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Archive for the ‘Evolution’ Category

“Dying the Christian Science way: the horror of my father’s last days”

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Religion, as a genus in the meme-sphere, evolves in some surprising directions (just as do lifeforms—cf. the peacock). In the Guardian Caroline Fraser describes one variant and the real-world consequences:

When I was a baby, my grandfather delighted me by playing a game. He made a fist sandwich, fingers laced together and hidden in his palms, showing me his thumbs closed upon them. Slowly, he would say, “Here’s the church, and here’s the steeple,” raising his index fingers together to form a peak. Then, throwing his thumbs apart, he flipped his interlaced fingers over, wriggling them and crying out, “Open the doors and see all the people!”

My grandfather was a Christian Scientist. His mother had been a Scientist. His only child, my father, was a Scientist. I was raised to be a Scientist.

Now I’m delighted by a different kind of game: counting the churches as their doors close. In 20 years, drastic changes have taken place, but the most arresting is the church’s precipitous fall. It’s getting harder and harder to see all the people, because they’re disappearing.

The early popularity of Christian Science was tied directly to the promise engendered by its core beliefs: the promise of healing. The overwhelming majority of those attracted to the movement came to be healed, or came because a husband, wife, child, relative or friend needed healing; the claims of Christian Science were so compelling that people often stayed in the movement whether they found healing or not, blaming themselves and not the church’s teachings for any apparent failures.

The teachings were radically simple. The founder and leader of the church, Mary Baker Eddy, taught that disease was unreal because the human body and the entire material world were mere illusions of the credulous, a waking dream. Those who awoke and knew the “Truth” could be instantaneously healed. (Eddy was big on capitalised generalities; “Life”, “Love” and “Spirit” were among her other “synonyms” for God.)

What was the “Truth”? We memorised it in Sunday School, the “Scientific Statement of Being”, which assured us that “there is no life, truth, intelligence, nor substance in matter”. Eddy’s definition of man was even more stark: “Man is not matter; he is not made up of brain, blood, bones, and other material elements.” We were instructed to repeat as needed for whatever ailment came along, from canker sores to cancer. The trick lay in the application: allow no hint of doubt, neither aspirin nor vitamin, a dogma so dire it was taken to absurd lengths. During the height of the London fad for the faith, in 1911, novelist VS Pritchett was indoctrinated into the mysteries by his father after “dying Cousin Dick” leapt from his deathbed, “miraculously cured”. Soon after, Pritchett, a lad of 11, was forced to walk to school on a sprained ankle.

As Pritchett discovered, Cousin Dick’s results were impossible to replicate in the real world, and the consequences of Eddy’s strictures – she demanded “radical reliance” on her methodology to the exclusion of all else – quickly caused havoc. Newspapers and prosecutors noticed the casualties, especially children dying of unreported cases of diphtheria and appendicitis. In the early years of the church, this touched off battles with the American Medical Association, which tried to have Christian Science healers, or “practitioners”, arrested for practising medicine without a licence. Since practitioners did nothing but pray, however, their activities were protected by the US constitution. Reacting with righteous zeal, Church leaders doubled down for decades, furtively slipping protections into the law and encouraging insurance companies to cover Christian Science “treatment”. Since it cost very little, the companies cynically complied.

As a result, by the 1970s – a high-water mark for the church’s political power, with many Scientists serving in Richard Nixon’s White House and federal agencies – the church was well on its way to accumulating an incredible array of legal rights and privileges across the US, including broad-based religious exemptions from childhood immunisations in 47 states, as well as exemptions from routine screening tests and procedures given to newborns in hospitals. The exemptions had consequences: modern-day outbreaks of diphtheria, polio and measles in Christian Science schools and communities. A 1972 polio outbreak in Connecticut left multiple children partially paralysed; a 1985 measles outbreak (one of several) at Principia College in Illinois killed three.

In many US states, Scientists were exempt from charges of child abuse, neglect and endangerment, as well as from failure to report such crimes. Practitioners with no medical training (they become “listed” after two weeks of religious indoctrination) were recognised as health providers, and in some states were required to report contagious illnesses or cases of child abuse or neglect, even as their religion demanded that they deny the evidence of the physical senses. Practitioners, of course, have no way of recognising the symptoms of an illness, even if they believe it existed, which they don’t.

A whole system of Christian Science “nursing” sprang up in unlicensed Christian Science sanatoriums and nursing homes catering to patients with open wounds and bodies eaten away by tumours. There, no medical treatment was allowed to interfere with prayer. Assigned only the most basic duties – feeding and cleaning patients – Christian Science “nurses” are not registered, and have no medical training either. Instead, they engage in bizarre practices such as leaving food on the mouths of patients who cannot eat. They provide no assistance for those who are having trouble breathing, administer no painkillers, react to no emergencies. “Do not resuscitate” is their default. But some of these facilities, and the incompetent care they provide, are covered by Medicare, the US’s national healthcare insurance programme.

Still, by this point, few people know or care what the Christian Scientists have been up to, since the average person can’t tell you the difference between a Christian Scientist and a Scientologist. The decline of the faith, once a major indigenous sect, may be among the most dramatic contractions in the history of American religion. Eddy forbade counting the faithful, but in 1961, the year I was born, the number of branch churches worldwide reached a high of 3,273. By the mid-80s, the number in the US had dropped to 1,997; between 1987 and late 2018, 1,070 more closed, while only 83 opened, leaving around a thousand in the US.

Prized urban branches are being sold off by the score, converted into luxury condominiums, museums and Buddhist temples. The branch I attended, on Mercer Island, near Seattle, is now Congregation Shevet Achim, a Modern Orthodox synagogue.

Worldly erosion eats away at the remainder. New York’s Third Church on Park Avenue is still open for spiritual business, but is leased for events during the week, sparking complaints about blocked traffic, paparazzi and partygoers attending celebrity galas in the four-storey neo-Georgian sanctuary. The phrase “God is Love” is traditionally affixed to an interior wall of every branch, but during secular events the words are concealed behind a faux-slate panel, lest they detract from, say, a runway show of Oscar de la Renta resort wear. Alcohol and coffee, shunned by Church members since Eddy’s day, are brought in by caterers.

The slide into irrelevance has been inexorable. The number of practitioners has fallen to an all-time low of 1,126, and during the last decade the Sentinel magazine has lost more than half its subscribers. The Monitor, the public face of the Church, has become a kind of zombie newspaper, laying off 30% of its staff in 2016. It is now available as a five-days-a-week emailed newsletter, or a thin print weekly that has been bleeding subscribers.

Principia, the Christian Science educational institution (a separate entity from the Mother Church), has shed so many students that its future is in question. Its college enrollment was down to 435 in 2018, the St Louis Post-Dispatch reported, while its school had 400 students, with just eight in the first-grade class. With an endowment of $680m, one official noted, “We are going to run out of kids before we run out of money. There just aren’t enough Christian Scientists on the planet.” . . .

Continue reading. There’s much more, and some of it is grim indeed. Lord, deliver us from “Christian” “Science.”

Written by LeisureGuy

10 August 2019 at 10:35 am

Are You There, Race? It’s Me, DNA

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Jonathan Jerry writes for McGill Office for Science and Society (“separating sense from nonsense”):

What would you say is Liam Neeson’s race?

I ask this question because in this era of the gene, of people swabbing their cheeks to know where their ancestors came from, and of racism glazed over with the shiny patina of science, many people feel confused about race. They have heard that it’s a social construct, but that can be hard to square with rumours that only Black people have sickle cell anemia. And if 23andMe can report on your ancestry, isn’t that proof that race exists at the biological level?

The concept of dividing humans into categories has been with us for a very long time. Greek philosopher Aristotle attempted to classify living things in a hierarchy. According to his thinking, some humans were born to be kings, whereas others were determined to be slaves. In the 1700s, Man was divided into a handful of races: Africans, Asians, Native Americans, and Caucasians (Pacific Islanders were thought of as a fifth race by some). It wasn’t just a horizontal classification, but a vertical one too. Thinking of Africans as biologically inferior to Caucasians certainly facilitated their treatment during the slave trade.

When participants to a focus group in 2004 were asked what exactly is a race, they ended up mirroring a debate that had been happening among scholars, because it’s not an easy concept to define. Physical appearance, especially skin colour, was often mentioned by the participants, but it wasn’t seen as sufficient. If we stop at skin colour, however—a common enough shortcut for anyone trying to categorize an individual by race—we quickly run into a problem:

To what races do these women belong? It turns out they are all from the African continent. From left to right, we have a Namibian, an Egyptian, a Malian, and a Kenyan. If “African” is one race, why do all these women look so different?

A useful definition of a race is a group of people who are perceived as sharing biological features. Importantly, this perception varies by culture, because this is not, please excuse the pun, a black-and-white ruling. If skin colour is used to distinguish race, where is the cut-off? It’s not obvious, because skin colour is on a gradient.

But skin colour, hair colour, eye colour, and other physical traits are all under the control of genes, so doesn’t our DNA have something to do with race?

Our eyes tell us lies that DNA can pulverize

The DNA in our cells is littered with variants, little changes from one individual to the next that are responsible for many of our physical attributes and our predispositions to disease. It’s like we all have the same book, except that my edition has a few typos and local spelling differences that yours doesn’t and vice versa (e.g. “color” versus “colour”). When we add up all of these variants, that is what we mean by “genetic variability”, the number of DNA differences from one person to another.

So do you think there is more genetic variability between these two penguins… or between Taylor Swift and Kanye West?

The answer is surprising. Even though our eyes tell us one thing, DNA analysis reveals the opposite. These penguins are more different at the DNA level than our two human superstars. It turns out that humans are less genetically diverse than many animals, including chimps.

In fact any two unrelated human beings on the planet are 99.9% identical in their DNA sequence. Only 0.1% varies, and here’s the most important takeaway message from all this. It also happens to be the most replicated finding in the scientific literature on human variation.

Of this 0.1% that varies, almost all of it (95.7% to be exact) is found between individuals within the same race. Despite what our eyes perceive, there is more genetic diversity within a race than between races

If you didn’t know that, don’t worry: you’re in good company. Three out of four college students taking an introductory course in biology and genetics also do not know this.

And since skull sizes are being discussed again in certain corners of the Internet, 90% of the variability in their volume also occurs within (and not between) human groups.

This is a big snag in the argument that race is a biological reality. This finding—that there’s more diversity within than between groups—is true for most physical traits, with one prominent exception: skin colour. Why? Because skin colour is under tremendous selective pressure. It varies depending on how far from the equator we are, because a darker skin offers better protection against sunburn, skin cancer and related damages. People with naturally darker skin were better adapted to their environment and were more likely to reproduce. The fact that a Maasai and an Aboriginal Australian both have very dark skin is not because they are part of the same biological race, but rather because both have lived under a very harsh sun for generations. So skin colour is not evidence of race being a biological reality.

But what about sickle cell anemia, I hear you ask. Isn’t that a disease that only affects Black people?

Race and medicine

The truth about sickle cell anemia is more complicated than that. The sickle cell trait is a variant in our DNA that offers protection against malaria. Over many generations, people who were exposed to malaria were more likely to reproduce if they had this trait, so this trait was selected for. When you have two copies of it, however, you can develop sickle cell anemia. So do only Black people carry the trait? No. While it is commonly seen in people of sub-Saharan African ancestry, it can also be found in Mediterraneans, Middle Easterners, and Indians. It is not restricted to one race but rather to many populations that were all exposed to malaria.

But there is another example where race seems to play a role in medicine: the drug BiDil, the first race-based prescription drug in the US which aims to treat heart failure. It was said to be a breakthrough for African Americans, but here’s the twist: the clinical trial that led to its approval only tested African Americans. How can you pretend your drug can only treat one race when you haven’t tested it in another?

One final argument for the existence of biological races is . . .

Continue reading. There’s much more.

Written by LeisureGuy

10 August 2019 at 10:15 am

Every Noise at Once, revised and expanded

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I’ve blogged this before, but they have continued to develop it. From the link (under the now-very-large music map):

Every Noise at Once is an ongoing attempt at an algorithmically-generated, readability-adjusted scatter-plot of the musical genre-space, based on data tracked and analyzed for 3,295 genres by Spotify as of 2019-08-01. The calibration is fuzzy, but in general down is more organic, up is more mechanical and electric; left is denser and more atmospheric, right is spikier and bouncier.

Click anything to hear an example of what it sounds like.

Click the » on a genre to see a map of its artists.

Be calmly aware that this may periodically expand, contract or combust.

How We Understand Music Genres explains how this thing got started.
A Retromatic History of Music (or Love) follows these genres across years.
Spotify New Releases by Genre uses them to scour this week’s new releases.
We Built This City On follows them to their cities of origin.
Genres by Country breaks them down by strength of association with countries.
Songs From the Edges flings you through a blast-tour of the most passionate genrecults.
Songs From the Ages samples demographic groups.
Songs From the Streets samples cities.
Drunkard’s Rock wanders around for a really long time.
The Sounds of Places plots countries as if they were genres.
Spotify World Browser shows Spotify editorial programming in different countries.
Every Place at Once is an index of the distinctive listening of individual cities.
Hyperspace House Concerts looks for music playing only in particular places.
Every School at Once is an index of the distinctive listening of students by school.
Genres in Their Own Words maps genres to words found in their song titles.
The Needle tries to find songs surging towards the edges of one obscurity or another.
The Approaching Worms of Christmas tries to wrap itself around things I usually fight.
Every Demographic at Once explores listening by country, age and gender.
Or there’s a dynamically-generated daily summary of Spotify Listening Patterns by Gender.

Written by LeisureGuy

2 August 2019 at 9:00 am

A Genetic Reason Why Humans Have More Heart Attacks than Other Mammals

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JvR emails an interesting newsletter from Dr. Gabe Mirkin, who writes:

Two to three million years ago, our pre-human ancestors had a single genetic mutation in their CMAH gene that protected them from a deadly form of malaria but set them up for risk for heart attacks that increases when they eat a lot of meat from any kind of mammal (PNAS, July 22, 2019). No other mammals developed this genetic mutation.

Apes, gorillas, chimpanzees, and other human progenitors were dying from a type of malaria called Plasmodium reichenowi. Then along came a pre-human with a CMAH gene changed from making a cell surface sugar-protein called Neu5Gc to another molecule called Neu5Ac (Proc Natl Acad Sci USA, Sept 6, 2005;102(36): 12819–12824). That pre-human did not die from malaria like other apes, monkeys and gorillas, so his or her children lived and proliferated, and today all humans have Neu5Ac instead of Neu5Gc. Chimpanzees share more than 99 percent of their genes with modern humans, but the CMAH gene is one of the areas of difference. As often happens in nature, the malaria parasite then modified its genetic makeup into a variant called Plasmodium falciparum which can infect humans, but not chimpanzees, so today humans can be infected only with Plasmodium falciparum and chimpanzees can be infected only with Plasmodium reichenowi.

Neu5Gc, Neu5Ac and Heart Disease
Heart disease causes one-third of the deaths in North America, and while risk factors for heart attacks can include high blood cholesterol, high blood sugar, high blood pressure, obesity, smoking, or lack of exercise, 15 percent of people who suffer heart attacks have none of these risk factors (CDC, NCHS, Underlying Cause of Death, 1999-2013). Other mammals can suffer heart attacks when they have these risk factors (often caused by human lifestyle habits), but they seldom suffer heart attacks if they do not have these risk factors (Evol Appl, 2009 Feb; 2(1): 101–112).

Mice that have been genetically modified to have the same CMAH gene mutation that is found in humans have the same:
• high risk for heart disease and arteriosclerosis, and
• increased heart attack risk from eating mammal meat that humans have (PNAS, July 22, 2019). These CMAH gene-modified mice suffered double the risk of atherosclerosis compared to unmodified mice. Like humans, they were also at increased risk for inflammation, heart attacks, strokes, diabetes, and some types of cancers.

How This CMAH Gene Modification Can Harm
Your immune system recognizes invading germs by the surface proteins on cell membranes. If the surface proteins are different from your own surface proteins, your immune system makes:
• proteins called antibodies that attach to and kill the invading germs, and
• immune cells that eat and destroy germs.

All mammals except humans have a surface sugar-protein on their cells called Neu5Gc, while humans have a surface sugar-protein called Neu5Ac. When humans eat mammal meat, their immune systems make antibodies and cells that attack the Neu5Gc that they absorb into their bloodstreams, so people who eat mammal meat regularly are likely to have an immune system that is overactive all the time, called chronic inflammation (Proc Natl Acad Sci USA, Jan 13, 2015;112(2):542–547). An overactive immune system can use the same cells and proteins that it uses to kill germs to attack and destroy your own cells. It can punch holes in the inner linings of your arteries to form plaques, and break plaques off to cause heart attacks and strokes. Inflammation can also damage your DNA to cause cancers, and damage various tissues to cause arthritis, fatty liver, diabetes and so forth.

My Recommendations
The theory of Neu5Gc in mammal meat causing chronic inflammation is strong enough that I believe you should not eat mammal meat regularly. We have extensive data to show that regular meat eaters are at increased risk for heart attacks, strokes, diabetes, cancers (Genome Biol Evol, Jan 1, 2018;10(1):207-219). We do not have enough data to know if eating mammal meat on occasion is harmful. I recently reported on Neu5Gc and other theories that may help to explain the association between eating meat and heart attacks in Heart Attacks Again Linked to Red Meat

Written by LeisureGuy

1 August 2019 at 9:48 am

Quantum Darwinism, an Idea to Explain Objective Reality, Passes First Tests

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Darwin’s insight seems to have been much deeper than we knew: it’s a look into the heart of how nature works. Philip Ball writes in Quanta:

It’s not surprising that quantum physics has a reputation for being weird and counterintuitive. The world we’re living in sure doesn’t feel quantum mechanical. And until the 20th century, everyone assumed that the classical laws of physics devised by Isaac Newton and others — according to which objects have well-defined positions and properties at all times — would work at every scale. But Max Planck, Albert Einstein, Niels Bohr and their contemporaries discovered that down among atoms and subatomic particles, this concreteness dissolves into a soup of possibilities. An atom typically can’t be assigned a definite position, for example — we can merely calculate the probability of finding it in various places. The vexing question then becomes: How do quantum probabilities coalesce into the sharp focus of the classical world?

Physicists sometimes talk about this changeover as the “quantum-classical transition.” But in fact there’s no reason to think that the large and the small have fundamentally different rules, or that there’s a sudden switch between them. Over the past several decades, researchers have achieved a greater understanding of how quantum mechanics inevitably becomes classical mechanics through an interaction between a particle or other microscopic system and its surrounding environment.

One of the most remarkable ideas in this theoretical framework is that the definite properties of objects that we associate with classical physics — position and speed, say — are selected from a menu of quantum possibilities in a process loosely analogous to natural selection in evolution: The properties that survive are in some sense the “fittest.” As in natural selection, the survivors are those that make the most copies of themselves. This means that many independent observers can make measurements of a quantum system and agree on the outcome — a hallmark of classical behavior.

This idea, called quantum Darwinism (QD), explains a lot about why we experience the world the way we do rather than in the peculiar way it manifests at the scale of atoms and fundamental particles. Although aspects of the puzzle remain unresolved, QD helps heal the apparent rift between quantum and classical physics.

Only recently, however, has quantum Darwinism been put to the experimental test. Three research groups, working independently in Italy, China and Germany, have looked for the telltale signature of the natural selection process by which information about a quantum system gets repeatedly imprinted on various controlled environments. These tests are rudimentary, and experts say there’s still much more to be done before we can feel sure that QD provides the right picture of how our concrete reality condenses from the multiple options that quantum mechanics offers. Yet so far, the theory checks out.

Survival of the Fittest

At the heart of quantum Darwinism is the slippery notion of measurement — the process of making an observation. In classical physics, what you see is simply how things are. You observe a tennis ball traveling at 200 kilometers per hour because that’s its speed. What more is there to say?

In quantum physics that’s no longer true. It’s not at all obvious what the formal mathematical procedures of quantum mechanics say about “how things are” in a quantum object; they’re just a prescription telling us what we might see if we make a measurement. Take, for example, the way a quantum particle can have a range of possible states, known as a “superposition.” This doesn’t really mean it is in several states at once; rather, it means that if we make a measurement we will see one of those outcomes. Before the measurement, the various superposed states interfere with one another in a wavelike manner, producing outcomes with higher or lower probabilities.

But why can’t we see a quantum superposition? Why can’t all possibilities for the state of a particle survive right up to the human scale?

The answer often given is that superpositions are fragile, easily disrupted when a delicate quantum system is buffeted by its noisy environment. But that’s not quite right. When any two quantum objects interact, they get “entangled” with each other, entering a shared quantum state in which the possibilities for their properties are interdependent. So say an atom is put into a superposition of two possible states for the quantum property called spin: “up” and “down.” Now the atom is released into the air, where it collides with an air molecule and becomes entangled with it. The two are now in a joint superposition. If the atom is spin-up, then the air molecule might be pushed one way, while, if the atom is spin-down, the air molecule goes another way — and these two possibilities coexist. As the particles experience yet more collisions with other air molecules, the entanglement spreads, and the superposition initially specific to the atom becomes ever more diffuse. The atom’s superposed states no longer interfere coherently with one another because they are now entangled with other states in the surrounding environment — including, perhaps, some large measuring instrument. To that measuring device, it looks as though the atom’s superposition has vanished and been replaced by a menu of possible classical-like outcomes that no longer interfere with one another.

This process by which “quantumness” disappears into the environment is called decoherence. It’s a crucial part of the quantum-classical transition, explaining why quantum behavior becomes hard to see in large systems with many interacting particles. The process happens extremely fast. If a typical dust grain floating in the air were put into a quantum superposition of two different physical locations separated by about the width of the grain itself, collisions with air molecules would cause decoherence — making the superposition undetectable — in about 10−31 seconds. Even in a vacuum, light photons would trigger such decoherence very quickly: You couldn’t look at the grain without destroying its superposition.

Surprisingly, although decoherence is a straightforward consequence of quantum mechanics, it was only identified in the 1970s, by the late German physicist Heinz-Dieter Zeh. The Polish-American physicist Wojciech Zurek further developed the idea in the early 1980s and made it better known, and there is now good experimental support for it.

But to explain the emergence of objective, classical reality, it’s not enough to say that decoherence washes away quantum behavior and thereby makes it appear classical to an observer. Somehow, it’s possible for multiple observers to agree about the properties of quantum systems. Zurek, who works at Los Alamos National Laboratory in New Mexico, argues that two things must therefore be true.

First, quantum systems must have states that are especially robust in the face of disruptive decoherence by the environment. Zurek calls these “pointer states,” because they can be encoded in the possible states of a pointer on the dial of a measuring instrument. A particular location of a particle, for instance, or its speed, the value of its quantum spin, or its polarization direction can be registered as the position of a pointer on a measuring device. Zurek argues that classical behavior — the existence of well-defined, stable, objective properties — is possible only because pointer states of quantum objects exist.

What’s special mathematically about pointer states is that the decoherence-inducing interactions with the environment don’t scramble them: Either the pointer state is preserved, or it is simply transformed into a state that looks nearly identical. This implies that the environment doesn’t squash quantumness indiscriminately but selects some states while trashing others. A particle’s position is resilient to decoherence, for example. Superpositions of different locations, however, are not pointer states: Interactions with the environment decohere them into localized pointer states, so that only one can be observed. Zurek described this “environment-induced superselection” of pointer states in the 1980s.

But there’s a second condition that a quantum property must meet to be observed. Although immunity to interaction with the environment assures the stability of a pointer state, we still have to get at the information about it somehow. We can do that only if it gets imprinted in the object’s environment. When you see an object, for example, that information is delivered to your retina by the photons scattering off it. They carry information to you in the form of a partial replica of certain aspects of the object, saying something about its position, shape and color. Lots of replicas are needed if many observers are to agree on a measured value — a hallmark of classicality. Thus, as Zurek argued in the 2000s, our ability to observe some property depends not only on whether it is selected as a pointer state, but also on how substantial a footprint it makes in the environment. The states that are best at creating replicas in the environment — the “fittest,” you might say — are the only ones accessible to measurement. That’s why Zurek calls the idea quantum Darwinism.

It turns out that the same stability property that promotes environment-induced superselection of pointer states also promotes quantum Darwinian fitness, or the capacity to generate replicas. “The environment, through its monitoring efforts, decoheres systems,” Zurek said, “and the very same process that is responsible for decoherence should inscribe multiple copies of the information in the environment.”

Information Overload

It doesn’t matter, of course, whether information about a quantum system that gets imprinted in the environment is actually read out by a human observer; all that matters for classical behavior to emerge is that the information get there so that it could be read out in principle. “A system doesn’t have to be under study in any formal sense” to become classical, said Jess Riedel, a physicist at the Perimeter Institute for Theoretical Physics in Waterloo, Canada, and a proponent of quantum Darwinism. “QD putatively explains, or helps to explain, all of classicality, including everyday macroscopic objects that aren’t in a laboratory, or that existed before there were any humans.”

About a decade ago, . . .

Continue reading.

Written by LeisureGuy

22 July 2019 at 12:26 pm

Posted in Evolution, Science

Prebiotics: Tending our inner garden

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Evolution produces some clever mechanisms, but if the environment changes, they can stop working.

Written by LeisureGuy

19 July 2019 at 2:06 pm

Wired Bacteria Form Nature’s Power Grid

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Carl Zimmer reports in the NY Times:

At three o’clock in the afternoon on September 4, 1882, the electrical age began. The Edison Illuminating Company switched on its Pearl Street power plant, and a network of copper wires came alive, delivering current to a few dozen buildings in the surrounding neighborhood.

One of those buildings housed this newspaper. As night fell, reporters at The New York Times gloried in the steady illumination thrown off by Thomas Edison’s electric lamps. “The light was soft, mellow, and grateful to the eye, and it seemed almost like writing by daylight,” they reported in an article the following day.

But nature invented the electrical grid first, it turns out. Even in 1882, thousands of miles of wires were already installed in the ground in the New York region — in meadows, in salt marshes, in muddy river bottoms. They were built by microbes, which used them to shuttle electricity.

Electroactive bacteria were unknown to science until a couple of decades ago. But now that scientists know what to look for, they’re finding this natural electricity across much of the world, even on the ocean floor. It alters entire ecosystems, and may help control the chemistry of the Earth.

“Not to sound too crazy, but we have an electric planet,” said John Stolz, a microbiologist at Duquesne University in Pittsburgh.

In the mid-1980s, Dr. Stolz was helping to study a baffling microbe fished out of the Potomac River by his colleague Derek Lovley. The microbe, Geobacter metallireducens, had a bizarre metabolism. “It took me six months to figure out how to grow it in the lab,” said Dr. Lovley, now a microbiologist at the University of Massachusetts at Amherst.

Like us, Geobacter feed on carbon compounds. As our cells break down these compounds to generate energy, they strip off free electrons and transfer them to oxygen atoms, producing water molecules. Geobacter couldn’t use oxygen, however, because it lived at the bottom of the Potomac, where the element was in short supply.

Instead, Geobacter transfers its electrons to iron oxide, or rust, Dr. Lovley and his colleagues discovered. The process helps turn rust into another iron compound, called magnetite.

The finding left the scientists with a puzzle. We humans draw oxygen into our cells to utilize it, but Geobacter does not import rust. So the microbe must somehow get the electrons out of its cell body and attach them to rust particles. How?

The researchers struggled for years to find the answer. Dr. Stolz eventually turned to other microbes to study. But Dr. Lovley soldiered on. Over the years, he and his colleagues have come across Geobacter in many places far beyond the Potomac. They’ve even encountered the bacteria in oil drilled from deep underground. “It’s basically found everywhere,” Dr. Lovley said.

In the early 2000s, Dr. Lovley’s team discovered that Geobacter could sense rust in its neighborhood. The microbe responded by sprouting hairlike growths.

Maybe each of those growths, known as a pilus, was actually a wire that latched onto the rust, Dr. Lovley thought. Electrons could flow from the bacterium down the wire to the receptive rust. “It seemed like a wild idea at the time,” Dr. Lovley said.

But he and his team found several clues suggesting that the pilus is indeed a living wire. In one experiment, when Geobacter was prevented from making pili, the bacteria couldn’t turn rust to magnetite. In another, Dr. Lovley and his colleagues plucked pili from the bacteria and touched them with an electrified probe. The current swiftly shot down the length of the hairs.

Subsequent research revealed that Geobacter can deploy its wires in different ways to make a living. Not only can it plug directly into rust, it can also plug into other species of microbes.

The partners of Geobacter welcome the incoming flow of electrons. They use the current to power their own chemical reactions, which convert carbon dioxide into methane.

Discoveries like these raised the possibility that other bacteria might be dabbling in electricity. And in recent years, microbiologists have discovered a number of species that do.

“When people are able to dig down at the molecular level, we’re finding major differences in strategy,” said Jeff Gralnick of the University of Minnesota. “Microbes have solved this issue in several different ways.”

In the early 2000s, a Danish microbiologist named Lars Peter Nielsen discovered a very different way to build a microbial wire. He dug up some mud from the Bay of Aarhus and brought it to his lab. Putting probes in the mud, he observed the chemical reactions carried out by its microbes.

“It developed in a very weird direction,” Dr. Nielsen recalled.

At the base of the mud, Dr. Nielsen observed a buildup of a foul-smelling gas called hydrogen sulfide. That alone was not surprising — microbes in oxygen-free depths can produce huge amounts of hydrogen sulfide. Normally, the gas rises the surface, where oxygen-breathing bacteria can break most of it down.

But the hydrogen sulfide in the Aarhus mud never made it to the surface. About an inch below the top of the mud, it disappeared; something was destroying it along the way.

After weeks of perplexity, Dr. Nielsen woke up one night with an idea. If the bacteria at the bottom of the mud broke hydrogen sulfide without oxygen, they would build up extra electrons. This reaction could only take place if they could get rid of the electrons. Maybe they were delivering them to bacteria at the surface.

“I imagined it could be electric wires, and I could explain all of this,” he said.

So Dr. Nielsen and his colleagues looked for wires, and they found them. But the wires in the Aarhus mud were unlike anything previously discovered.

Each wire runs vertically up through the mud, measuring up to two inches in length. And each one is made up of thousands of cellsstacked on top of each other like a tower of coins. The cells build a protein sleeve around themselves that conducts electricity.

As the bacteria at the bottom break down hydrogen sulfide, they release electrons, which flow upward along the “cable bacteria” to the surface. There, other bacteria — the same kind as on the bottom, but employing a different metabolic reaction — use the electrons to combine oxygen and hydrogen and make water.

Cable bacteria are not unique to Aarhus, it turns out. Dr. Nielsen and other researchers have found them — at least six species so far — in many places around the world, including tidal pools, mud flats, fjords, salt marshes, mangroves and sea grass beds.

And cable bacteria grow to astonishing densities. One square inch of sediment may contain as much as eight miles of cables. Dr. Nielsen eventually learned to spot cable bacteria with the naked eye. Their wires look like spider silk reflecting the sun.

Electroactive microbes are so abundant, in fact, that researchers now suspect that they have a profound impact on the planet. . .

Continue reading.

Written by LeisureGuy

2 July 2019 at 11:37 am

Posted in Evolution, Science

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