Worst Paper of the Year

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Alyrium Denryle
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Worst Paper of the Year

Post by Alyrium Denryle »

Thank you Anguirus for showing me this, as it made me laugh and cry at the same time... I dont have online access to this edition of PNAS yet, so I cant post a full review. However I will either get it shortly, or will just go to the library tomorrow and scan it in... then post it as images. Then give it the full treatment.
Worst paper of the year?

A new paper in the Proceedings of the National Academy of Sciencee makes the bizarre and completely unsupported claim that the two stages of the butterfly life cycle: caterpillar and volant adult, result from a hybridization event, with the caterpillar resulting from a butterfly mistakingly mating with an onycophoran (velvet worm). Instead of a single lineage evolving two different life stages, then, each stage reflects a completely independent evolutionary event.,

An article on this paper in Scientific American first explicates the theory:

In the current issue of Proceedings of the National Academy of Sciences (PNAS), Donald Williamson, a wheelchair-bound 87-year-old zoologist from the University of Liverpool in England, suggests that the ancestors of modern butterflies mistakenly fertilized their eggs with sperm from velvet worms, also known as onychophorans. “People have been trying to find one solution that covers all of metamorphosis,” Williamson says. “I say it’s a change in taxon during development.”

Velvet worms, which fall between worms and insects on the tree of life, have soft-bodies and superficially resemble caterpillars, particularly the larvae of an early butterfly relative known as Micropterix. Velvet worms have evolved a variety of elaborate fertilization procedures. Males are known to place sperm packets not on the female’s genital opening, but rather on skin tissue, which the sperm penetrates before migrating to the ovaries.

Williamson believes that an ancient insect accidentally picked up that sperm, and butterflies now contain two developmental programs so they live half their life as velvet worms and half their life as winged butterflies.

“Animals have been able to hybridize since they invented sex,” Williamson says. “With external fertilization, there’s always the possibility that some sperm will fertilize the wrong egg.”

and then gathers the reaction of other scientists, which is uniformly negative:

However, scientists asked to comment on Williamson’s theory were taken back by it and surprised it made it into such a prestigious journal. For example, from insect paleontologist Conrad Labandeira of the Smithsonian National Museum of Natural History in Washington, D.C.: “You’re kidding!”

After looking over the paper, Labandeira pointed out more substantial criticisms. Hybridization between closely related species sometimes occurs in the animal kingdom, but it is highly unlikely that the sperm of a velvet worm could fertilize a distantly related insect egg and produce a viable embryo. He also raises the question of where the genetic program controlling metamorphosis would come from.

“If I was reviewing [this paper] I would probably opt to reject it,” he says, “but I’m not saying it’s a bad thing that this is published. What it may do is broaden the discussion on how metamorphosis works and…[on]…the origin of these very radical life cycles.”

Insect developmental biologist Fred Nijhout of Duke University took a less diplomatic view of the article saying it would be better suited for the “National Enquirer than the National Academy.

Besides being inherently implausible, the theory can be easily refuted by DNA analysis, which should show, in butterflies, two completely disparate genomes, one resembling that of onycophorans.

Now who communicated this bizarre, unsupportable paper to one of the world’s most prestigious journals? Think about it: who has made their careeer asserting that all of evolution results from lateral gene transfer and hybridization?

Lynn Margulis.

Margulis had some great ideas early in her carreer, most famously the bacterial endosymbiont idea of the origin of mitochondria. She’s deservedly famous for pushing those ideas in the face of serious doubt. But lately she’s been spreading bizarre ideas about hybridogenesis being the main driver of evolution.(I was particulary distressed by the book on speciation she wrote with her son Dorian Sagan — also son of Carl Sagan, to whom Margulis was married — Acquiring Genomes: A Theory of the Origins of Species [2002], which argued that hybridization is a pre-eminent driver of speciation. Fortunately, the book has had zero impact on the field of speciation.)

Margulis is showing symptoms of what I call the Big Idea Syndrome, to wit: “Whatever I study is the most important thing in evolution — in fact, the driving force of evolution.” We’ve seen it before with developmental plasticity, epigenesis,evo devo, and other such buzz-fields. It’s all too tempting to think that one’s pet idea applies widely, or even universally.

PNAS of course, permits elected members of the Academy to promote papers they like by “communicating” them and adjudicating the reviews, which were often solicited by friends of the member or those known to be favorable to a paper’s results. This has resulted in the journal’s publication of some egregious work on the past; Linus Pauling’s papers on vitamin C are the most famous example.

Fortunately, this situation is changing, and soon PNAS manuscripts will receive the same rigorous review as regular journals offer — and bigwigs will no longer be able to push substandard work into publication.
on the face of it.. this is utter bullshit. The nuclear-cytoplasmic incompatibilities alone, to say nothing inter-genome incompatibilities, recessive lethals now expressed etc would make this impossible. Oh, and lets not forget the gene regulation of metamorphosis, and how this would basically make genome regulation a Genome Acquisition Cluster-Fuck.

Hybridogenesis is only really possible between closely related taxa, or because of endosymbiosis or parasitism in very simple organisms. Oh, and lets not forget about pathogens and transposons, but... not like this....

Oh, and here is a simplified image of the most up to date phylogeny of major insect taxa.

Image

You will note how what he is saying is an ancestral clade, the Lepidopterans for the homometabalous insects is actually highly derived relative to the coleoptera, which he claims are in fact derived from lepidopterans...

in the words of Anguirus' girlfriend

"Who needs evidence when you have stupidity?"
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Samuel
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Re: Worst Paper of the Year

Post by Samuel »

I don't have an indepth knowledge of biology but...
result from a hybridization event, with the caterpillar resulting from a butterfly mistakingly mating with an onycophoran (velvet worm).
:wtf:

How the hell would that work? Are species defined as not being able to have fertile offspring?
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Re: Worst Paper of the Year

Post by Alyrium Denryle »

Samuel wrote:I don't have an indepth knowledge of biology but...
result from a hybridization event, with the caterpillar resulting from a butterfly mistakingly mating with an onycophoran (velvet worm).
:wtf:

How the hell would that work? Are species defined as not being able to have fertile offspring?

Not anymore... the definition is more nuanced than that now. It is defined now (save by a few holdouts, we cladists are pretty much ruling the roost now), as a distinct lineage which is on a clear evolutionary "trajectory" so speak, distinct from other closely related lineages. This is because some organisms dont use sexual reproduction, and some groups are more genetically labile than others. For example it is possible for most toads to hybridize if brought into proximity during mating. Same with a lot of reptiles. Pythons are notorious for it, so are water snakes. Just too many exceptions for the biological species concept to be a rule.
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Re: Worst Paper of the Year

Post by Anguirus »

On the other hand, you can't get a working organism from mating members of two different phyla, which have been distinct since the Cambrian period.

I'll do a more detailed review when I'm not dead tired, my professors were absolutely appalled that this got into PNAS. We grad students, on the other hand, took the lesson to heart that you don't have to write a good paper to get into a prestigious journal, just write some crap about some high-placed wingnut's favorite idea.
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Alyrium Denryle
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Re: Worst Paper of the Year

Post by Alyrium Denryle »

Anguirus wrote:On the other hand, you can't get a working organism from mating members of two different phyla, which have been distinct since the Cambrian period.

I'll do a more detailed review when I'm not dead tired, my professors were absolutely appalled that this got into PNAS. We grad students, on the other hand, took the lesson to heart that you don't have to write a good paper to get into a prestigious journal, just write some crap about some high-placed wingnut's favorite idea.
I think I have found a way to save my dignity as a scientist. Maybe they printed it in order to properly throw it into the proverbial giant Mulcher of science.
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Re: Worst Paper of the Year

Post by The Episiarch »

Oh man, *this* paper by *that* guy. Funny, we just read this last week for the postgraduate journal club.

This guy, Donald I. Williamson has been writing the same shit year after year. And I don't mean that in the sense of "He does phylogeography, all his papers are about phylogeography of one thing or another" - Williamson has literally written basically the same thing ever since his book "Evolution of Larvae" came out in 1993 (I think?) - which is a rehash of "ancestral butterfly and velvet worms did the nastie in the pastie and all of a sudden...caterpillars!" He has maybe 3 or 4 papers and 2 books - and they all read like they were just copied and pasted from each other with minor tweaks here or there. No experimental results - at all.

Williamson has ignored *everything* that has come out in the years since his book came out (and no doubt will continue to do so until he dies) regarding developmental biology, genomics, phylogenetics and *so* many aspects of molecular biology. There's people like that everywhere, but the really bad thing was that it got into PNAS which is a high-fucking-impact journal that's just a tier below the likes of Nature and Science where all the cool kids get published. He keep suggesting experiments people can do to show whether his hypothesis is correct and just ignore all the mountain of evidence that shows him "Er, interesting idea - but WRONG!". Just as well PNAS is changing their submission policy...

If you have a look at the paper, you can find out who was reponsible for getting this piece of shit into PNAS - it was "communicated" by Lynn Margulis. I really admire Lynn Margulis for coming up with the endosymbiosis theory and thus revolutionising the way we viewed the evolution of the eukaryotic cell and yes, horizontal gene transfers does give us all kinds of wonderfully crazy things like sea slug with algal symbionts *and* algal genes, and asexual bdelloid rotifers which are ironically enough is really slutty with horizontal gene transfer that it ends up with genes from everything from bacteria to fungi and plants in its genome. But it most definitely does not give us butterfly-velvet worm hybrids.

Lynn Margulis had a really good idea, one on par with Dawkin's Extend Phenotype-selfish replicator combo, but she *really* over extended herself with thinking "Oh, eurkayotes came from the merging of 2 cell types! Then everything else must have came from the merging of everything else!!!"

Sheesh. Epic Fail PNAS.
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