August 8, 2012 | David F. Coppedge

The Fish Explosion

Fish are exploding in the kitchen of evolutionary phylogenomics.

“The Age of Fishes” – the phrase immediately brings to mind your biology textbook or natural history museum.  What is it, class?  “The Devonian Period.”  Wrong.  Fish exploded onto the scene in the Devonian (300 million years ago on the evolutionary timeline), but diversified rapidly again in the Mesozoic to Cenozoic, 120 to 60 million years ago on the timeline – a virtual “Second Age of Fishes,” according to the authors of a new paper in PNAS that tried to paper over a “lack of a single comprehensive phylogeny” that “has limited our understanding of the evolution and diversification of this radiation” of our finny friends (Near et al., “Resolution of ray-finned fish phylogeny and timing of diversification,” PNAS August 6, 2012, doi: 10.1073/pnas.1206625109).

Is it inaccurate to call these explosions?  After all, the paper discussed the “radiation” or “diversification” of fish.  Perhaps.  But the abstract and the summary on PhysOrg used evasive words that amount to “abracadabra” incidents: we are told that the fish “appeared” and “arose.”   The scientists used the more clever word “occurred” (without explaining what mutations were preserved by natural selection), while unveiling some dirty laundry in the evolutionary fish camp:

This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the “bush at the top of the tree” that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the “Second Age of Fishes.”

If they were to use the word radiation the way physicists do, it travels at the speed of light – a pretty explosive speed.  Naturally, they define it differently; nevertheless, their imprecise words continue to invoke visions of instantaneous change.  As with the Cambrian explosion, no transitional forms were mentioned.  While lead author Dr. Thomas Near boasted, “The new family tree of ray-finned fish comes close to completing the book on the evolutionary relationships of vertebrates,” it is doubtful he rebuked the press release writers for saying that the fish “appeared” in the Devonian then “appeared” again later – doubtful, indeed, because he said so himself:

“Half of all animals that have backbones are ray-finned fish, but we know little about their evolutionary history in contrast to other vertebrate lineages like frogs, lizards, birds, and mammals,” said Thomas Near of the Department of Ecology and Evolutionary Biology at Yale and lead author of the paper. “Fish are usually viewed as primitive in origin, but we are learning that most of the familiar living lineages of fish arose more recently — during what we might call the Second Age of Fishes.”

Speaking of fish, there’s news about the alleged fish-to-limb transition, and it’s not good (for evolutionists).  “Paddlefish’s doubled genome may question theories on limb evolution,” PhysOrg announced.  The first paragraph summarizes the furrow-browing concern in the evolution camp:

The American paddlefish — known for its bizarre, protruding snout and eggs harvested for caviar — duplicated its entire genome about 42 million years ago, according to a new study published in the journal Genome Biology and Evolution. This finding may add a new twist to the way scientists study how fins evolved into limbs since the paddlefish is often used as a proxy for a more representative ancestor shared by humans and fishes.

These means trouble for the fish line and the human line holding the pole.  “This creates extra genetic material that adds complexity to comparative studies,” explained Karen Crow (San Francisco State).  “It may change the way we interpret studies on limb development.” How so?

In the last decade, paddlefish have become a useful benchmark in evolutionary studies because their position on the evolutionary tree makes them a reasonably good proxy for the ancestor of the bony fishes that evolved into tetrapods such as humans. However, the fact that paddlefish underwent a genome duplication could complicate what its genes tell us about the fin-to-limb transition, says Crow.

“Our findings suggest that the results of previous studies using paddlefish as a comparative species may need to be re-interpreted,” Crow said.

You may have thought that humans were bipeds, not tetrapods (“four-foot”), even admitting that babies walk on all fours in their transitional form to adults.  The study basically tosses the paddlefish back into the river as the transitional form that got away.  But casting a good spin with this tangle of phylogeny filament, Crow found new possibilities to bring home a good fish story:

Whole genome duplications are game-changing events in evolutionary history that give rise to new species or novel features within a species. They occur when a series of unlikely circumstances coincide, resulting in twin copies of every gene. When this happens, one scenario that could take place is that one gene in the pair keeps its designated function while the other is either lost or takes on a new purpose.

This extra genetic material provides the canvas for evolution to paint with,” said Crow, who studies the evolution of novelty and diversity.

In short, she gave up fishing for art.

It’s hard not to laugh at these people.  Their concoctions explode in the kitchen, they can’t find the ingredients, and they can’t paint, either.  Like some other famous magicians, they are always learning and never able to come to the knowledge of the truth.  There’s always truck driving for the desperate.  Use laughter charitably; it may be the quickest and softest way for them to get the hint that they are clueless.  Let them know that the ID community will welcome them into a better fellowship once they quit the Darwin cult and kick the naturalistic magic habit that is its central ritual.

Where have all the fishies gone?

Long time passing;

Where have all transitions gone?

Long time ago.

Where have all our stories gone?

Facts have kicked them, everyone.

When will they ever learn?

When will they ever learn?

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