Deconstructing a 'just so' story

Gegenbaur Revisited: Assessing the "Limbs from Gills" Scenario
Michael Denton 

Science Daily announces:

Sonic hedgehog gene provides evidence that our limbs may have evolved from sharks' gills

Latest analysis shows that human limbs share a genetic programme with the gills of cartilaginous fishes such as sharks and skates, providing evidence to support a century-old theory on the origin of limbs that had been widely discounted.

An idea first proposed 138 years ago that limbs evolved from gills, which has been widely discredited due to lack of supporting fossil evidence, may prove correct after all -- and the clue is in a gene named for everyone's favourite blue hedgehog.

Unlike other fishes, cartilaginous fishes such as sharks, skates and rays have a series of skin flaps that protect their gills. These flaps are supported by arches of cartilage, with finger-like appendages called branchial rays attached.

In 1878, influential German anatomist Karl Gegenbaur presented the theory that paired fins and eventually limbs evolved from a structure resembling the gill arch of cartilaginous fishes. However, nothing in the fossil record has ever been discovered to support this.

Now, researchers have reinvestigated Gegenbaur's ideas using the latest genetic techniques on embryos of the little skate -- a fish from the very group that first inspired the controversial theory over a century ago -- and found striking similarities between the genetic mechanism used in the development of its gill arches and those in human limbs.

Scientists say it comes down to a critical gene in limb development called 'Sonic hedgehog', named for the videogame character by a research team at Harvard Medical School.

The intriguing paper in the journal Development is here, and a very lucid description by one of the authors, J. Andrew Gillis, is here.

Gillis and his co-author Brian K. Hall provide evidence showing that in the development of the gill or branchial arches (a paired series of skeletal elements that support the gills and run down either side of the pharynx in fishes) and of the branchial rays (cartilaginous rods that articulate at their base with the gill arches in sharks and rays and protrude laterally from the gill arches), the common toolbox gene sonic hedgehog (Shh) establishes the anterior-posterior axis and the proliferative expansion of branchial endoskeletal progenitor cells. Those are the cells that give rise to the internal support system in vertebrates, composed of bone (in bony fishes and tetrapods) or cartilage (in sharks and rays).

What is the significance of their report? It is that precisely the same gene establishes the anterior-posterior axis in the tetrapod limb (in the human hand this is the axis from the thumb to the little finger) and promotes proliferation of the endosketal progenitor cells. This, as mentioned, supports a notion first proposed more than a century ago by the great German morphologist Carl Gegenbaur. As Gillis and Hall point out in a recent PNAS paper:

Gegenbaur drew parallels between the organization of the gill arch skeleton with that of the paired appendage skeletons of gnathostomes [jawed fishes], homologizing the appendage girdle with the proximal branchial arch, and the endoskeleton of paired fins proper with the distal branchial rays.

On this theory, the fin and limb girdles of vertebrates would be homologous to and derived from gill or branchial arch skeletal elements. Meanwhile the lateral appendages, the fins and limbs themselves, would be homologous to and derived from branchial rays.

In light of Gillis and Hall's research, Gegenbaur might turn out to have been right. However, as with so many other evolutionary transitions, one of the major problems in assessing his "arch to fin" scenario is, as Gillis and Hall confess, the absence of any known intermediates between branchial arches and fins. The gap between a branchial ray and a fish fin is certainly considerable (as is obvious in figure 1 in the Gillis and Hall paper). And the existence of developmental homologies throws no light on the question of how the evolutionary transformations might have come about.

Was it, as Darwin envisaged, via a long series of adaptive intermediates, i.e., imposed by external constraints? Or did it occur via a sudden, or series of relatively saltational events, driven by internal causal factors or constraints?

Intriguingly, there is a similar gap between fins and tetrapod limbs. And once more, although no one doubts that fins and limbs are homologous, how the fin-to-limb transition came about is not known. Again as with the considerable gap between branchial rays and fins, there is a considerable morphological gap between fins and limbs while no intermediate fossils are known that might throw light on the transition.


Thus the familiar question arises: Was the fin-to-limb transition gradual or sudden? And was the tetrapod limb imposed by the external pressure of natural selection or by internal causal factors? The same might be asked about the origin of many other novelties in nature even where, as would seem to be the case here, a novelty is clearly homologous to some preexisting structure.

Beyond the scroll.

All in the family? III

The Little Lady of Flores Spoke from the Grave. But Said What, Exactly?
Denyse O'Leary

If Darwinian evolution is true, the human race should evolve into different species. Indeed, Darwin said that in Descent of Man. It is a feature, not a bug. But there is no clear evidence that it is happening. Thus, it would be most helpful to the argument if a new species (i.e., clearly human but not homo sapiens) was unearthed. Or at least, if the evidence was mixed, a species that could be argued into existence.In 2003, an international archeology team was excavating the Liang Bua limestone cave (pictured above) on the Indonesian island of Flores, between Sumatra and East Timor. At a six meters depth, they unearthed the skeleton of a tiny ancient woman, about thirty years old. She was a meter in height (a little over a yard), with the brain capacity of a small chimpanzee.

When the discovery was announced in October 2004, the buzz was that she represented a new human species. As such, she was "extreme," "spectacular," "startling," and "incredible." The Return of the King was released that year, so she was dubbed the "hobbit."

One researcher hoped that a "male" would turn up. His wish was swiftly granted -- by a National Geographic artist who offered an imaginative drawing of a "male" returning from the hunt, looking impressively feral, and distinctly other than human. By August 2007, Science was calling the dig "hallowed ground." In that year, modern humans were predictably fingered as the villains that wiped out Flores man. In addition, the find answered another unmet need: To Henry Gee, writing in Nature, it posed "thorny questions about the uniqueness of Homo sapiens."

The cave turned up more than bones; it revealed stone tools, remains of fires, and the bones of pygmy elephants and other feasts. So the hobbit woman and the other individuals later unearthed -- the oldest dating from perhaps 94,000 years ago -- apparently followed the same lifestyle as other ancient human groups. But then how did we decide that they were not just one of the vast variety of human types?

The key fossil's small brain was taken by many researchers as evidence that the Floresians must be a separate species. That and an odd-shaped wrist bone. But almost immediately, a competing narrative appeared. In November, leading Indonesian scientist Teuku Jacob (1929-2007) announced that the Flores hobbit was an "ordinary human" and "just like us," but possibly with mental defects. Jacob took the bones to his own lab, and returned most of them the following February, amid charges that he had severely damaged them.

He also damaged the orthodox narrative. And Nature wasn't having any of that "just like us" stuff. In March 2005, it triumphantly reported the results of a computer simulation that bolstered the new species claim, in a story titled "Critics silenced by scans of hobbit skull." But the critics' silence did not dispel lingering doubt about "Homo floresiensis."

Concern was raised that the ongoing controversy might be good for creationism. One researcher offered that "we certainly make it easy for them when we have disagreements like this one. I think that a lot of what has been said is going to have to be retracted. Given the amount of media attention, it just makes the field look incompetent." He concluded: "Nobody is on the side of the angels now."

Not even the angels, it seemed.

By March 2008, the scene had changed again. New Scientist told us, "Researchers have uncovered bones that could drive another nail into the Homo floresiensis coffin." The magazine's nail-and-coffin metaphor is a signal: Doubt is now fashionable, not forbidden. Why? Apparently, diminutive humans had "overrun" a nearby island as recently as 1400 years ago -- "but despite their size these people clearly belonged to our species."

Meanwhile, more recent reconstructions have suggested that Flores man looked like us, and that earlier artists' reconstructions may have distorted this fact:

Basically, chimps don't have human cheeks, the study argues, so past reconstructions of the hobbit's face botched its likely looks. Or past efforts fell into the trap of assuming all early modern human species resembled "wild men," "missing links" or "ape-men."

And on it goes. The old bones told no new tale.

To get a sense of the breadth of positions in the controversy, see "Is the Hobbit's Brain Unfeasibly Small?" (maybe not); "Compelling Evidence Demonstrates that 'Hobbit' Fossil Does Not Represent A New Species of Hominid"; "Researchers offer alternate theory for found skull's asymmetry" (malformed individual); "'Hobbit' Was an Iodine-Deficient Human, Not Another Species, New Study Suggests."

Meanwhile, the Neanderthals were becoming ever more dissatisfied with their treatment at the hands of taxonomists.

Original v.evidence lite physics?

What Does Beauty Have To Do with Physics?
By Sarah Scoles

As a Harvard undergraduate, Sarah Demers—now a professor at Yale University—didn’t have the job you would imagine of a young student of particle physics. She wasn’t running code, writing equations on whiteboards, or trawling data for statistically significant signals. Instead, she was sitting in a basement, transforming 10,000 sheets of gold-coated Mylar into an instrument that would go inside the Fermilab particle accelerator.

It was menial, tedious labor, and she was the only woman in the windowless room. Even after the transformation was complete, the work and the instrument itself didn’t scream “glamorous.” In its DIY, basement-built glory, the detector looked less like a sophisticated science instrument and more like someone toppled over a set of cheap garage shelves.

Before the job started, she thought she would hate it, and—worse—that she wouldn’t understand the underlying physics, that she was just messing around with foil sheets.


But she found that she did understand, and soon she could comprehend not only how the strange instrument worked, but also how it would help reveal fundamentals of physics. “I gave myself permission to think about underlying questions,” she says.
Inside the Fermilab particle accelerator, her instrument looked on as protons collided at near light-speed with their opposites—antiprotons—and the resulting particle shards decayed after the cataclysmic blast. By rewinding that action, physicists could dissect it in slow motion. From there, they could pick up its pieces, discover what matter is made of and the forces that hold it together, and pry it apart.

Despite the foil-wrapped contraption’s messiness, those close observations of the femtoscale explosions are what helped her see she beauty. “A lot of us go into science partly driven by how beautiful the theories are,” Demers says.

Physicists often describe their earliest experiences with the field as borderline spiritual, moments in which they realized that they—they!—can represent the world with math. They can describe how stars shrink to black holes, how hard you will hit your head if you slip on a banana peel, and how protons fall apart inside particle accelerators. That ability gives them a sense of control in the way that describing something gives humans dominion over it.

For many physicists, this fosters a desire to get to the very, very bottom of things: the theory of everything. Such a theory, many physicists often believe, should be beautiful, simple, elegant, aesthetically pleasing. All of the forces should fit under one umbrella; all particles need to emerge from a nested set of equations. No ifs, ands, buts, or loopholes. Physicists sometimes use these qualities, and their opposites—ugliness, caveats, asymmetries—as respective hot-and-cold indicators to guide them on the path toward understanding, describing, and conquering the universe.

The current gold standard for describing the nature of reality, the Standard Model, isn’t physicists’ ideal because, among other blemishes, it isn’t perfectly symmetric, and the way it glues fundamental forces together is a little kludgy. That’s partially why scientists have developed a new idea, called supersymmetry, which smooths and extends the Standard Model, giving each of those old-school particles a new-school “supersymmetric” counterpart.

Despite the fact that particle physicists have found no evidence of supersymmetry, they continue hunting for the elusive supersymmetric partners—partly because the theory is more aesthetically appealing than the Standard Model.

But not all physicists believe that beauty should count as indirect evidence in favor of an idea.

As Demers dug in to her research, she began to have doubts. Maybe it was okay for the universe to be a little bit ugly. And with that thought, Demers joined a faction of physicists who believe that the pursuit of beauty as truth may be leading the field of particle physics astray.

Semi-Symmetry
Marcelo Gleiser, a professor of physics at Dartmouth College, began his career the same way as Demers: searching for the underlying explanations of why the universe is the way it is. But about a decade ago, he felt Demers’s same uncertainty tugging at him. “You look outside, and what you see in nature is not really perfection and symmetry,” he says. “You see patterns and formats which are not exactly perfect. Animal, tree, cloud, face: They obviously have symmetry but not perfect symmetry. It’s not really perfection, but near perfection.”

“How contrived is too contrived? And how fine-tuned is too fine-tuned?”
He saw the blemishes in physics, too. There is more matter than antimatter, for example. If the two were perfectly balanced and symmetric, they would have annihilated each other like the particles in Demers’ detector, and the universe would be empty—there’d be no physicists to wonder why, or to high-five each other after the discovery of a beautiful but deadly cosmic balance. “Something happened during the history of the early universe to cause this,” he says. “That got me thinking that perhaps the insistence that we have in search of perfect symmetry is not a physics idea, but a bias.”

Demers’s epiphany took place as she was composing grant applications to fund her work after graduate school with the Large Hadron Collider, where the so-called “God particle” Higgs boson was discovered. Around 3,000 people worked on the ATLAS instrument team with her—attempting to discover physics that’s beyond the well-established Standard-Model. In the grant application, she also had to justify her experiment and the motivations behind it. Some of the reasons she jotted down, she realized, were purely aesthetic. It made her uncomfortable. “I personally had been sloppier about that than I should have been,” Demers says. “It struck me: You wonder, how equipped are we to be making aesthetic judgments given what we know now?” she adds. “How contrived is too contrived? And how fine-tuned is too fine-tuned?”

Millennia of Aesthetics
The human desire for a fine-tuned, aesthetically pleasing cosmos goes much further back than our ability to build particle accelerators. Plato believed the universe was made of geometry: simple, pure shapes that some deus snapped together to form a Lego-like reality. A sufficiently smart person, he reasoned, could unsnap those building blocks to reveal the fundamental forms.


Early astronomers also believed that planetary orbits were perfect circles. After all, in their view, God wouldn’t have doomed the planets to orbit along an imperfect path. Because every early astronomer started with this belief, it took Johannes Kepler six years to figure out that the evidence pointed to unappealing elliptical orbits instead. But when he allowed the experimental data to lead him toward a conclusion, he discovered a truth about the universe.After Kepler’s data-driven discovery, Isaac Newton created the theories of gravitational force that described how and why orbits actually trace ellipses, though his ideas again reached back toward aesthetic pleasure. The same gravity that makes apples fall onto our heads also makes Earth go around the Sun. One beautiful force to control them both.

In this kind of thinking, Gleiser sees a different version of the ancients’ god-driven commitment to perfect circles. And in modern scientists’ pursuit of further unification—like making the physics of atoms and subatomic particles work with the classical physics that governs the everyday world—he sees a renewed religious impulse. “The idea that there is a force that describes everything is sort of a monotheistic cultural vice that we have,” he says. “Growing up in a culture for two or three thousand years where there is a god and a central command of things—I think that’s deeply ingrained in people’s heads.” In some sense, physicists have replaced their one true, symmetrically-faced God with one true, symmetric theory.

Take Einstein, who in the early 1900s said that general relativity was too beautiful to be wrong. Or physicist Paul Dirac, who in the 1960s said that the elegance of an equation outweighed the outcome of an experiment. It’s as though they had both taken to heart what poet John Keats wrote in 1820: “Beauty is truth, truth beauty.”

For Demers and Gleiser, aesthetics as evidence loses its appeal when it is taken as…well…on par with evidence. For example, when the Large Hadron Collider failed to find any evidence of supersymmetry, many theorists tweaked their ideas about supersymmetry—saying, “Here’s why we don’t see any evidence”—rather than accepting that perhaps the evidence was pointing them elsewhere.Demers believes particle physics is in a data-rich era and that physicists should let data lead the way. As the Large Hadron Collider continues its run, it produces more and more evidence for experiments physicists like her to analyze—and then for theorists explain. “I think we may be more likely to win by the data just forcing us in a direction, as opposed to having some great idea that’s aesthetically motivated that pans out to be true,” she says. In other words, it isn’t a physicist’s job to write mathematical poetry expounding upon the platonic “universeness” of the universe. It’s their job to describe the physical reality that we interact with, that we have concrete experimental data about.

And so, while beauty may be truth, the science of physics isn’t actually the pursuit of truth, nor the quest for beauty. The universe may be, at its most fundamental, as perfectly balanced as a Shakespearean sonnet. But if the data from experiments suggests not a sonnet but a modern prose poem—which is no less pretty, just different, unconventional, and more complicated—it is still physicists’ duty as scientists to analyze it.

Agnostic Quests
In April 2015, after a two-year break for an upgrade, the Large Hadron Collider spooled back up. This summer, the accelerator—including the ATLAS experiment that Demers is part of—will conduct its second data-taking run at these higher energies with more particle collisions. By the end of the season, it will have recorded twice as much information as it did in all of 2015. In that data, says Demers, physicists should still search for evidence of the Standard Model and supersymmetry—she’s not opposed to those theories. But they should also go on “agnostic quests,” she says, where they don’t go looking for something in particular. Instead, they should just look, and see what they find.But some physicists may be reluctant to give up their beautiful theories, even if the data dictates they should. For example, while the Large Hadron Collider has so far failed to show evidence of supersymmetry, many have essentially said that the collision wasn’t powerful enough or that some small modifications are all that’s needed to fit the theory they love with the data they gathered.

“Supersymmetry has been around since 1974, for 42 years, and it doesn’t really have any evidence that it’s there. But people really bet their careers on this,” Gleiser explains. “Many physicists have spent 40 years working on this, which is basically their whole professional life.”

That may change in in ten years or so, he says, when further advances to the LHC could force the hangers-on to let go if the data they need doesn’t materialize. “If we don’t find evidence, people who still stick to it after that are doing it as a philosophical practice,” he says.

Of course, it’s certainly possible that the answers to life, the universe, and everything will be elegant. To physicists like Demers and Gleiser, that’s not the problem: The problem is the a priori assumption that it is so. And if the foundational principles of the universe turn out to be ugly or tedious, perhaps we can find the beauty beneath the mess.

Not as black as once thought?

Stephen Hawking says escape from a black hole is possible — kind of

Ali Sundermier 


Stephen Hawking has shaken up our understanding of black holes by announcing that actually, it might be possible to escape these greedy pits of spacetime.

"They are not the eternal prisons they were once thought," Dr. Hawking said in a talk last year. "If you feel you are trapped in a black hole, don't give up. There is a way out."

He posted his paper on arXiv, a pre-peer review site, in January. This month, the paper was finally published in the peer-reviewed journal Physical Review Letters.

Hawking's assertion that it is, in fact, possible to escape a black hole will not only transform our definition of them, it will also solve a longstanding riddle about what happens to the information that these mysterious space beasts devour.

Hawking radiation
A black hole is a monstrous warping of the fabric of space and time. It's a region where matter is almost infinitely compacted, and anything that gets too close is indiscriminately devoured.

And for a while, we believed that nothing - not even light - could escape its intense gravity.

In the 1970s, Stephen Hawking proposed that some things actually do wiggle free from the grasp of a black hole. When a black hole gulps up part of a particle-antiparticle pair, one half might escape, carrying away a tiny bit of the black hole's energy in the form of Hawking radiation.

Over time, a black hole will slowly leak out this energy, evaporating until it inevitably vanishes. Nothing would be left of the black hole except this mysterious radiation.


But then, what happens to all the information that swirled helplessly past the black hole's point of no return?
The information paradox
Until recently, Hawking believed that this information was lost forever. But our current understanding of modern physics states that it should always be possible to reverse time and piece together the present from the past like a puzzle.

"The Universe, like a kind of supercomputer, is supposed to be able to keep track of whether one car was a green pickup truck and the other was a red Porsche, or whether one was made of matter and the other antimatter," the New York Times reports. "These things may be destroyed, but their 'information' - their essential physical attributes - should live forever."

So if this is the case, all of the information inside the black hole should actually be preserved somehow. And if not, that means that black holes disobey the laws of modern physics. Then what's to say that other things don't do the same? That means that our memories might not be real: the "past" might be an illusion.


This is called the black hole information paradox, and it's been confounding scientists for decades. But Hawking thinks he might be on track to finding a solution to this.
'Hairy' black holes
Up until now, scientists thought that black holes were bald. But Hawking says that black holes might actually be surrounded by halos of 'soft hair,' Science Alert reports. This peach fuzz would preserve all the information of everything that ever fell into the black hole.

"That pattern, like the pixels on your iPhone or the wavy grooves in a vinyl record, contains information about what has passed through the horizon and disappeared," the New York Times reports.

But that doesn't mean you can dive headfirst into a black hole and expect to make it out alive. What's actually preserved is your information, not your physical body. And it doesn't have to be preserved intact, it can be all jumbled up beyond repair.


It's kind of like burning a book, the New York Times reports. The book might be reduced to nothing but smoke and ashes, but "with the right calculations, you should be able reconstruct the patterns of ink, the text."