Sunday, July 26, 2015

Caution: This is NOT a Falsification

I love this stuff.
Four-Legged Snake Shakes Up Squamate Family Tree – Or Does It?

"Some would argue that the origin of snakes was pretty much settled back in May, when a landmark paper by Allison Hsiang and her colleagues was published in BMC Evolutionary Biology. “We put together a large dataset comprising both fossil and living snakes and used mathematical models and computer programs to infer ‘ancestral states,'” explains Hsiang, a postdoctoral researcher in the Department of Geology and Geophysics at Yale University. "
OK, then. It's got computer models going for it.
"The diagram of snake evolutionary relationships they produced, called a phylogenetic tree, is the most robust analysis of snake evolution to date, and it strongly supported the land-based evolution of serpents.

Ancestral state analyses, which essentially use math and science to estimate the biological and ecological traits of the most recent common ancestor of a group of species, suggested that early snakes were nocturnal hunters, preying upon the small vertebrates of their era through stealth, not constriction. Their analysis didn’t find that snakes were burrowers, however — there was no strong support of a fossorial lifestyle, just that the snakes lived on land.

According to Hsiang, morphological data “strongly influenced” the snake tree. “Our study helped to demonstrate how important and essential it is to include fossils when we are trying to understand how and when organisms evolved.”"

Well, now. Computer models, math AND science, plus morphology AND fossils. Got it nailed then.
"Though there was some excitement when Hsiang and her colleagues published their analysis in May, a paper published a little over a month earlier in PLoS ONE slipped by the press unnoticed. The analysis, led by Tod Reeder from San Diego State University, looked beyond snakes to reconstruct the evolutionary relationships within the squamates, the group of reptiles that contains lizards and snakes. Using the largest dataset to date which, like Hsiang, included both genetic and morphological markers, Reeder and his colleagues affirmed one of the crucial pieces of evidence of a marine snake origin: the close relationship between mosasaurs and snakes.

“The most comprehensive analysis of the lizard evolutionary tree now reinstates these aquatic mosasaurs as the nearest relatives to snakes,” explains Michael Lee, associate professor at the University of Adelaide, who was one of the first scientists to suggest that snakes may have started in the water."

Oh NO! Are math AND science AND computer programs failing us?
"Because of this, Reeder et al. calls into question the methods used by Hsiang et al., specifically one of the core assumptions in the paper: the closest relatives of snakes. When constructing evolutionary trees, assumptions have to be made to “root” the tree, or put the relationships into the context with regards to time. Scientists must compare their data to what is called an “outgroup”, which is ideally the closest relative or relatives to the group of interest. Hsiang and her colleagues used a subset of a group of lizards called anguimorphs, which includes land dwelling lizards like the Komodo dragon.

“The Hsiang paper was a terrific analysis of the evolution within snakes, but the fundamental core assumption they made in the paper was that terrestrial lizards were ancestral to snakes,” said Lee. “The direction of evolution was determined by that assumption. But if you assume, as the Reeder paper suggests, that mosasaurs are ancestral to snakes, then some of the inferences by Hsiang might not hold.”
Since when are core assumptions questioned when using math AND science AND computers?? Is this not heresy? Or is it turf protection?
"Hsiang admits that there are differences between the phylogenies in her paper and Reeder’s, and that the choice of outgroup may have skewed their results. “There are differences between the Reeder et al. phylogeny and our phylogeny — it would be interesting to conduct an in-depth analysis to try and determine why the differences in phylogeny exist,” she said. While her team’s tree was strongly influenced by morphology, Reeder’s team found that genetics most strongly predicted the results. “In fact, the morphological data are really ambiguous,” co-author John Wiens said in a press release. “Or in some cases, even worse than ambiguous.”"
Hold up right there buddy. Morphology is the core, the very core, the essence, the truth centering at the very heart of Darwinism and 150 year of evolutionary theorizing. This is very close to hate speech here, pal. Remember, Darwinism is protected by law, so watch your step.

Hsiang strikes back and then makes this statement:
"“Of course, we’d have to actually run the analysis to know for sure.”"
And there's the problem. No one will ever, ever, ever, "know for sure". So I think neither camp actually will admit to this. It is a struggle to establish contingent knowledge which probably won't last more than a few years, decades at most.

It's arguable that there are no longer any sciences which can produce objective knowledge, period. So scientists get paid, probably from tax payer largesse, to squabble over things which cannot be objectively and unambiguously proven, and which make no real difference in the human objective knowledge base.

And here comes another one, examining visual pigments:
"“Visual pigments, like opsin and rhodopsin, are basically the business front-ends of the visual pathway,” says Simões. “So basically if anything is happening in the visual system, the visual pigments will be the first to be impacted.” Burrowing mammals, for example, have lost some visual pigment genes, as they no longer need them underground. But even more impressively, scientists can connect genetic changes in these pigment genes to ecology and function. “By checking their amino acid composition, you can estimate what kind of wavelengths the animal can see,” says Simões.

When Simões et al. compared the visual pigment genes in snakes to other lizards, they found something exciting: snakes have lost two of the five pigments found in the rest of the squamates. They retain the same three that we have. Simões explained that this means snakes likely went through an “ancestral nocturnal bottleneck,” just like mammals did. “Snakes have this contrasting pattern from lizards that converges with mammals.”"

Whatever you think that means, forget it; here's the ancestor... maybe:
"Which brings us back to the most recent finding, what Martill and his colleagues claim is a four-legged snake ancestor from Brazil. Though there’s no concrete information about where this fossil originated, the color and texture of the limestone it is encased in suggests it’s from the Crato Formation, a fossil deposit which was laid down some 100 million years ago when the area was a shallow sea."
From that two sentence statement one can see this: they don't know where the fossil is from (!) They think that it's four legs occurred in a shallow sea (!) Why four legs confers selectability in a sea is not even speculated here.
"“This thing is much much more of a snake than it is of a lizard,” he concluded. But some scientists don’t buy it. “I think the specimen is important, but I do not know what it is,” University of Alberta paleontologist Michael Caldwell told Ed Yong from National Geographic. But Lee is willing to give Martill the benefit of the doubt. “I’m prepared to provisionally accept that it’s a very unusual small snake,” he said. “But the specimen is so small and the skull is so badly crushed that I think there is going to be a lot of debate until all interested researchers are able to look at it.”
So whether it is a snake or not merely depends upon who you can convince. Science is what scientists do, scientists say.
“It does seem to have some pretty intriguing snake features,” Lee admits. “Snake teeth have a very distinct curvature to them… and this animal does seem to have that. So that’s one feature that really makes me think this is probably a snake.” He’s also impressed by the animal’s spine. “It’s got a very large number of vertebrae — 160 backbone elements — which is also a very snake-like feature,” he added. “None of the other features that they list do I find particularly compelling.”

Hsiang, on the other hand, is entirely convinced. “Tetrapodophis does seem to possess many anatomical features that are unique to snakes — the recurved teeth, intramandibular joint, vertebral characters, et cetera,” she said. “So, based on Martill et al.’s report of the anatomy, it seems likely that Tetrapodophis is indeed an early snake.” She’s especially intrigued by what else is visible in the new fossil: its last meal. Martill et al. report that inside the snake’s stomach are a collection of vertebral bones, likely from a small mammal or lizard that it ate just before it died — the same diet that Hsiang et al. predicted with their ancestral state analyses. “The new fossil provides empirical confirmation of some of our results,” she noted. “For instance, the discovery of
vertebrate bones in the stomach contents of Tetrapodophis aligns with our inference that the earliest snakes likely ate small vertebrates.”
So the snake ate a mammal or a not-mammal. I'm convinced.

Evolution is just like the monkeys on the typewriters, typing up stuff which makes sense only to themselves. It can't be falsified, so, of course, it won't be falsified; thus it must be true, right?

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