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Monday, 21 March 2016

The appearance of evenhandedness?

Larry Moran -- Voice of Reason


The salmon vs. Darwin



Another Fine-Tuned Mechanism Gets Salmon Home


Evolution News & Views March


What is carbonic anhydrase and why does it matter? The presence of this enzyme in salmon hearts points to another case of intelligent design in these remarkable fish that were depicted in Illustra Media's film Living Waters. News via the Journal of Experimental Biology explains the challenge salmon face swimming upstream:
Fish plumbing is contrary. As the heart is the last organ that blood passes through before it returns to the gills, and with little direct blood supply to the ceaselessly contracting muscle, there are occasions when it could be on the verge of failure. 'We know this can happen under certain conditions like exhaustive exercise in combination with hypoxia or elevated water temperature', says Sarah Alderman from the University of Guelph, Canada. Added to the challenge of keeping the heart supplied with oxygen, Alderman explains that the haemoglobin that carries oxygen in fish blood is finely tuned to blood pH: the more acidic the red blood cells, the less able haemoglobin is to carry oxygen, which could prevent the red blood cells of exercising fish from picking up oxygen at the gills if they didn't have an effective pump to remove acid from the cells and restore the pH balance. [Emphasis added.]
Here we see a double challenge the salmon faces. It has to avoid excess acid so that the hemoglobin can carry oxygen, and it has to get the oxygen all the way from the gills through its entire body to the heart. Here's where carbonic anhydrase comes to the rescue:
But Alderman and her colleagues, Till Harter, Tony Farrell and Colin Brauner from the University of British Columbia, Canada, also knew that fish can take advantage of a sudden drop in red blood cell pH to release oxygen rapidly at tissues -- such as red muscle and the retina -- when required urgently. An enzyme called carbonic anhydrase -- which combines CO2 and water to produce bicarbonate and acidic protons, and vice versa -- lies at the heart of this mechanism. Normally there is no carbonic anhydrase in blood plasma; however, the enzyme has been found in salmon red muscle capillaries, where it facilitates the reaction of protons -- that have been extruded from the red blood cell -- with bicarbonate to produce CO2, which then diffuses back into the red blood cell. The CO2 is then converted back into bicarbonate and protons in the blood cell, causing the pH to plummet and release a burst of O2 from the haemoglobin. Could salmon take advantage of this mechanism to boost oxygen supplies to the heart when the animals are working full outPossibly, but only if carbonic anhydrase was accessible to blood passing through the heart.What is carbonic anhydrase and why does it matter? The presence of this enzyme in salmon hearts points to another case of intelligent design in these remarkable fish that were depicted in Illustra Media's film Living Waters. News via the Journal of Experimental Biology explains the challenge salmon face swimming upstream:
Fish plumbing is contrary. As the heart is the last organ that blood passes through before it returns to the gills, and with little direct blood supply to the ceaselessly contracting muscle, there are occasions when it could be on the verge of failure. 'We know this can happen under certain conditions like exhaustive exercise in combination with hypoxia or elevated water temperature', says Sarah Alderman from the University of Guelph, Canada. Added to the challenge of keeping the heart supplied with oxygen, Alderman explains that the haemoglobin that carries oxygen in fish blood is finely tuned to blood pH: the more acidic the red blood cells, the less able haemoglobin is to carry oxygen, which could prevent the red blood cells of exercising fish from picking up oxygen at the gills if they didn't have an effective pump to remove acid from the cells and restore the pH balance. [Emphasis added.]
Here we see a double challenge the salmon faces. It has to avoid excess acid so that the hemoglobin can carry oxygen, and it has to get the oxygen all the way from the gills through its entire body to the heart. Here's where carbonic anhydrase comes to the rescue:
But Alderman and her colleagues, Till Harter, Tony Farrell and Colin Brauner from the University of British Columbia, Canada, also knew that fish can take advantage of a sudden drop in red blood cell pH to release oxygen rapidly at tissues -- such as red muscle and the retina -- when required urgently. An enzyme called carbonic anhydrase -- which combines CO2 and water to produce bicarbonate and acidic protons, and vice versa -- lies at the heart of this mechanism. Normally there is no carbonic anhydrase in blood plasma; however, the enzyme has been found in salmon red muscle capillaries, where it facilitates the reaction of protons -- that have been extruded from the red blood cell -- with bicarbonate to produce CO2, which then diffuses back into the red blood cell. The CO2 is then converted back into bicarbonate and protons in the blood cell, causing the pH to plummet and release a burst of O2 from the haemoglobin. Could salmon take advantage of this mechanism to boost oxygen supplies to the heart when the animals are working full outPossibly, but only if carbonic anhydrase was accessible to blood passing through the heart.
Well, what do you know! That's what Alderman's team found: the enzyme is present on the surface of the heart chambers. Using the heart itself as their "reaction vessel," they were able to see the pH plummet as the enzymes went into gear. 
Working closely together, the duo painstakingly developed a technique where they could measure the pH in the beating heart with pH probes that were thinner than a human hair. Eventually, the duo's persistence paid off and the pH in the heart plummeted as they fed CO2 into the pulsating chambers. And when they added a carbonic anhydrase inhibitor (produced by Claudia Supuran) to the fluid, the pH fall slowed dramatically. Carbonic anhydrase was responsible for the drop in pH.
The Protein Data Bank 101 website shows pictures of this enzyme and describes its mode of action. 
An enzyme present in red blood cells, carbonic anhydraseaids in the conversion of carbon dioxide to carbonic acid and bicarbonate ions. When red blood cells reach the lungs, the same enzyme helps to convert the bicarbonate ions back to carbon dioxide, which we breathe out. Although these reactions can occur even without the enzyme, carbonic anhydrase can increase the rate of these conversions up to a million fold.
There's an evolutionary conundrum about this enzyme: functional equivalence without sequence similarity:
This ancient enzyme has three distinct classes (called alpha, beta and gamma carbonic anhydrase). Members of these different classes share very little sequence or structural similarity, yet they all perform the same function and require a zinc ion at the active site. Carbonic anhydrase from mammals belong to the alpha class, the plant enzymes belong to the beta class, while the enzyme from methane-producing bacteria that grow in hot springs forms the gamma class. Thus it is apparent that these enzyme classes have evolved independently to create a similar enzyme active site.
Further complicating the picture, there are different forms of the enzymes depending on the tissue or cellular compartment they are located in. These allow fine tuning of the enzyme's activity: "Thus isozymes found in some muscle fibers have low enzyme activity compared to that secreted by salivary glands," in the case of mammals.Carbonic anhydrase (CA) was the first enzyme found to contain zinc, abiochemistry textbook says; now, hundreds are known. Zinc and other metals are often essential for function in metalloenzymes. The PDB-101 article explains,
Zinc is the key to this enzyme reaction. The water bound to the zinc ion is actually broken down to a proton and hydroxyl ion. Since zinc is a positively charged ion, it stabilizes the negatively charged hydroxyl ion so that it is ready to attack the carbon dioxide.
It's not surprising that this enzyme is present in the salmon, since it exists in all three domains of life. What's amazing is that the salmon's heart is studded with these enzymes that are "at the ready" when the large fish is fighting with all its might to leap above cascades and waterfalls, facing daunting challenges without the benefit of food. (Living Waters says, "The sockeye are so focused on their objective that after leaving the ocean, they do not eat again.")
If the pH dropped too early as the blood travels through the salmon's body, it would be less able to carry its precious oxygen cargo. But right when it is needed during that Olympic high jump over a waterfall or away from a hungry bear, the fish uses its CA enzymes in its heart to drop the pH and release the oxygen it needs. The spent blood then travels to the gills to load up with more oxygen. In the original paper in the Journal of Experimental Biology, the authors summarize what they found:
Combined, these results support our hypothesis of thepresence of an enhanced oxygen delivery system in the lumen of a salmonid heart, which could help support oxygen delivery when the oxygen content of venous blood becomes greatly reduced, such as after burst exercise and duringenvironmental hypoxia.
How many independent systems do we see at work in the remarkable migration of the salmon? The fish has a built-in map of its destination. It has the ability to memorize waypoints by smell. It can navigate by the earth's magnetic field. It has a sixth sense, the lateral line. It can distinguish odors by parts per trillion. Each of its body systems contain thousands of molecular machines like carbonic anhydrase that are located just where they need to be, doing what they need to do to support the whole organism.
If any one of these systems is a testament to intelligent design, how much more the composite? The only fish story here is the notion that all this came together by unguided natural processes -- sheer dumb luck.


Thursday, 17 March 2016

On taking on big science's gatekeepers.

Is There a Scientific Establishment?

Yet more on pre evolutionary design.

Collective Motion: A New Level of Design Found in Proteins

On Charles Darwin and Rube Goldberg

My Debate with Michael Ruse -- Evolution as a Rube Goldberg Machine

Monday, 14 March 2016

On the hunt for the biggest cryptid of them all.

Are Black Holes Real?

An Earth-Sized Telescope

That’s where the EHT comes in. Since the EHT first started taking data, it has been building its telescope roster, and with each new member, it gets closer to making the first true image of a black hole shadow.
The EHT is like an all-star team of telescopes: Most days, its millimeter-wave dishes run their own experiments independently, but for one or two weeks a year, they team up to become the EHT, taking new data and running tests during the brief window when astronomers can expect clear weather at sites from Hawaii to Europe to the South Pole.
“It sounds too good to be true that you just drop telescopes around the world and ‘poof!’ you have an Earth-sized telescope,” says Avery Broderick, a theoretical astrophysicist at University of Waterloo and the Perimeter Institute. And in a way, it is. The EHT doesn’t make pictures. Instead, it turns out a kind of mathematical cipher called a Fourier transform, which is like the graphic equalizer on your stereo: it divvies up the incoming signal, whether its an image of space or a piece of music, into the different frequencies that make it up and tells you how much power is stored in each frequency. So far, the EHT has only given astronomers a look at a few scattered pixels of the Fourier transform. When they compare those pixels to what they expect to see in the case of a true black hole, they find a good match. But the job is like trying to figure out whether you’re listening to Beethoven or the Beastie Boys based only on a few slivers of the graphic equalizer curve.
Now, the EHT is about to add a superstar player: the Atacama Large Millimeter Array, a telescope made up of 66 high-precision dishes sited 16,000 feet above sea level in Chile’s clear, dry Atacama desert. With ALMA on board, the EHT will finally be able to make the leap from fitting models to seeing a complete picture of the black hole’s shadow. EHT astronomers are now rounding up time at all of the telescopes so that they can take new data and assemble that first coveted image in 2017.
And if they don’t see what they expect? It could mean that the black hole isn’t really a black hole at all.
That would come as a relief to many theorists. Black holes are mothers of cosmic paradox, keeping physicists up at night with the puzzles they present: Do black holes really destroy information? Do they really contain infinitely dense points called singularities? Black holes are also the battlefield on which general relativity and quantum mechanics clash most dramatically. If it turns out that they don’t actually exist, some physicists might sleep a little better.
But if they’re not black holes, then what could they be? One possibility is that they are dark stars made up of bosons, subatomic particles that, unlike more familiar electrons and protons, obey strange rules that allow more than one of them to be in the same place at the same time. Boson stars are highly speculative—astronomers have never seen one, as far as they know—but theorists like Vitor Cardoso, a professor of physics at Técnico in Lisbon and a distinguished visiting researcher at Sapienza University of Rome, hypothesize that some or all of the objects we think are supermassive black holes could actually be boson stars in disguise.
Physicists classify particles into two different categories: fermions, which include protons, electrons, neutrons, and their components; and bosons, like photons (light particles), gluons, and Higgs particles. Every star that we’ve ever seen shining is dominated by fermions. But, Cardoso says, given a starting environment rich in bosons, bosons could “clump” together gravitationally to form stars, just as fermions do. The early universe might have had a high enough density of bosons for boson stars to form.
But not every boson is a suitable building block for a boson star. Gravity won’t hold together a clump of massless photons, for instance. Higgs particles are massive enough to be bound together by gravity, but they aren’t stable—they only exist for tiny fraction of a second before decaying away. Theorists have speculated about ways to stabilize Higgs particles, but Cardoso is more intrigued by the prospect that other, yet-undiscovered heavy bosons, like axions, could make up boson stars. In fact, some physicists hypothesize that massive bosons like these could be responsible for dark matter—meaning that boson stars wouldn’t just be a solution to the riddle of black holes, they could also tell us what, exactly, dark matter is.

Gravastars

Boson stars aren’t the only black hole doppelgänger that theorists have dreamed up. In 2001, researchers proposed an even more speculative oddity called a gravastar. In the gravastar model, as a would-be black hole collapses under its own weight, extreme gravity combines with quantum fluctuations that are constantly jiggling through space to create a bubble of exotic spacetime that halts the cave-in.
Theorists don’t really know what’s inside that bubble, which is both good and bad news for gravastars: Good news because it gives theorists the flexibility to revise the model as new observations come in, bad news because scientists are rightly skeptical of any model that can be patched up to match the data.
When the data does come in, physicists have a checklist of sorts that should help them know which of the three—black hole, boson star, or gravastar—they’re looking at. A gravastar should have a bright surface that’s distinguishable from the glowing ring predicted to loop around a black hole. Meanwhile, if the object at the center of the Milky Way is actually a boson star, Cardoso predicts, it will look more like a “normal” star. “Black holes are black all the way through,” Cardoso says. “If really the object is a boson star, then the luminous material can in principle pile up at its center. A bright spot should be detected right at the center of the object.”

A New View

Most physicists have placed their bets on Saggitarius A* and other candidates being black holes, though. Boson stars and gravastars already have a few strikes against them. First, when it comes to scientific credibility, black holes have a major head start. Astronomers have a solid understanding of the process by which black holes form and have direct evidence that other ultra-dense objects, like white dwarfs and neutron stars, which could merge to form black holes, really do exist. The alternatives are more speculative on every count.
Furthermore, Broderick says, astronomers have looked for the telltale signature of boson stars and gravastars at the center of the Milky Way—and haven’t found it. “The stuff raining down on the object will give up all its kinetic energy—all the gravitational binding energy tied up in the kinetic energy of its fall—resulting in a thermal bump in the spectrum,” Broderick says —that is, a signature spike in infrared emission. In 2009, astrophysicists reported that they had found no such bump coming from Sagittarius A*, and in 2015, they announced that it was missing from the nearby massive galaxy M87, too.
Cardoso doesn’t see this as a death-knell for the boson star model, though. “The field that makes up the boson star hardly interacts with matter,” he says. To ordinary matter, the surface of a boson star would feel like frothed milk. “We do not yet have a complete model of how these objects accrete luminous matter,” Cardoso says, “so I think that it’s fair to say that this is still an open question.” He is less optimistic about gravastars, which he describes as “artificial constructs” that are likely ruled out by the latest observations.
As the LIGO experiment gathers more data, theorists will get more opportunities to test their exotic hypotheses with gravitational waves. As two massive objects—say, a supermassive black hole and a star—spiral toward each other on the way toward a collision, gravitational waves carry away the energy of their motion. If one member of the spiraling pair is a black hole, the gravitational wave signal will cut off abruptly as the star passes through the black hole’s event horizon. “It gives rise to a very characteristic ringdown in the final stages of the inspiral,” Cardoso says. Because the alternative models have no such horizon, the gravitational wave signal would keep on reverberating.
Most astronomers believe that the waves LIGO detected were given off by the collision of two black holes, but Cardoso thinks that boson stars shouldn’t be ruled out just yet. “The data is, in principle, compatible with the two colliding objects being each a boson star,” he says. The end result, though, is probably a black hole “because it rings down very fast.”
LIGO is not designed to pick up signals at the frequency at which supermassive objects like Sagittarius A* are expected to “ring.” (LIGO is tuned to recognize gravitational waves from smaller black holes and dense stars like neutron stars.) But supermassive black holes and boson stars are in the sweet spot for the planned space-based gravitational wave telescope eLISA (the Evolved Laser Interferometer Space Antenna), slated for launch in 2034. “To confirm or rule out boson stars entirely, we need ‘louder’ observations,” Cardoso says. “EHT or eLISA are probably our best bet.”

Taking the Pulse

In the meantime, astronomers could measure waves from these extremely massive objects by precisely clocking the arrival times of radio pulses from a special class of dead stars called pulsars. If astronomers spot pulses arriving systematically off-beat, that could be a sign that the space they’ve been traveling across is being stretched and squeezed by gravitational waves. Three collaborations—NANOGrav in North America, the European Pulsar Timing Array, and the Parkes Pulsar Timing Array in Australia—are already scanning for these signals using radio telescopes scattered around the globe.
To Broderick, though, the big question isn’t which model will win out, it’s whether these new experiments can find a flaw in general relativity. “For 100 years, general relativity has been enormously successful, and there’s no hint of where it breaks,” he says. Yet general relativity and quantum mechanics, which appears equally shatterproof, are fundamentally incompatible. Somewhere, one or both must break down. But where? Boson stars and gravastars might not be the answer. Still, exploring these exotic possibilities forces physicists to ask the questions that might lead them to something even more profound.
“We expect that general relativity will pass the EHT’s tests with flying colors,” Broderick says. “But the great hope is that it won’t, that we’ll finally find the loose thread to pull on that will unravel the next great revolution in physics.”

Immortality on the cheap?

Your Personality Uploaded to a Robot Wouldn't Be "You"