece of work, and resolved several questions that had long puzzled students of fly biology.

But the creationists—that is, the oxymoronically named Institute for Creation Research—have got their dirty mitts on the paper, and have published a “critique” (read “distortion”) of the results in a piece called “Periodic table of flies is guesswork, not science.”  Here’s a screenshot: note their LOLzy slogan at the upper right:

You can read their short critique on the ICR site.  Their basic claim is that there’s no scientific basis for constructing phylogenies (family trees): it’s all guesswork, and basically a scam by scientists who use unreliable and constantly changing methods to buttress their “faith” in evolution.  The ICR concludes:

And in all of the research conducted to fit fly data into a preconceived notion of fly evolution, the researchers have yet to find any data that challenge the concept that flies were created.

Of course one can wonder why the Creator, in His ineffable wisdom, made flies and mosquitoes to torment and kill the object of creation.

What I’m going to do is put up an analysis by a professional systematist of how duplicitious this ICR article is.  Christian creationists won’t, of course, be swayed by scientific counterarguments, but perhaps it will be instructive to see how creationists distort data in a field that’s unfamiliar to most laypeople: systematics.

The analysis below the line is by my friend Phil Ward, a professor in the Entomology Department at the University of California at Davis.  He works on ant systematics, but is also deeply knowledgeable about evolution in general.   I’ve asked him to respond to the ICR piece in a way that biologically interested laypeople could understand. Many thanks to Phil for the following (the indented parts are taken from the ICR piece):

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The Wiegmann et al. paper is the most comprehensive study to date on the evolutionary history of two-winged flies or Diptera. It provides a well supported “backbone” phylogeny of this large and diverse group of insects, based on analysis of a newly generated and quite substantial molecular data set. I think that any insect systematist would consider this a very significant contribution to the field. The criticisms and distortions of the study by the Creation Research Institute (CRI) are laughable and are hardly worthy of serious consideration—except that they will be taken seriously by some misguided souls.

At the outset the CRI article mischaracterizes the Wiegmann et al. study as one in which the investigators attempted to determine “which types of fly likely evolved into other types”. This exemplifies a fallacious view, apparently widespread among creationists, that evolution posits the origin of one extant kind of organism from another extant kind (e.g., that chimps evolved into humans).

The procedure for building evolutionary trees requires many assumptions, and one of them is the decision of which fly best represents the “first” flies at the “root” of the fly evolutionary tree.

Again this reflects a misunderstanding of how the phylogenetic analysis was carried out. The root of the tree (the common ancestor of all flies) was inferred by including in the data matrix other non-dipteran insects belonging to a more inclusive group known as the Endopterygota (these are insects with holometabolous development, that is to say, those whose life cycle encompasses four stages: egg, larva, pupa and adult). Wiegmann et al. did not arbitrarily “decide” that the strange flies belonging to the family Deuterophlebiidae would be at the base of the tree as sister to all other Diptera. This emerged from the phylogenetic analysis that included both ingroup taxa (flies) and outgroup taxa (non-dipteran holometabolous insects). Moreover it would be incorrect to say that the study concluded that Deuterophlebiidae represent the “first” flies – they are simply an old, species-poor lineage that is sister to all other Diptera. They no more represent the ancestral fly than the duck-billed platypus (or echidna) represents the first mammal.

Many prior evolutionary tree studies have amply demonstrated that the different “trees” that can be built from the same genetic and structural data are as numerous and varied as the investigators who construct them.

The estimation of evolutionary trees is affected by the quality of the data and the assumptions that accompany the analyses. But as we accumulate more data (particularly abundant and informative DNA sequence data from the genomes of different species) there is increasing stability and consensus about the major features of the tree of life. Of course there remain some contentious areas, especially the placement of old and long isolated branches in the tree, but the progress that has been made in the last decade is truly remarkable.

Despite the use of scientific-sounding words like “phylogenomics”—which attempts to reconstruct the supposed evolutionary history of an organism using its gene sequence data— this constantly changing structure is a clear sign that the trees are subjective inventions that only masquerade as observable “science.” The new fly tree shows no signs of breaking this mold.

As if the modification or replacement of hypotheses is a bad thing! Actually the new fly tree confirms many long-standing traditional views about dipteran phylogeny. It provides strong evidence that many kinds of flies previously delimited by morphological attributes are in fact monophyletic groups (a monophyletic group is an assemblage of species that comprises their most recent common ancestor and all its descendants). At the same time the study generates a number of novel findings, revealing for example that the family Drosophilidae (containing Drosophila) is closely related to two rather odd groups of flies that parasitize bees and other insects. Other contentious questions about fly phylogeny are addressed and provisionally answered. More generally, the Wiegmann et al. study provides a clearer picture of the changes in life history traits and rates of diversification that have occurred during the 260 million year history of these fascinating organisms.

Finally Wiegmann et al. point out that there is still much to be learned about the tempo and mode of fly evolution, especially in the species-rich group known as Schizophora which radiated in the early Tertiary (65-40 million years ago). This will require much more intensive sampling of flies and genes. How much more satisfying and intriguing than “Biblical, Accurate, and Certain”!

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and a h/t to Phil Ward:

Wiegmann, B. M. et al. (many authors). 2011.  Episodic radiations in the fly tree of life. Proc. Nat. Acad. Sci. USA, doi:10.1073/pnas.1012675108

Click and weep

March 20, 2011 • 12:23 pm

The dire state of scientific knowledge in America, from an article by Mark Roth in today’s Pittsburgh Post-Gazette:

It’s stupefying that nearly half of Americans don’t think that regular tomatoes have genes!

Although scientific literacy is increasing, it’s still quite low.  Roth identifies several causes for this reprehensible state of affairs, but of course we know the real ones. They are:

  1. The stridency of Gnu Atheists, which makes Americans refuse to learn science and flee to religion instead
  2. The lack of scientific “rock stars” and cheerleaders to make science sexy for the average American

h/t: Hempenstein

Michael Ruse: New Atheism is as bad as the Tea Party

March 20, 2011 • 9:19 am

I can’t deal with this diatribe at the Chronicle of Higher Education:

If I say my love is a red, red rose, I am saying nothing about her mathematical abilities, and if I say (as today’s scientists do say) that the world is a whacking big machine, I am saying nothing about such questions as why there is something rather than nothing, why morality, or (and this is more controversial) why computers made of meat (aka brains) produce sentience.

I think science leaves these questions open, and if religion wants to try to answer them, it is perfectly legitimate for it to do so.  It doesn’t mean that we have to accept the answers of the religious, and it doesn’t mean that religion cannot be criticized – I have said that for me personally the problem of evil is beyond solution – but I don’t think it can be criticized by science.

Science has tentative answers for the “something rather than nothing” question, and we’re working on the evolution or morality (its secular origin is also an empirical question) and the evolutionary and physiological bases of consciousness.  The questions may be “open,” but they’re not in principle beyond the purview of science.  The “answers” of religious people boil down to this: all these phenomena came from God.  End of story.  As Anthony Grayling notes, we may as well say that all these phenomena came from Fred. Religion has not, and cannot, provide good explanations for real-world phenomena.

And then there’s this ridiculous alarmism:

This is why, whatever is said about me, I am not about to change my mind – at least not without some arguments.  And this is why I think the New Atheists are a disaster, a danger to the wellbeing of America comparable to the Tea Party.  It is not so much that their views are wrong – I am not going to fall into the trap of labeling those with whom I disagree immoral because of our disagreements – but because they won’t make any effort to think seriously about why they hold their positions about the conflict between science and religion.

Because, of course, the New Atheists are philosophically unsophisticated:

Perhaps it is just a turf war, but I don’t think philosophy is something to be ignored or done after a day’s work in the lab over a few beers in the faculty club.  I think if you want to show that science and religion are inherently in contradiction, then you should show why people like Kuhn (and indeed Foucault) are wrong about the nature of science.  That I think is morally wrong, namely taking positions with major political and social implications, without doing your serious homework.  Just mentioning Galileo’s troubles with the Church or Thomas Henry Huxley’s debate with the Bishop of Oxford is no true substitute for hard thinking.

No, we don’t have to show that Kuhn and Foucault are wrong about the nature of science.  All we have to show—and have shown—is that religion and science use different and incompatible ways to “understand” the universe, and that the religious way isn’t really a way of understanding at all.  All we have to show is that there is only one science, which is practiced by researchers of all creeds and nationalities, but that there are elebenty gazillion religions, all of which disagree about their “truths.”  All we have to show is that religious “truths”, like resurrection and parthenogenetic humans, violate scientific ones.  All we have to show is that we know a lot more about physics and biology than we did 200 years ago, but don’t know a jot and tittle more about the nature of supposed gods.  And all we have to show is that faith is considered a virtue in religion, but a vice in science.  We’ve already shown these forms of incompatibility.  QED.

I love it that Ruse, like Jeremy Stangroom and Jean Kazez, characterizes our philosophical naivité and so-called stridency as “immoral.”  Do these philosophers even know what “immorality” is?

Who’s related to fruit flies?

March 20, 2011 • 7:23 am

I’ve spent my entire life as an academic working with “fruit flies” in the genus Drosophila. (Note that the true fruit flies are not Drosophila, but rather members of family Tephritidae, which includes the much-feared Mediterranean fruit fly. Drosophila are more accurately called “vinegar flies”.)  Drosophila is surely the best-studied genus of insects, at least from an evolutionary and genetic point of view.  Most people don’t realize, when I tell them or show them what I work on, that many of the principles of modern genetics, including sex linkage and the physical linkage of genes on chromosomes, came from research on Drosophila.

Flies (insects of the order Diptera) are important numerically and in relation to humans.  One in ten of all named multicellular species, and that includes plants, are flies: Diptera contains 152,000 named species and many more that are undescribed. And they are of medical and agricultural importance, for Diptera includes mosquitoes, tsetse flies, Medflies, horseflies, botflies and, of course, houseflies.  But up to now, the family tree of flies—and of my beloved Drosophila—has been contentious.  Drawing family trees using morphological traits—body parts and the like—has been helpful, but the higher-order relationships remained mysterious.

This has largely been resolved, though, with the publication of a new paper in Proceedings of the National Academy of Sciences by Brian M. Wiegmann et al. (there’s free access).  The paper, called “Episodic radiations in the fly tree of life,” used molecular data (DNA sequences) from more than 200 species to draw the family tree of Diptera.  The major findings:

  • Diptera is indeed “monophyletic”; that is, the group contains all living descendants of a single common ancestor.
  • A new and unexpected finding: the oldest groups (or, as the authors call them, “the earliest extant fly lineages”) are semi-aquatic: they are two families (Deuterophlebiidae and Nymphomyiidae) in which both larvae and adults are associated with water.  These habits, and similar aquatic tendencies in nearby dipteran groups, suggest that the ancestors of all modern flies were also semi-aquatic.  The authors call the Deuterophlebiidae and Nymphomyiidae “rare and anatomically bizarre.” Here’s a Nymphomyia alba adult and larva:

  • There were three large radiations of flies, characterized not such much by higher rates of species formation, but lower rates of extinction.
  • And, of greatest interest to me, they found two groups that appear to be the closest relatives of Drosophilidae (the family that contains Drosophila and allied genera).  First, here’s a fly that I’ve worked on for years: the undergraduate genetics star Drosophila melanogaster:

Molecular data showed, surprisingly, that the closest relatives of Drosophila (by this I mean the sister groups of the family Drosophilidae) are two strange groups,  the Braulidae (bee lice) and the Cryptochetidae.  Here’s the authors’ phylogeny:

Bee lice are bizarre wingless flies that are parasites; they cling to bees (one per bee, except for the queen, who can have many), and their larvae live on honey from the hive.  They’re not regarded as major bee pests unless there’s a serious infestation of a hive.  Here’s the bee louse fly Braula coeca; you can see that it doesn’t look at all like a fly, for its wings are gone and it looks for all the world like a louse (lice are in a completely different order of insects, the Phthiraptera).

This is a FLY!

Here’s a true louse, one that some of us may have had—the pubic louse Phtirus pubus.  The resemblance between this and the fly above is a great example of convergent evolution.  Parasitic clinging insects don’t need wings, and develop bodies and legs good for holding onto insect setae (bristles) and hairs:

Here’s some bee louse flies on a queen.  The flies are about the size of a small pinhead:

The other group of Drosophila relatives, the Cryptochetidae, look more conventional as adults, but their larvae are also parasites—in this case endoparasites of scale insects.  The larvae have been used as biocontrol agents.

The rest of the paper’s results will excite systematists and entomologists, but won’t thrill the rest of us.  But they’re solid results, since they’re based on lots of molecular data and the branch positions are well supported.  In the next post we’ll see how creationists have taken this paper and, in trying to show their fellow Jebus-lovers that its results—and evolution itself—are wrong, have wilfully misunderstood and distorted what the paper showed.

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Wiegmann, B. M. et al. (many authors). 2011.  Episodic radiations in the fly tree of life. Proc. Nat. Acad. Sci. USA, doi:10.1073/pnas.1012675108

Catheology

March 19, 2011 • 5:43 pm

Dr. Jim Linville is Chairman of the Department of Religious Studies at the University of Lethbridge in Alberta, Canada, and owner of the cat- and atheism-infused website Dr. Jim’s Thinking Shop and Tea Room (how does he get away with that?)

More important, inspired by our discussion of natural selection and theology, he posted a theological LOLcat.:

What a sophisticated cat!

More Darwinian theodicy

March 19, 2011 • 9:20 am

UPDATE: Over at Choice in Dying, ex-Anglican priest Eric MacDonald analyzes Harrell’s nonsense, calling it “contemptible special pleading”—and worse.

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I can’t resist dealing with evolutionary theodicy again, for BioLogos has just put up a LOLzy two-minute video showing the Reverend Daniel Harrell explaining exactly why God used natural selection to accomplish His aims.  Here it is; below it I’ve transcribed the important bits:

The amount of death and waste that evolution requires was a big stumbling block for a lot of Christians who began to dig into it . . . Why all this waste or death?

And one of this things that was so helpful to me was this realization of how death is part of the character of God.  That it is—his supreme expression of love is an act of death:  that he gives himself fully for the sake of us, whom he loves.  And inasmuch as he does that through Christ—you see an analogy to that sort of in evolution, that all of this is spent by God, you know, for the sake of life, as we come to enjoy it and appreciate it. . .

It’s just a different thing, because we expect that what God do would be just to do everything as we would do it if we were God, you know, perfectly, and in just this straight row.  But in fact what we have is, you know, a God who does things in ways we would never expect.  Why would you ever save the world by becoming human and dying yourself?  So, all the more—why would you ever create a world that exists, as it does, through dying and in a sense giving yourself (obscure)?

So, you know, these kinds of analogies are helpful to me because you’re able to see, you know, that theology can be writ large upon the biological narrative, even though that’s something that science itself would never write.

His supreme expression of love involves a monkey being eaten alive by chimpanzees?  What kind of love is that?

When I see stuff like this, I realize that there is no limit to how tortuously the human mind can twist itself into knots to make everything in the world comport with a ludicrous faith.  It’s positively Orwellian how they can turn horror and death into manifestations of God’s love.  Haven’t they ever realized that it’s a lot easier to assume no god at all?  Or how stupid they look when they talk like this?

Natural selection: God’s tool?

March 19, 2011 • 7:31 am

Accommodationists are often schizophrenic:  they want to claim that religion and science are completely separate spheres of inquiry, but at the same time argue that “sophisticated” theology shows scientific processes to be perfectly comprehensible as god’s way of creating his world. And as for the mutually helpful “dialogue” between science and faith, I have yet to hear about anything that faith does for science.  Science, of course, does plenty for faith: it shows that its doctrines are ridiculous.  Do religious people then reconsider their faith?  Well, some of us—as we saw on yesterday’s thread—do: many atheists gave up belief in god because the facts of physics and biology made belief insupportable.  But most religious people simply regroup and tinker with their dogmas.  Ultimately, no facts—even the horrors of the Holocaust—can dispel true faith.

The best example of theology making scientific necessities into theological virtues is Darwin’s idea of natural selection.  As natural selection demolished Abrahamic faith’s most important empirical evidence for god, the faithful simply regrouped and, after a frenzied confab, began claiming that, don’t you know, natural selection was not only god’s tool for making life and humans, but it was in fact a much better tool than simply creating ex nihilo.  It was all natural!  Driven by laws instead of constant intervention! God could just set evolution in motion (making sure, of course, that it would eventually cough up humans), sit back, and enjoy.  Of course, there were all those nasty “natural evils” to deal with: all the suffering, extinctions, and other byproducts of evolution.  This has lead to theology’s cottage industry of reconciling the waste and suffering of selection with the plan of a benevolent god.

These reconciliations are laughable of course, and not convincing to any sentient being.  What appalls me, though, is that some atheists, perceiving these problems, try to help theologians with this reconciliation!  There are two examples this week: Michael Ruse writing at HuffPo, and Josh Rosenau posting on his blog and commenting at Jason Rosenhouse’s website, EvolutionBlog.

I briefly considered critiquing Ruse’s piece, but I couldn’t stomach having to read it more than once, especially after he called Jason and I “junior New Atheists.” (Ruse is the most obviously jealous critic of Gnu Atheists like Dawkins and Sam Harris: he’s always whining about how poorly his books sell compared to theirs.  Has he ever wondered why?)

So, after this long preamble, let me just point you to Jason’s labor-saving critique, “Evolution and the problem of evil,” focusing specifically on natural selection.  Ruse, for instance, argues that god chose to “create through law” (i.e., natural selection).  Jason responds:

I’m afraid I don’t see how this makes any sense at all. Imagine the state of the universe at some moment shortly after evolution has produced modern human beings. God, presumably, could have created the world supernaturally in a state that was identical in every morally relevant way. That world would contain free human beings embedded within a natural world adequate for their needs. Had He done so we would have been spared the millions of years of evolutionary bloodsport that has horrified everyone who has ever considered it. That universe would differ from ours only in that it would lack that awful history, which seems to me a clear improvement over the world we have. There would be no evidence of evolution to erase because evolution would never have occurred.

Furthermore, the whole idea of “creating through law” needs to be clarified. Whatever you think God did, it seems clear that He did certain things supernaturally and allowed certain other things to unfold by natural law. The only question is the balance He employed. In Ruse’s version God’s moment of supernatural intervention ended with the Big Bang. My version simply has God fast-forwarding the tape and letting natural laws take over from a later stage. What theological purpose was served by Ruse’s scenario that would not be served by mine?

I would note, incidentally, that for most of Christian history people thought that humans were created supernaturally and instantaneously, without noticing, apparently, that such a notion was theologically problematic. Ruse, writing a short blog post, can be forgiven for not exploring these details. But if you would care to read his two books on this subject you will find that he provides scarcely more detail in either one of them.

Pwned!

Rosenau, on the other hand, helpfully tells the faithful that their problems are considerably ameliorated if one assumes god isn’t omnibenevolent.  Jason’s response:

But I do think it is incorrect to claim that the problem of evil does not present itself unless we assume an omnibenevolent deity. Such an assumption only seems necessary if you are putting forth the logical problem of evil (that there is a logical contradiction entailed by the statements, “God exists” and “Evil exists”). The inductive argument (that evil is strong evidence against God) can get by with something less. God is often said to be perfectly just, for example, which is not the same thing as perfectly good but which would certainly make us wonder about what justice is exemplified by letting animals suffer simply as links in an evolutionary chain. We could also point to the sheer profligacy of evil and suffering in natural history and argue that any God presiding over this is not only not perfectly good, but is actually downright sinister.

Thanks, Jason, for saving me a lot of work.  It’s bad enough that accommodationists dip their toes into theology by repeatedly arguing that evolution can be easily reconciled with faith, and that many denominations agree. But it’s far worse for them to try to help the faithful reconcile God and science by propping up their theodicy.  Why on earth would atheists engage in such puffery?  Only, I think, so they can appear “reasonable.”  It’s a betrayal of their own beliefs, and a form of intellectual cowardice.  After all, there are presumably reasons why these people are atheists.

I swear, when you read this kind of stuff coming out of the mouths of professed atheists, you finally want to ask, “Why don’t you just go to church?”