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
Biblical – Accurate – Certain: Insects have four legs.
Lev 11:21-23: Yet these may ye eat of every flying creeping thing that goeth upon all four, which have legs above their feet, to leap withal upon the earth;
Even these of them ye may eat; the locust after his kind, and the bald locust after his kind, and the beetle after his kind, and the grasshopper after his kind.
But all other flying creeping things, which have four feet, shall be an abomination unto you.
That line has always seemed to me to be intended to be read as, “Of the set of flying creeping things, the subset which have four feet are an abomination.”
Which, on the face of it, would seem to imply that only eating a Pegasus-type animal would be an abomination.
Mmmm…buffalo wings….
b&
But the specific call-out of the locust, bald locust, beetle and grasshopper speaks against that. If the author was clear that these things had more than 4 legs, they would not have to be exempted.
And of course it would be presumptuous for a Biblical literalist like those at ICR to be second guessing the author’s true intent.
Creationist: ‘If the Bible says that insects have four legs then they have four legs.’
One can wonder indeed.
That was wonderful–thank you for that!
Mark Twain–Gnu before it was even coyned.
Don’t at least some Creos say flies were not created by God but by the Lord of the Flies?
If they do, do they realize that they’ve just posited *two* Creators? I wonder whether they realize that they don’t really want to go down that road…
Another thanks– *adore* his essays. Always wondered why adolescents have to be tortured with his short stories instead delighted with his brilliant essays (personal fave: The Awful German Tongue)…
“Of course one can wonder why the Creator, in His ineffable wisdom, made flies and mosquitoes to torment and kill the object of creation.”
You are, no doubt, paraphrasing the great philosopher, Ogden Nash:
God in His wisdom made the fly, and then forgot to tell us why.
I went to their article; turns out you can’t comment…
I’ve written to their webmaster asking why?
Any guesses on the response or lack thereof…?
You might ask the author of the article, Brian Thomas, M.S. * (the asterisk was there when I got there, and refers the reader to the note that Mr. Thomas is a science-writer for ICR.)
Apparently, when you got a big degree like that MS thing, you put in your by-line so your readers understand you’re an AUTHORITY.
The ICR bio for Brian Thomas doesn’t have anything to say about his research history or papers published (presumably there is nothing to report)
According to wiki Stephen F. Austin is one of four “independent” public universities in Texas (i.e., those not affiliated with one of Texas’ six university systems)
As a UK observer it seems strange to me that there are colleges/universities with religious roots (yes, I know the UK also has this disease a little)
Ahh, Nacogdoches. That makes him an authority on bugs, if you recall what Groucho Marx had to say about Nacogdoches.
I didn’t know about that, but I looked it up ~ funny ! & thanks for the roach reference
I did discover that Nacogdoches (A.K.A. “Nac-a-nowhere” ) is not too far from Waco ~ bet you didn’t know that 🙂
Thanks for doing the research. 😀
I recall plenty of references to Nacodoches when I lived in TX.
Virtually no Creationist websites allow commenting, for obvious reasons: Their position is dependent on ignorance. If they allowed commenting, a small but non-trivial minority of their readers would realize they were full of shit.
They have a FaceBook page where comments can be made…
Just once, I’d like to see a publicity photo of a Drosophilia researcher, decked out in all his field gear, standing a suburban kitchen and peering intently at an overripe banana.
What? Did I miss something? Did we get magically transported back to 1811, because the Idiots for Creation Research must think that is WHEN we are!
As the Cramps sang in Human Fly –
“I got a garbage brain, it’s drivin’ me insane”
Professor Coyne: A proverbial gadfly in the soup of biblical sophistry.
“Periodic table of flies is guesswork, not science.” Projection, if I ever saw it.
This gambit is certainly not restricted to Creationists. From religious fundamentalists to alt-med mavens to Republicans, a willingness to change one’s mind in the face of new data is considered a weakness and a demonstration that your conclusions must be wrong; while paradoxically a stubborn pig-headed insistence on your initial uninformed opinion is considered the mark of someone who really knows their shit.
This particular example reminds me in style of the missing link gambit:
“Science has failed to identify the missing link between organism A and organism C, therefore evolution is dubious at best.”
“But you’re wrong. See here, we just discovered fossil B which is a perfect transitional specimen between the two.”
“Ah hah! Now you have TWO missing links, one between A and B, and another between B and C. Now evolution is proved to be false!”
Similarly, here we have:
“There are all sorts of problems with this phylogenetic tree. You’re just guessing!”
“Well, it’s true that we have to speculate to fill in the gaps in our knowledge, but we’re getting better data all the time. See here, we just completed this study that answered a whole bunch of questions about fly phylogeny (flylogeny?) and as a result we’ve been able to replace some of the guesswork in our tree with a different ordering that is probably correct.”
“Ah hah! Now you have two random guesses, the old tree and the new tree. Which is it, Einstein? If you’re so smart, how come you keep trying to make your answers more accurate, huh?”
I note that you are willing to adjust your mind in the face of new steak data
I will be conducting a steak experiment based on your information & that provided by ‘serious eats’ a little later. I’m just testing a South African Chardonnay before I begin…
Next we’ll have creationist protesters showing up at evolutionary conferences brandishing flip flops…
Come to think of it, geocentricism is really just a bunch of assumptions based on which solar system bodies are orbiting around which. Genesis clearly says the sun, stars and planets move in the firmament around the earth.
Doh, that should read “heliocentricism” above.
Of course those people think the universe is Bibliocentric…
On a science-y note, I have to recommend Dawkins’ The Ancestor’s Tale as a great resource to help laypeople like me understand this concept of using an outgroup taxa in order to calibrate the root of your tree.
Paradoxically, the fact that Dawkins more often than not takes a stab at describing the common ancestor at each step — and being very up front about the reasons for his guess, and the shortcomings in attempting this type of speculation — really drives home the extent to which the common ancestor is truly a mystery, a crucial mathematical construction in phylogenomics, but an entity for which we can rarely say much about the actual organism with any certainty.
Fun stuff.
Agreed–Ancestor’s Tale helped me there, too. Very clear–as he ‘most always is:-). Chapter two of Futuyma’s Evolution textbook is good, too (just finished that part a couple of weeks ago, so it was relatively fresh). These are the concepts that need to get hit *hard* in jr high and high school biology classes, and generally aren’t. I don’t remember that idea being discussed at *all* in HS bio, or in the college-level course I had, either–unfortunate, because if the basic idea of “common-ancestor-distinct-from-extant-species” were more generally understood, we’d hear fewer “if-monkey-turned-into-humans-why-are-there-still-monkeys” comments coming from grown-ups who should know better.
Forgot to add– Dr. Phil, that hat is simply dashing! 😉
Thank you – as the fashion queen of myrmecology I appreciate your comment.
Even before I understood the idea that the ancestors of extant species are almost never extant species themselves, I still found the “Why are there still monkeys?” gambit baffling. With the shallow understanding of evolution I had at the time, I didn’t see any necessary contradiction in monkeys still being around. Two populations separate, one starts to evolve, the other stagnates. I now understand that it would be extraordinarily unlikely for the main population to stagnate for any significant length of time on an evolutionary time scale… but surely Creationists aren’t making that argument!
In other words, in my mind, in order to even make a coherent argument that “it can not possibly be true that humans evolved from monkeys if both are extant”, that requires a deeper understanding of evolution than most laypeople have. At least that’s how I see it.
I suppose it depends what you mean by ‘stagnate’? If there is a body type that fits a niche & is successful, there is little pressure for change, so an isopod today may be much like its ancestor 325 million years ago –
http://en.wikipedia.org/wiki/Phreatoicidea
That’s right. This business of inferring ancestral conditions is tricky, but there is no doubt that some organisms undergo much less phenotypic change than others. And sometimes (not always, but sometimes) these old species-poor lineages apparently retain a lot of ancestral features. The common ancestor of lancelets (aka amphioxus) and Homo sapiens almost certainly looked more like a lancelet than an ape.
Even when I was a Young Earth Creationist, I didn’t think the “why are there still monkeys” was a valid argument.
I remember being about ten years old, and my grandmother said that “evolutionists seem to think that male and female species that just happened to match evolved at the same time by chance!” and my little yeccer mind thought “I’m pretty sure that’s not what evolutionists actually believe…”
None of the responses from the ICR are for our consumption, and they know it. These guys don’t give a rubber rats-ass what Coyne, or anyone else for that matter, make of their answers to scientific papers.
All of ICR’s trash is for their readers, non-thinkers, (and I’m being kind here.)
Thank you Jerry Coyne, Ph.D & Phil Ward, Ph.D (or Phi ??) for the freely given primer
I got stuck with “monophyletic groups” & a few other concepts, but I got my crayons out & I’ve got it down now
Is it “Phi” for short (as per link) or Phil ?
Nitpicking: “a monophyletic group is an assemblage of species that comprises their most recent common ancestor and all its descendants.”
This definition is common, but problematic for reasons pointed out way back in 1966 (or 1950 if you read German) by Hennig. Some of the problems involved are: 1) in a fully resolved tree, nearly 50% of the members of any given clade are hypothetical; 2) it ceases to be possible under this definition to divide a tree exhaustively into clades, as some ancestral branches cannot be assigned. Both problems undermine the logical coherence of phylogenetic systematics. For instance, if we only include extant species in a taxon, by this definition our taxon cannot be monophyletic. So, what do we do? Maybe we create binomials for unobserved species? The ICZN and ICBN would not look fondly on this enterprise, and it’s not clear what would be accomplished by this set of pro forma names in any case.
Most recent critiques of phylogenetic systematics in botany (there aren’t a lot of them published, but there are a few diehards; search google scholar for “Brummitt” and “paraphyletic”, for instance) rely on precisely this kind of confusion to argue that the whole enterprise is logically inconsistent and untenable.
So, please, “a monophyletic group is an assemblage of species that comprises all descendants of a common ancestor.”
By your proposed definition a monophyletic group comprises “all descendants of a common ancestor”. But which common ancestor? Assemblages of species have many common ancestors, going all the way back into the mists of time. The necessary precision is achieved by saying “all descendants of their most recent common ancestor”. But then the definition is identical to mine except that the most recent common ancestor (MRCA) is not explicitly included.
Of course any given clade (= monophyletic group) will have unobserved ancestral species and, for species-rich groups like insects, many as-yet-undiscovered extant species. So what? None of this bankrupts the concept of monophyly.
It is sometimes useful to make a distinction between a “crown clade” (MRCA and all descendants) and the more inclusive “stem clade” (all taxa more closely related to the crown clade than to any other living taxa). Stem clades have also been referred to as “total clades”. The stem clade is more inclusive because it includes the ancestral branch (and extinct offshoots therefrom) below the crown clade down to the point where it splits from another extant clade. See further discussion of these concepts here: http://sysbio.oxfordjournals.org/content/56/6/956.full
There was indeed something missing from my definition. I’ll go with this: “A monophyletic group is one that includes all extant descendants of a common ancestor”. In treatment of ancestral species we just need to keep in mind that a stem species is logically equivalent to the group of its descendants; they’re the same thing at different times.
“Of course any given clade (= monophyletic group) will have unobserved ancestral species and, for species-rich groups like insects, many as-yet-undiscovered extant species. So what? None of this bankrupts the concept of monophyly.”
Well, then, exactly what purpose does the explicit requirement that the most recent common ancestor be included in the membership of a clade serve?
BTW, I’ve read that de Queiroz paper, but it’s been a while. It seems to provide unnecessary terminological proliferation. “Crown clades” and “stem clades” are just different groupings. Terminology that treats them as somehow different forms of the same group is a rather oblique approach to the issue at best.
Is any of this applicable in Lybia, now it is a No-Fly zone?
Libya
Oh my–that is so bad, I might have to tell my father (and if a pun is bad enough to merit repeating it to my dad, that is high praise indeed;-)).