Butterflies for design

Defects on Purpose Make Butterfly Wings Shine
Evolution News & Views

Illustra Media's film Metamorphosis: The Beauty and Design of Butterflies showcased many dazzling butterfly wings, but didn't have time to discuss the secrets behind those colors. Scientists have long identified the source of the colors as not coming from pigments, but from light interference patterns at the nanoscale. A regularly repeating 3-D structure called a "photonic crystal" reinforces some colors and interferes with others. That's how the dazzling blue of a Morpho butterfly is produced: crystals in the scales of the wings play tricks with light. Grind up the scales and you won't get a pile of blue dust, just brown or gray material. It's the highly-organized nanostructure that generates the brilliant blue of the living insect flapping in the sunlight.

But how does a butterfly grow those crystals? Something has to guide them into position as the wing develops in the chrysalis. Metamorphosis showed the wings taking shape but only touched on the complexity involved. Now, scientists at the University of California, San Diego, have shined some X-ray light onto the process. In a paper in the AAAS open-access journal Science Advances, they used X-ray diffraction to examine the properties of individual scales.

Many organisms in nature have evolved sophisticated cellular mechanisms to produce photonic nanostructures and, in recent years, diverse crystalline symmetries have been identified and related to macroscopic optical properties. However, because we know little about the distributions of domain sizes, the orientations of photonic crystals, and the nature of defects in these structures, we are unable to make the connection between the nanostructure and its development and functionality. [Emphasis added.]
As Illustra showed with electron micrographs, the wings are composed of scales that overlap like shingles on a roof. The scales, made of the protein chitin, begin as individual cells. The cells must manufacture chitin and place it in the right orientation. The scientists found that the crystals of chitin are strongly oriented normal to the plane of the scale (i.e., perpendicular). The crystals apparently grow from the edges of the cell toward the middle, where they meet at domain boundaries.

We report on nondestructive studies of the morphology of chitinous photonic crystals in butterfly wing scales. Using spatially and angularly resolved x-ray diffraction, we find that the domains are highly oriented with respect to the whole scale, indicating growth from scale boundaries. X-ray coherent diffractive imaging reveals two types of crystalline domain interfaces: abrupt changes between domains emerging from distinct nucleation sites and smooth transitions with edge dislocations presumably resulting from internal stresses during nanostructure development. Our study of the scale structure reveals new aspects of photonic crystal growth in butterfly wings and shows their similarity to block copolymer materials. It opens new avenues to exploration of fundamental processes underlying the growth of biological photonic nanostructures in a variety of species.
The domain boundaries, they found, are randomly oriented, yet each crystal is highly organized within each domain. "The photonic crystal is reminiscent of a thin polycrystalline film, with the domains being highly oriented in the direction normal to the scale boundary, which suggests a layer-by-layer crystal growth process starting at the cell membrane," the paper says. The boundaries, furthermore, are "extremely sharp," on the order of one unit cell. "The preferred orientation of the domains, normal to the scale plane, is quite remarkable and is consistent with crystal nucleation at the scale boundary and crystal growth outward." This gives the researchers some ideas about how to manufacture artificial photonic crystals. Again, it's remarkable as well as intriguing:

The discovery of the edge dislocations in the biological photonic crystals is particularly remarkable because artificially manufactured topological defects in photonic crystals lead to interesting optical properties such as Anderson localization of light. Two intriguing questions are whether nature-engineered defects for a particular purpose and whether mimicking similar growth conditions allows for controlled manufacturing of defects in artificial photonic structures.
"Nature-engineered defects for a particular purpose"? Can it be that defects have a function? Indeed they can. The press release from UCSD describes why scientists sometimes "engineer" defects to improve their strength and function:

These crystal dislocations or defects occur, the researchers say, when an otherwise perfectly periodic crystal lattice slips by one row of atoms. "Defects may have a negative connotation, but they are actually very useful in improving materials," explains Singer. "For example, blacksmiths have learned over centuries how to purposefully induce defects into metals to make them stronger. 'Defect engineering' is also a focus for many research teams and companies working in the semiconductor field. In photonic crystals, defects can enhance light-scattering properties through an effect called light localization."
The bug is a feature. Defects consisting of random domain boundaries in the butterfly scale actually enhance the light-scattering properties. Post-doc Adrej Singer describes "tiny crystal irregularities that may enhance light-scattering properties, making the butterfly wings appear brighter."

It looks like we will have to add "defect engineering" to our list of intelligent design sciences in action. How strange that the butterfly figured this out before mankind did:

"In the evolution of butterfly wings," he adds, "it appears nature learned how to engineer these defects on purpose."

We can dismiss the references to evolution. Nature does not learn to engineer things for a purpose. Organisms do not evolve sophisticated cellular mechanisms in order to produce optical properties. Minds do that. If our best optical engineers look to butterflies for inspiration to improve their manufacturing, what does that tell you? It implies that engineers do not employ unguided, aimless Darwinian processes of chance. They use intelligent design. By arguing from lesser to greater, we explain what goes on in the "black box" of the chrysalis, where "remarkable" and "sophisticated" engineering generates structure, function, and beauty.

Nature's navigators for design

Oh, Deer: Mammals Use Magnetic Navigation, Too
Evolution News & Views

You're in a herd of deer when a mountain lion is seen approaching. What's your safest retreat? Is it to run directly away? Is it to scatter in all directions? Or is it to run according to a predetermined orientation?

Scientists in Europe were intrigued that roe deer seem to orient in a north-south direction when grazing and when startled, so they decided to investigate. What they uncovered was a novel case of magnetic navigation in the animal kingdom. A Springer news item says:

Why do deer in a group, when startled, suddenly bolt away together and never collide with each other? It's because these deer have an inner compass that allows them to follow a certain direction in order to make their escape. Their getaway is almost always along a north-south axis, thanks to their ability to sense the magnetic field, says Petr Obleser of the Czech University of Life Sciences in the Czech Republic. He and Hynek Burda of the University Duisburg-Essen, Germany, are lead authors of a study in Springer's journal Behavioral Ecology and Sociobiology. [Emphasis added.]
This is a first for large mammals. Illustra Media has shown in Metamorphosis how butterflies use the magnetic field to get to Mexico. They showed in Flight how Arctic Terns navigate from pole to pole, and in Living Waters how salmon and sea turtles use magnetosensing in their long-distance migrations. Suggestions of magnetosensing had been reported for bats and mole rats, but large mammals like deer -- who would have thought they use an inner compass for everyday safety?

One of the authors of the new paper, Dr. Hynek Burda of University of Duisburg-Essen, had contributed to a 2008 study published in PNAS that used Google Earth to find cattle and deer preferentially orienting on a north-south axis. BBC News commented on this finding, saying that this phenomenon "has apparently gone unnoticed by herdsmen and hunters for thousands of years." At the time, the function of this orientation was unknown. One biologist remarked, "We need to think about some really fundamental things that this sensory ability provides in animals."

Since then, Obleser and Burda monitored roe deer from April to August 2014. This species of deer tends to congregate in flat areas on agricultural land, making them easy to observe with binoculars. From 60 locations, they recorded data on the deer's orientation at rest and when startled, monitoring 188 escape behaviors under a variety of conditions.

It was found that roe deer tend to align their bodies along the north-south axis when grazing. When startled, the animals generally fled away from observers. They did not merely make their getaway in the direction directly opposite to the approaching threat, but consistently did so north- or southwards. In fact, they seemed to actively avoid escaping westwards and eastwards, says Obleser. Wind direction or the position of the sun had no influence on the direction of their escape route.
The authors took note of the time of day, odor, wind and other factors; the magnetic orientation still prevailed. If a forest shelter was nearby, however, the herd could override the magnetic tendency and escape directly toward the shelter.

Is there a reason for this behavior? The north-south escape strategy was especially pronounced when the deer were congregated in groups. The authors feel the strategy helps the deer avoid collisions that would be more likely to occur if each animal took off in a random direction. Other possible functions include keeping group cohesion, guiding the deer get back to the previous grazing spot after the danger has subsided, and helping a mother find its fawn it left hiding in the grass.

For the strategy to work, an animal needs hardware and software programmed into its body and brain.

The researchers believe that the tendency of deer to align their bodies with respect to a north-south magnetic field line confirm that they are magnetosensitive and magnetoreceptive. This assists the animals to "read" and comprehend the mental maps they hold of the landscapes they occupy.
The authors did not speculate about the predator. What if it has a compass, too? What if it knows the strategy? Just speculating, it would seem the deer still have an advantage. The lion can't run north and south at the same time, and would have no way of knowing in advance which direction the deer will choose to run. If they split directions, the deer in both groups would still have some safety in numbers. Most of the advantages would appear to accrue to the prey; the wide angle of 180 degrees "would maximize the distance between the animal and the danger," the authors say.

The authors feel this pioneering study points to magnetosensing being common in mammals. It might even reside in us humans!

This is the first study of escape behavior in animals which considers also the role of absolute compass direction. Our findings confirm existence of magnetic alignment and thus magnetosensitivity in the roe deer and provide first evidence for its role as the so-called direction indicator in control of escape behavior in roe deer in particular and in mammals in general. Our results make the speculations more plausible that the magnetic alignment helps to organize and read the mental (cognitive) map of space. (In analogy, humans are more efficient in reading and commenting the map, if it is held in an accustomed direction: with north pointing upwards and if the person aligns with the map and with the visible landmarks.)
Many of us can probably relate to that: facing north and holding a map to try to find our way around when vacationing in an unfamiliar city. It's just by "analogy" the authors say we might also have directional sensing. That deserves further study. Could a latent human ability for magnetosensing be trained? Could it augment orienteering by the sun and the stars? Fascinating thought. Maybe it will put compass makers out of business.

In the new open-access paper, the authors make no use of evolutionary theory to explain the coordinated escape strategy of roe deer with its requirements for magnetosensing equipment. There's no mention of natural selection, fitness or phylogeny. Why would that be, if nothing in biology makes sense except in the light of evolution?

As design theorists, we can identify prerequisites for magnetically-based escape strategy in roe deer and other mammals:

Construction of crystals of iron or protein that respond to the earth's magnetic field.

Neurons that can sense the response of the crystals.

Brain receptors that can process the neural inputs and interpret them.

Mental maps to place the interpretations in a regional context.

Brain regions that can coordinate the magnetic data with other sensory data.

Stored instincts to activate body systems to respond appropriately.

Genes to encode the construction of all the above.

Epigenetic systems to guide the development of the genetic information.

That's a bigger parts list than in the classic mousetrap model of irreducible complexity. In fact, each item on the list could itself be called irreducibly complex.

Needless to say, magnetosensation presupposes a planet with a strong magnetic field. Of the rocky planets in our solar system, the Earth is unique in that regard; Mercury's magnetic field is too weak, Venus has none, and Mars has only patches of magnetism. Many regard a strong magnetic field as a requirement for habitability, to act as a shield from stellar and cosmic radiation. It's one of at least twenty improbable factors listed in The Privileged Planet that point to fine-tuning for habitability.


Intelligence is the only cause we know that is capable of arranging multiple independent factors for a function. The design inference strengthens with the improbability or specified complexity of each factor. With Darwinian evolution apparently of no use in explaining why roe deer know how to escape along a north-south axis, an inference to intelligent design beckons.

Transhumanism's brave new world.

When Atheists Meet Creationism, You Get Creatheism
Brendan Dixon 

Creathiest: It is not a word that rolls easily off the tongue. But I am at a loss for one that better describes the atheists Daniel Jackson describes in a condescending post at The Spectator ("Atheists are embracing Gods and creationism").

No bleak darkness for these disbelievers. No existential angst enters their minds. No despair over the vast emptiness in which Earth floats, seemingly alone with life. Creathiests have the comforts of religion without the commitment of a creed. Post-humanity will bring an end to all ills. Eternal life arrives when we can upload ourselves into a machine. And Elon Musk admitted to a Creator when, a couple of weeks ago, he suggested that the odds of our living in a simulation to be "a billion to one."

Jackson writes:

Elon Musk, the billionaire inventor and entrepreneur, the twenty-first century's answer to Howard Hughes, believes we are living in a computer simulation.

...

His argument -- that, given the increasing pace of progress in computer technology, we will eventually be able to synthesise reality and consciousness -- is an abbreviated version of a 2003 paper by Nick Bostrom, a philosophy Professor at Oxford.

The paper suggests that if we aren't living in a simulation, civilisation will end before we are able to reach the 'posthuman' age. The detail and the terminology isn't important; the idea is bunkum, the sort of thing that's fun to think about on psilocybin, but not much use otherwise.

What's interesting is the way in which atheists are embracing the idea -- or at least the possibility -- of creationism. If we are living in a simulation, someone or something had to create it.

It brings a kind of pleasure to watch someone apparently without religion call attention to the religiosity of the supposedly irreligious devoted to demolishing religion. It is, truly, ironic.

After all, only the religiously devoted would shut down rational discussion over their creation myth: evolution by means of random change and natural selection. Why else would otherwise very smart, well-read, articulate people fall for and promote the silly, unfounded "just so" stories with which evolutionary research is generously stocked? What else can explain the consistent misrepresentation of alternative views and the refusal to engage counterarguments? Only because it serves creathiests as their creation myth is evolution held with such irrational passion against the evidence of design.

The same fervor promotes the ungrounded faith in a coming Singularity, when computers will transcend us, perhaps leading to our demise. It is not a logical result drawn from the data. It is a wild extrapolation that fails to admit the vast amount we don't know and the limits of our technological successes. It is not a short leap from a pattern-matching, game-playing machine -- such as Google's AlphaGo -- to awe-inspiring AI super-intelligence. It is a blind leap of religious faith.


For everyone engaged in the evolution debate, a calm, rational discussion would be best. Religious devotion, no matter how sincere, cannot alter the evidence or up-end the challenge. Let's leave our a priori commitments behind and look closely at what we're seeing, following the evidence wherever it leads.

Darwinism Vs.the real world XXXIV

The Kidney's Irreducibly Complex Systems
Howard Glicksman

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind,Evolution News is delighted to offer this series, "The Designed Body." For the complete series, see here. Dr. Glicksman practices palliative medicine for a hospice organization.

If a unicellular organism is like a microscopic island that can get what it needs and get rid of what it doesn't need through its surrounding water, the body, consisting of trillions of cells, is like a huge land mass that must move what it needs and doesn't need in and out of its interior so it can survive. The cells of the body need the right amount of oxygen and carbon dioxide to work right, so the lungs, at the direction of the respiratory center in the brain, take care of that.

They also need to have the right amount of water, sugar, salt, and other nutrients, which is taken care of by the gastrointestinal system, at the direction of the nervous system. And to transport what it needs into and out of its continental mass of cells, the body uses the cardiovascular system to move blood containing these chemicals to where they need to go so they can be on- or off-loaded.

Evolutionary biologists are good at imagining how the molecular structures for life may have come about, as long as they don't have to reckon with the objective standards those structures must meet to keep the cells and the body alive. To survive within the laws of nature, the cell must be able to control its volume and chemical content. So too, for the body to survive within the laws of nature, it must also control its volume and chemical content.

Stephen Meyer has described the complexity of the cell, the numerous systems within it, and what they must do for it to work properly. But each cell, no matter where it is located, is blind to the overall needs of the body. We have seen this in how the water content and blood levels of sodium, potassium, calcium, and nitrogen (protein) affect organ function and body survival. The common pathway the body uses to control all of these chemical parameters leads through the kidney.

The functioning unit in the kidney is the nephron, and there are about one million per kidney. The nephron filters fluid out of the blood by squeezing it through a specialized capillary system called the glomerulus. The kidneys filter about 7.5 liters of fluid, with its chemical content, out of circulation per hour. This fluid enters tubules, which wind their way through the tissue of the kidney on its way to becoming urine. As the fluid moves along the cells lining, the tubules reabsorb or secrete different chemicals to the degree that is necessary for body survival.

The body is always taking in different amounts of various chemicals through the gastrointestinal system, while simultaneously losing them through metabolism. Therefore, the ongoing chemical needs of the body are always in flux and the kidneys must constantly adjust to these changes by changing how much of a given chemical they keep or release from the body through the urine. We will look at the five vital chemicals mentioned above, water, sodium, potassium, calcium, and nitrogen, and explain how the body, through the kidneys, adjusts them to stay alive.

Evolutionary biologists may be good at describing how kidneys look and imagining how they evolved, but they never seem to mention how they work or what they would have had to do to keep the transitional organisms they belonged to alive.

Water is vital for life and is the commonest molecule in the body, making up sixty percent of its weight. Two-thirds of the body's water is inside the cells and one third is outside, either between the cells or inside the blood. If the body loses one-quarter of its water (10 liters), it dies. Since the kidneys filter 7.5 liters of fluid per hour this means that if they didn't take back any of it, the body would die in about ninety minutes.

Water can move freely in and out of the cell, so cell volume reflects the body's water content. In general, if the body's water content is below normal, then the volume of its cells will be below normal as well. The hypothalamus contains shrink-sensitive cells that can detect this drop in cell volume. These osmoreceptors react to worsening cell shrinkage by making more Anti-Diuretic Hormone (ADH) be released. ADH travels in the blood and attaches to specific receptors on certain tubules within the kidneys and tells them to bring more water back into the body from the urine in production. By using osmoreceptors in the brain, ADH, and its specific receptors on certain kidney tubules, the body is able to take of control of its water content.

Sodium is vital for life and dissolves in the body's water as an Na+ ion. The fluid outside the cells contains about ninety percent of the body's total sodium and is ten times more concentrated than the fluid inside the cells. Since water generally follows Na+ ions wherever they go in the body, this means that the relatively high concentration of sodium in the fluid outside the cells is responsible for not only its water content but also the blood volume. Much like water, if the body loses about one-quarter of its sodium, it dies. The amount of sodium in the blood is so high that the 7.5 liters of fluid the kidneys filter out per hour contains about one-half of the body's total sodium. If the kidneys didn't take back any of this filtered sodium, the body would die in about a half hour.

Since blood volume is dependent on water content and water content is dependent on sodium content, this means that the wall motion that takes place as blood flows into a blood vessel or chamber is a reflection of the body's sodium content. One set of sensors, called mechanoreceptors, detect this wall motion within the kidneys, where blood enters to be filtered, and another is in the walls of the atria. The sensory cells in the kidneys release a hormone, called renin. The amount of renin released is inversely related to how much wall motion the sensors detect. The more the walls stretch, indicating more blood volume, the less renin is sent out, and the less the walls stretch, indicating less volume, the more renin is sent out. In contrast, the atrial cells send out a hormone, called Atrial Natriuretic Peptide (ANP), in an amount that is directly related to how much wall motion they detect. The more the walls stretch, indicating more blood volume, the more ANP is sent out, and vice versa.

Renin results in the formation of a hormone called angiotensin II which binds to specific receptors in the adrenal glands and tells them to release another hormone called aldosterone. Aldosterone travels to the kidneys and attaches to specific receptors on the cells lining some of its tubules. This tells them to bring more sodium back into the body. So, the less blood volume, the more renin, resulting in more angiotensin II and aldosterone, and more sodium the kidneys reabsorb. In contrast, the more blood volume, the more ANP attaches to specific receptorson the same tubules in the kidneys and tells them to release more sodium. In other words, the effects of renin and ANP counterbalance each other. By using mechanoreceptors in the kidneys and atria, renin and ANP and specific aldosterone and ANP receptors on certain kidney tubules, the body is able to take of control of its sodium content.

Potassium is also vital for life and dissolves in the body's water as a K+ ion. The fluid inside the cells contains about ninety-eight percent of the body's total potassium and is over thirty times more concentrated than the fluid outside the cells. The relatively low K+ ion level in the fluid outside the cells must be maintained within a very narrow range to make sure the difference between the electrical charge inside and outside the cell allows for proper heart, nerve, and muscle function. The relative amount of potassium in the blood is a lot lower than it is for sodium, and if the kidneys did not bring any of it back from the 7.5 liters of fluid it filters per hour, the body would die in about a day.

The body uses sensors in specialized cells within the adrenal glands to detect the ratio between the K+ and Na+ ion concentration in the blood. If the ratio rises, due to an increase in K+ ion concentration or a decrease in Na+ ion concentration, these cells send out more aldosterone. Conversely, if the ratio drops, due to a decrease in K+ ion concentration or an increase in Na+ ion concentration, it sends out less aldosterone.

Aldosterone travels in the blood and attaches to specific receptors on the cells lining certain tubules in the kidneys and tells them to release K+ ions out through the urine and bring Na+ ions back in. More aldosterone, due to an increase in the ratio between K+ ions and Na+ ions, makes more K+ ions leave the body and more Na+ ions come back in. Less aldosterone, due to a decrease in this ratio, makes less K+ ions leave the body and less Na+ ions come back in. By using receptors that detect the ratio between K+ and Na+ ions in the adrenals and aldosterone and its specific receptor on certain tubules in the kidneys, the body is able to take control of its potassium content.

Calcium is vital for life and the bones of the body house over ninety-nine percent of its content. However, the remaining one percent is just as important for survival. Calcium dissolves in the body's water as Ca++ ions and its concentration in the blood is about ten thousand times more than within the cell. Besides creating the skeleton, bone also acts as a reservoir for the calcium needs of the body, which include heart, nervous, glandular, muscle function, and clotting. The total content of calcium is over one thousand milligrams and if the kidneys did not bring back any of it from the 7.5 liters of fluid that it filters per hour, the body would lose its entire supply in about two months.

The cells of the four parathyroid glands have sensors that can detect the calcium level in the blood. In response to a drop in serum calcium, they release more parathormone (PTH). PTH travels in the blood and not only makes the bone release more Ca++ ions into the circulation but tells the kidneys to activate Vitamin D so the gastrointestinal tract can absorb more calcium. It also attaches to specific receptors within the tubules and tells them to bring more calcium back into the body. By using calcium sensors, PTH, and its specific receptors in the kidneys, the body is able to take control of its calcium content.


Nitrogen is mainly present in the amino acids that make up the proteins of the body. Protein metabolism produces a highly toxic nitrogen-containing molecule called ammonia, which the liver converts into less toxic urea to be released from the body through the kidneys. The amount of fluid filtered by the glomeruli of the kidneys is called the Glomerular Filtration Rate (GFR) and is normally about 125 mL/min (7.5 liters/hr). The body's ability to keep its blood level of nitrogen-containing substances under control is directly related to its kidney function.

Especially in people with long-standing hypertension and diabetes, worsening kidney function causes the level of urea and other nitrogen-containing substances to rise. In fact, when the GFR is less than ten percent of normal, severe weakness, nausea, and confusion are common symptoms. In addition, there is often retention of sodium and water. This results in fluid build-up in the lungs, which in turn can cause shortness of breath and high levels of potassium, both of which can lead to cardiopulmonary arrest. It is at this time that a person may be considered for dialysis, which artificially cleans the blood of urea and other nitrogen-containing substances and stabilizes its water, sodium, and potassium levels.

The kidney may not be as sophisticated as the brain or the liver, but it definitely has a lot of roles to play when it comes to human life. Each of the control systems mentioned above is irreducibly complex in that all of the parts must be present for it to do its job. And to get the job done right so the body can survive within the laws of nature requires a natural survival capacity -- an inherent knowledge of what is required.

The word intelligence comes from the Latin words inter and lego which means to choose between, to choose one outcome from all possible outcomes. Most people would look at the complicated structure of the kidney and what it takes for the body to control its water content and blood levels of sodium, potassium, calcium, and nitrogen, and conclude that an intelligent agent, a mind, was at work here.


Funny thing about intelligence though; you must have it in order to detect it. One hopes, in the near future, students will learn the truth about how life really works, and not just how it looks, and with this knowledge see the inadequacy of neo-Darwinism as an explanation for biological origins.

universal common ancestry in the hot seat VII

The Placenta Problem: How Common Descent Fails
Ann Gauger 

Editor's note: For previous replies by Dr. Gauger to Dr. Torley in this series, see here, here, and here.

Philosopher Vincent Torley (and Washington University's Professor Josh Swamidass) have been trying to persuade me that common descent is the only rational view to affirm, the only intellectually consistent and respectable choice. What they don't seem to realize is that I see the evidence for common descent. I know its strength. The reason I doubt common descent is not because of the ways that it succeeds, but the ways that it fails.

Writing at Uncommon Descent, Torley poses the following challenge in "Consider the Opossum," thinking to trap me into either accepting the argument for common descent as the only evidence-based conclusion, or denying the evidence in order to escape the logic:

Do you accept that if hypothesis A readily explains an empirical fact F and hypothesis B does not, then F (taken by itself) constitutes scientific evidence for A over B? Or putting it another way, if a fact F is predicted by hypothesis A, and compatible with hypothesis B but not predicted by B, then do you agree that F constitutes scientific evidence for A over B? If not, why not?

Do I accept Torley's logic? Yes. Do I think common descent is explanatory (A) and design is not (B)? No. Do I think that common descent is predictive (A) and design not (B)? No. The reason is that the syllogisms cut both ways. Design is both explanatory and predictive, particularly when dealing with pattern breaking observations in biology, where common descent doesn't work as an explanation. Thus the onus of proof is not on design alone, as Professor Swamidass thinks, but on common descent as well.

Let me show you. According to the theory of common descent, all true mammals are supposed to have descended from a common ancestor with a placenta. This is a trait common to all mammals. However, it has been a puzzle for some time that placentas differ in the form they take among different mammalian clades.

In the year 2000, French researcher Thierry Heidmann and coworkers found that genes derived from endogenous retroviruses (ERVs) appear to have been coopted to perform an essential role in placental formation. These genes, which resemble the ERV envelope gene env, make a protein that originally promoted fusion of the virus with its host cell's membrane, but now acts to promote fusion of membranes between the embryo and the lining of the uterus. These "repurposed" proteins are called syncytins. They are essential for placental formation, yet are of independent origin in different kinds of mammals -- primates have one kind, mice another, rabbits, cows, and carnivores yet others. They are clade-specific. In fact, in 2015 a functional syncytin was found in several marsupials, extending the presence and essential function of the protein to all placental mammals examined. All syncytins are lineage-specific, meaning that each mammalian clade has its own syncytin, with a unique sequence and location in the genome. They must have inserted themselves (or been placed there) after the separation of the mammals into different clades! This means there must have been multiple independent acquisitions of these syncytins to participate in an essential process that is common to all mammals. Why should there be unique syncytins in each clade?

What we have to explain is the unique and independent group-specific cooption of syncytins for a function that is essential for placental development, a feature common to all mammalian groups. Six independent origins for the placenta! There is no evidence of a grand ancestral syncytin shared by all groups that was later replaced by other syncytins, so the common descent explanation of the placenta in mammals fails.

I repeat: distinct syncytins for cows, carnivores, rodents, primates, rabbits, and even tenrecs (a species thought to retain features of primitive mammals). We all recognize these clades based on their traits -- cows are different from carnivores, which are different from rodents, which are different from chimpanzees. Even nursery school children can tell the difference. And they are all thought to have descended from a common ancestor, the proto-mammal. Well, apparently, these well-defined clades of mammals make their placentas using analogous but distinct proteins. This perhaps explains why the placentas of each clade differ in their structures. But it flies in the face of the idea that all mammals are descended from a single kind of ancestor with a single kind of placenta.

I'll quote a review paper on syncytins. These are the people who discovered syncytins, and they have done great work. Yet they are forced into a corner by their own work and the idea of common descent. I have italicized the key features of syncytins that must be explained, and bolded the explanations offered:

... syncytins are 'new' genes encoding proteins derived from the envelope protein of endogenous retroviral elements that have been captured and domesticated on multiple occasions and independently in diverse mammalian species, through a process of convergent evolution. Knockout of syncytin genes in mice provided evidence for their absolute requirement for placenta development and embryo survival, via formation by cell-cell fusion of syncytial cell layers at the fetal-maternal interface. These genes of exogenous origin, acquired 'by chance' and yet still 'necessary' to carry out a basic function in placental mammals, may have been pivotal in the emergence of mammalian ancestors with a placenta from egg-laying animals via the capture of a founding retroviral env gene, subsequently replaced in the diverse mammalian lineages by new env-derived syncytin genes, each providing its host with a positive selective advantage.

Rather than postulating six independent, random capture events in placental development, they are now postulating at least one more, a founding syncytin leading to a primitive placenta, then the other syncytins to replace that one in each lineage. Each replacement must have had a clear selective advantage as time went on to make the replacement possible, and each must be the outcome of a random series of events. To say it again, the common descent prediction is that there must have been a founding syncytin in the first mammal with a placenta, or something else that functioned in syncytin's place, in order for the primitive placenta to arise and subsequently be passed to all mammalian clades. For which there is no evidence, and may never be.

Can common descent explain the unexpected observation of six independent origins for the placenta? No. Could it predict it? No.

Common design has an explanation, but not one that will be palatable to my interlocutors. The designer used the same idea six different times to produce the same outcome in six different "designs" (clades). That's another way of saying all these clades have the same outcome, the placenta, but achieved by independent uses of the same idea.

This can be stated as a general principle. Design predicts that we should find other examples where there are similar but independent ways of performing an essential function or of solving a common biological problem. The means may differ between groups, but the outcome is the same across groups. Or to put it another way, multiple independent paths converge on a common solution. There are many examples of this known already, at the molecular and organismal level. It's known in evolutionary terms as convergent evolution, but I'll call it convergent design.

Convergent design is to be expected under the design hypothesis because the designer is not constrained by an evolutionary tree. He can reuse ideas that work in one setting in a different place. In fact, he can mix and match his methods to get to any outcome he wants. I am thinking of echinoderms (sea stars and sea urchins) that look alike as adults but get there by very different developmental paths, or two very different animal groups that come up with similar molecular solutions to create a new function, echolocation.

Convergent design is clearly observable across biology but has no evolutionary mechanism. There are proposed reasons for it but no demonstration. I can hear in my head the arguments of evolutionary biologists: intrinsic constraints, canalization, living in similar environments or ecological niches, you have no demonstration either...

So then maybe the answer comes down to probability.

In considering these alternative explanations, ask yourself, how likely is it that a retrovirus would infect, invade the germ line (the cells that make eggs and sperm), then insert itself at random in locations in the genome that are expressed in the developing embryo or primitive uterus at the proper time, then promote fusion of membranes to permit the formation of a placenta, with all this happening at least six separate times in the six lineages tested so far? We should also make clear, expressing a syncytin by itself is unlikely to be enough to make a placenta, which is a complex organ requiring interactions between mother and embryo, and the ability to exchange nutrients and oxygen.

Let me close by posing Torley's questions to him, concerning syncytins:

Do you accept that if hypothesis A readily explains an empirical fact F and hypothesis B does not, then F (taken by itself) constitutes scientific evidence for A over B? Or putting it another way, if a fact F is predicted by hypothesis A, and compatible with hypothesis B but not predicted by B, then do you agree that F constitutes scientific evidence for A over B? If not, why not?


Evidence for and against common descent. It's not nearly so open and shut a case as some believe, unless there is an a priori commitment to materialistic explanations.

Electric bacteria for design.

By Jasmin Fox-Skelly

 

Some microbes have developed the ultimate stripped-down diet. They do not bother with food or oxygen. All they need to survive is pure electrical energy.
They often live in muddy seabeds or along the banks of rivers. Finding them is easy: biologists can coax them out of hiding by sticking an electrode into the sediment. The bacteria nearest to the electrode will even grow biological equivalents of electrical wires out of their bodies, so that other microbes further away can hook up to the electricity source. It is effectively a living power grid.
What's more, it appears that we can all benefit from this microscopic grid. Among other things, it might provide an effective way to deal with toxic waste and other forms of environmental pollution.
 

Electricity-eating microbes might sound like something straight out of a science fiction novel. In fact their behaviour is not quite as exotic as it might first appear.

                
All lifeforms on Earth – even humans – must harness energy if they are to remain alive. This energy comes in the form of electrons, the same tiny negatively-charged particles that create a current when they zip around electrical wires in a circuit.
We humans, along with most other organisms on this planet, get our electrons from sugars in the food that we eat. In a series of chemical reactions that happen inside our cells, the electrons are released, and ultimately flow into oxygen – the same oxygen which we have just breathed in through our lungs. That flow of electrons is what powers our bodies.
This means that the challenge for all creatures is the same. Whether the organism is a single-celled bacterium or a blue whale, it has to find a source of electrons, and a place to dump them to complete the circuit.
But what happens when there is no oxygen to dump your electrons onto?
Many organisms live in low-oxygen environments and so must use alternative electron dumps. For some, that means "breathing" metals instead of oxygen.
In 1987 Derek Lovley and his lab at the University of Massachusetts stumbled across the first of these bacteria on the banks of the Potomac River near Washington DC.
The microbes, called Geobacter metallireducens, were getting their electrons from organic compounds, and passing them onto iron oxides. In other words they were eating waste – including ethanol – and effectively "breathing" iron instead of oxygen.
Of course, this is not breathing as we would recognise it. For one thing, bacteria do not have lungs. Instead, the bacteria pass their electrons to metal oxides that lie outside the cell.
They do this through special hair-like wires that protrude from the cell's surface. These tiny wires act in much in the same way that copper wire does when it conducts electricity. They have been dubbed "microbial nanowires".

 

Geobacter bacteria are able to survive on energy sources entirely unavailable to most lifeforms.

They are even able to effectively "eat" pollution. They will convert the organic compounds in oil spills into carbon dioxide, or turn soluble radioactive metals like plutonium and uranium into insoluble forms that are less likely to contaminate groundwater – and they will generate electricity in the process.
In fact, some even see a future in which microbial fuel cells power devices like smartphones using seaweed, urine or sewage as their only food source: the ultimate in recycled energy.
In 1988, a year after Lovley's discovery, microbiologist Kenneth Nealson of the University of Southern California found a second electron-excreting bacterium.He was investigating a strange phenomenon in Oneida Lake in New York State. The lake contains manganese, which reacts with the oxygen in the air to form manganese oxide.
However, Nealson did not find as much manganese oxide as he was expecting. Some of it was missing. The culprit, it turns out, was Shewanella oneidensis.
This bacterium breathes oxygen when it is available, but in the muddy banks of the lake where oxygen is scarce it instead passes its electrons directly onto manganese oxide, producing a stream of electricity. It can do the same thing with other metals like iron.
Just how the bacteria were doing this was a mystery until very recently.
Under the microscope, Shewanella appear to have long thin hair-like extensions of their outer membrane. These filaments were at first thought to conduct electrons along them like a copper cable, much like Geobacter. However, it turns out that the long filaments are only conductive when dried out in a lab.
Instead Shewanella appear to shuttle electrons out of their cells using transport molecules called flavins and "stepping stone" proteins embedded in the outer membrane called cytochromes.

So far we have only talked about bacteria that produce electricity when they breathe. But these electron-excreting microbes are not the only ones that researchers have found.
While most organisms get their electron fix from carbohydrates, some bacteria can harvest electrons in their purest form. They can effectively "eat" electrons from minerals and rocks. In a way, they are getting their electrical energy straight from the socket.
Annette Rowe, a graduate student of Nealson, has found six new bacterial species on the ocean floor that can live off electricity alone. All are very different to one another, and none of them is anything like Shewanella or Geobacter.Rowe took samples of sediment from the seabed in Catalina Harbour off the Californian coast, brought them back to the lab and inserted electrodes into them. She then varied the voltage of the electrodes to see whether the bacteria in the sediment would "eat" electrons from the electrode, or discharge electrons on to it.
She found that, when no other food source was available, the bacteria would happily take electrons directly from the electrodes. In their natural habitat, the bacteria likely take their electrons directly from iron and sulphur in the seabed.
Examples of electron-eating bacteria found by Rowe include Halomonas, Idiomarina, Marinobacter, and Pseudomonas of the Gammaproteobacteria, and Thalassospira and Thioclava from the Alphaproteobacteria.

Many more electron-loving bacteria have now been found. In fact all you have to do is stick an electrode in the ground and pass electrons down it, and soon the electrode will be coated with feeding bacteria. Experiments show that these bacteria essentially eat or excrete electricity.
The holy grail of electricity-loving bacteria would be having a species that could both eat and excrete electrons, and so could exist entirely on electricity alone without any other energy source
According to Lovley, that grail has already been discovered. Some species of Geobacter, he says, can both directly transfer electrons to electrodes and also directly accept electrons from them.
In 2015, we learned that electron-eating and electron-excreting microbes can actually team up and pass electrons between each other, wiring themselves into a common electrical grid.
At the bottom of the ocean lie vast reserves of methane, released by microbes feeding on the remains of dead algae and animals as they sink down from the surface. If the methane escaped into the atmosphere the gas would exacerbate global warming, but luckily a consortium of microbes seem to keep it in check.
Different species of bacteria and archaea – ancient single-celled microbes similar to bacteria in many ways – team up to degrade the methane before it can get the surface.Gunter Wegener from the Max Planck Institute for Marine Microbiology in Bremen wondered how the process worked. He collected samples of the microbes
, which live at temperatures of 60C on the ocean floor, and put them under a scanning electron microscope.
The microscope revealed thin wire-like structures protruding from the bacterial cells. Although only a few nanometres wide, the wires were several micrometres long, which is much longer than the cells themselves.
It seems that the bacteria use these nanowires to hook up with the archaea.
The archaea feed on electrons from methane, oxidising the gas to generate carbonate. They then pass the electrons on to their partner bacteria along the nanowires, which act like power cables. Finally the bacteria deposit the electrons onto sulphate, producing energy that the cell can use in the process.
The researchers have now identified the genes that coded for the production of these nanowires. It is only when methane is added as an energy source that the genes are switched on and the nanowires form between bacteria and archaea.
This ancient form of electronic cooperation between the two types of microbe may have evolved billions of years ago, when the Earth's atmosphere was oxygen-free.
"One of the most interesting developments in the area of microbes eating and breathing electrons is the concept of direct interspecies electron transfer," says Lovley. "This is when microorganisms wire themselves together to share electrons, permitting them to carry out reactions that neither would be able to carry out individually."
Lovley and his lab have also discovered other communities of bacteria that are able to pass electrons directly to each other.

In the lab, Lovley showed that two species of Geobacter – G. metallireducens and G. sulfurreducens – survive by forming a conductive network of nanowires, through which electrons can be shuttled. G. metallireducens takes electrons from ethanol and then passed them directly to G. sulfurreducens using this electrical grid.                     
Cable bacteria live on sea floors and river beds where there is little oxygen. Without oxygen, they have nowhere to donate their electrons.
In a more extreme version of this process, some bacteria can link up to form long "cables".To cope with this the cable bacteria, which belong to the family Desulfobulbaceae, form chains, one cell in diameter, extending thousands of cells and distances of several centimetres – a huge distance for a bacterium only 3 or 4 micrometres long – until they finally reach a habitat with oxygen.
The first bacterium in the chain, which lives in a low-oxygen habitat, takes electrons from sulphide and passes them onto the next bacterium. This bacterium then passes the electrons on to the next cell, and so on until the final bacterium in the chain can finally pass the electrons onto oxygen.
This means that bacteria living in seabed mud where no oxygen penetrates can access oxygen dissolved in the seawater above simply by "holding hands" with other bacteria. Running along the chains of bacteria are ridges that connect the cells together, possibly allowing electrons to flow between them.
Other bacteria rely on rocks and minerals to do all the hard work for them when it comes to eating and dumping electronsBacteria have been seen to attach themselves to conductive materials, such as the iron-rich mineral magnetite, in order to pass electrons between each other through the magnetite. It is thought that chains of magnetite can form, bridging the gap between the electron-donating and the electron-accepting bacteria.
The environments these bacteria occupy may seem exotic, but electron-eating and -breathing microbes can also be found in more familiar settings.
For instance, they have been discovered in the digesters that convert brewery wastes to methane. Inside one such brewery, Geobacter metallireducens was directly transferring electrons to another bacterium, Methanosaeta harundinacea, which was then passing the electrons on to carbon dioxide.
It is even possible that microorganisms in the human gut electrically interact with cells in the gut lining.Just why have the bacteria evolved this neat trick?Being able to survive on electrons alone is a smart way of coping when resources and food are scarce, as can be the case at the bottom of the ocean or deep underground. Here, there is not quite enough energy for an organism to grow, or compete, but there is enough for it to exist – just about.
If life exists on other worlds, such as Mars or Jupiter's moon Europa, it will probably be in similarly sparse environments. Astrobiologists searching for evidence of extraterrestrial life might be particularly interested in electricity-eating and electricity-excreting microbes.
Whether or not such alien life is ever found, electricity-eating and -excreting bacteria here on Earth are still a significant discovery. All you need to do is provide them with an electrode onto which they can "breathe" electrons, and they have the potential to steal electrons from toxic waste, oil spills and nuclear waste, cleaning up our waste and generating electricity in the process.
Not bad for simple single-celled organisms.BBC Earth

Has nutritition science let cholesterol out of the dog house?

High cholesterol 'does not cause heart disease' new research finds, so treating with statins a 'waste of time'

Henry Bodkin

 

Cholesterol does not cause heart disease in the elderly and trying to reduce it with drugs like statins is a waste of time, an international group of experts has claimed.

A review of research involving nearly 70,000 people found there was no link between what has traditionally been considered “bad” cholesterol and the premature deaths of over 60-year-olds from cardiovascular disease.
Published in the BMJ Open journal, the new study found that 92 percent of people with a high cholesterol level lived longer.The authors have called for a re-evaluation of the guidelines for the prevention of cardiovascular disease and atherosclerosis, a hardening and narrowing of the arteries, because “the benefits from statin treatment have been exaggerated”.
The results have prompted immediate scepticism from other academics, however, who questioned the paper’s balance.
High cholesterol is commonly caused by an unhealthy diet, and eating high levels of saturated fat in particular, as well as smoking.

It is carried in the blood attached to proteins called lipoproteins and has been traditionally linked to cardiovascular diseases such as coronary heart disease, stroke, peripheral arterial disease and aortic disease.
The authors have called for a re-evaluation of the guidelines for the prevention of cardiovascular disease and atherosclerosis, a hardening and narrowing of the arteries, because “the benefits from statin treatment have been exaggerated”.
The results have prompted immediate scepticism from other academics, however, who questioned the paper’s balance.
High cholesterol is commonly caused by an unhealthy diet, and eating high levels of saturated fat in particular, as well as smoking.

It is carried in the blood attached to proteins called lipoproteins and has been traditionally linked to cardiovascular diseases such as coronary heart disease, stroke, peripheral arterial disease and aortic disease.
Co-author of the study Dr Malcolm Kendrick, an intermediate care GP, acknowledged the findings would cause controversy but defended them as “robust” and “thoroughly reviewed”.
“What we found in our detailed systematic review was that older people with high LDL (low-density lipoprotein) levels, the so-called “bad” cholesterol, lived longer and had less heart disease.”
Vascular and endovascular surgery expert Professor Sherif Sultan from the University of Ireland, who also worked on the study, said cholesterol is one of the “most vital” molecules in the body and prevents infection, cancer, muscle pain and other conditions in elderly people.
“Lowering cholesterol with medications for primary cardiovascular prevention in those aged over 60 is a total waste of time and resources, whereas altering your lifestyle is the single most important way to achieve a good quality of life,” he said.
Lead author Dr Uffe Ravnskov, a former associate professor of renal medicine at Lund University in Sweden, said there was “no reason” to lower high-LDL-cholesterol.
But Professor Colin Baigent, an epidemiologist at Oxford University, said the new study had “serious weaknesses and, as a consequence, has reached completely the wrong conclusion”.
Another sceptic, consultant cardiologist Dr Tim Chico, said he would be more convinced by randomised study where some patients have their cholesterol lowered using a drug, such as a stain, while others receive a placebo.
He said: “There have been several studies that tested whether higher cholesterol increases the risk of heart disease by lowering cholesterol in elderly patients and observing whether this reduces their risk of heart disease.
“These have shown that lowering cholesterol using a drug does reduce the risk of heart disease in the elderly, and I find this more compelling than the data in the current study.”
The British Heart Foundation also questioned the new research, pointing out that the link between high LDL cholesterol levels and death in the elderly is harder to detect because, as people get older, more factors determine overall health.
“There is nothing in the current paper to support the author’s suggestions that the studies they reviewed cast doubt on the idea that LDL Cholesterol is a major cause of heart disease or that guidelines on LDL reduction in the elderly need re-valuating,” a spokesman said.

On Learning to disagree without being disagreeable.

In the Evolution Debate, Not Listening Happens in One Direction, Not Two

David Klinghoffer

 

An eloquent post from Terry Teachout, the Wall Street Journal theater critic, might as well be a commentary on Doug Axe's observations this morning ("Public Opinion Is the Ultimate Peer Review"). Teachout (whom I had the privilege of working with at National Review long ago) laments the divorce between cultures symbolized by Red and Blue states. He recalls a time before half the country was so fiercely committed to regarding itself as Enlightened while dismissing the other half as Benighted, hopelessly so, or worse. Anyway that's how I would characterize it.

Many, perhaps most Americans of my generation (I was born in 1956) lived in places whose residents included people who read, liked, listened to, and thought all sorts of things, and who voted differently, even unpredictably, on election day. As a result, we learned to get along with one another, and sometimes we even learned from one another. At the very least, we learned -- up to a point -- to be reasonably tolerant of each other's crotchets.
More and more, though, we don't live together and we don't listen to each other. As a result, the modest but real tolerance of the past is increasingly giving way to attempts at outright repression, or (more often, at least for now) [a] sniggeringly dismissive attitude...

He refers to a Washington Post story deploring a prominent person's well-known appetite for fast food:

This "news" story is, in its minor but nonetheless revealing way, illustrative of the condition that now increasingly prevails in American society, which is that those who disagree no longer have anything to say to each other. Fact-based argument has been replaced by reflexive contempt. Nor should this be in any way surprising. In a totally polarized political environment, persuasion is no longer possible: we believe what we believe, and nothing matters but class and power. We are well on the way to becoming a land of jerking knees.
Never before have I felt so strongly that Americans are talking past instead of to one another.

The dividing line extends from food to faith, from politics to science. Oh, most certainly it includes science. Doug Axe, in his post, responds to a Caltech commencement address by Atul Gawande, the surgeon and New Yorker staff writer. To someone like Gawande, these sentences by Dr. Axe are a counterintuitive shot across the bow: "People aren't stupid. Science is a public enterprise, and public acceptance has always been its most significant seal of approval."
The theme of Axe's forthcoming book, Undeniable -- How Biology Confirms Our Intuition That Life Is Designed, is the validity of ordinary intuition as a tool in judging science. That idea is anathema to Americans on the other side of the worldview divide that Terry Teachout describes. For them, people -- "mere people," as Axe puts it ironically -- are indeed stupid.
In fact the deplorable stupidity of half the population is a pillar of faith for the Enlightened. The Benighted show their benightedness by trying to have a conversation with the Enlightened, not realizing that their "conversation" partner isn't even listening. For the Enlightened, it often seems, "nothing matters but class and power."
We see this in the discussion, such as it is, of intelligent design versus unguided Darwinian evolution. In this debate about an ultimate question, the mystery of human and biological origins, for one side "Fact-based argument has been replaced by reflexive contempt."
I would only offer this addendum to Terry's observations, from our experience in the context of the evolution controversy. Scientists open to evidence for design offer abundant "fact-based arguments," only to be greeted by a "sniggeringly dismissive attitude." They are not talking past us. By that I mean, design advocates genuinely register and understand, even if they reject, arguments from the other side. The "reflexive contempt" does not operate equally in both directions.