Ancient Viruses And The Origins Of Complex Life On Earth

scitechdaily |  The first discovery of viruses infecting a group of microbes that may include the ancestors of all complex life has been found, scientists at The University of Texas at Austin (UT Austin) report in Nature Microbiology. The incredible discovery offers tantalizing clues about the origins of complex life and suggests new directions for investigating the hypothesis that viruses were essential to the evolution of humans and other complex life forms.

There is a well-supported hypothesis that all complex life forms such as humans, starfish, and trees — which feature cells with a nucleus and are called eukaryotes — originated when archaea and bacteria merged to form a hybrid organism. Recent research suggests the first eukaryotes are direct descendants of so-called Asgard archaea. The latest research, by Ian Rambo (a former doctoral student at UT Austin) and other members of Brett Baker’s lab, sheds light on how viruses, too, may have played a role in this billions-year-old history.

 

Comparison of all known virus genomes. Those viruses with similar genomes are grouped together including those that infect bacteria (on the left), eukaryotes (on the right and bottom center). The viruses that infect Asgard archaea are unique from those that have been described before. Credit: University of Texas at Austin

“This study is opening a door to better resolving the origin of eukaryotes and understanding the role of viruses in the ecology and evolution of Asgard archaea,” Rambo said. “There is a hypothesis that viruses may have contributed to the emergence of complex cellular life.”

Rambo is referring to a hotly debated hypothesis called viral eukaryogenesis. It suggests that, in addition to bacteria and archaea, viruses might have contributed some genetic component to the development of eukaryotes. While this latest discovery does not settle that debate, it does offer some interesting clues.

The newly discovered viruses that infect currently living Asgard archaea do have some features similar to viruses that infect eukaryotes, including the ability to copy their own DNA and hijack protein modification systems of their hosts. The fact that these recovered Asgard viruses display characteristics of both viruses that infect eukaryotes and prokaryotes, which have cells without a nucleus, makes them unique since they are not exactly like those that infect other archaea or complex life forms.

“The most exciting thing is they are completely new types of viruses that are different from those that we’ve seen before in archaea and eukaryotes, infecting our microbial relatives,” said Baker, associate professor of marine science and integrative biology and corresponding author of the study.

The Asgard archaea, which probably evolved more than 2 billion years ago and whose descendants are still living, have been discovered in deep-sea sediments and hot springs around the world, but so far only one strain has been successfully grown in the lab. To identify them, scientists collect their genetic material from the environment and then piece together their genomes. In this latest study, the researchers scanned the Asgard genomes for repeating DNA regions known as CRISPR arrays, which contain small pieces of viral DNA that can be precisely matched to viruses that previously infected these microbes. These genetic “fingerprints” allowed them to identify these stealthy viral invaders that infect organisms with key roles in the complex origin story of eukaryotes.

QBism - Is Life But A Dream?

scientificamerican |  A newish interpretation of quantum mechanics called QBism (pronounced “Cubism,” like the art movement) makes subjective experience the bedrock of knowledge and reality itself. David Mermin, a prominent theorist, says QBism can dispel the “confusion at the foundations of quantum mechanics.” You just have to accept that all knowledge begins with “individual personal experience.”

According to QBism, each of us constructs a set of beliefs about the world, based on our interactions with it. We constantly, implicitly, update our beliefs when we interact with relatives who refuse to get vaccinated or sensors tracking the swerve of an electron. The big reality in which we all live emerges from the collisions of all our subjective mini-realities.

QBists hedge their mind-centrism, if only so they don’t come across as loons or mystics. They accept that matter exists as well as mind, and they reject solipsism, which holds that no sentient being can really be sure that any other being is sentient. But QBism’s core message, science writer Amanda Gefter says, is that the idea of “a single objective reality is an illusion.” A dream, you might say.

Proponents bicker over definitions, and physicists and philosophers fond of objectivity reject QBism entirely. All this squabbling, ironically, seems to confirm QBism’s premise that there is no absolute objectivity; there are only subjective, first-person viewpoints.

Physicists have more in common than most would like to admit with artists, who try to turn the chaos of things into a meaningful narrative. Some artists thwart our desire for meaning. T. S. Eliot’s poem The Waste Land is an anti-narrative, a grab bag of images that pop in and out of the void. The poem resembles a dream, or nightmare. Its meaning is that there is no meaning, no master narrative. Life is a joke, and the joke is on you if you believe otherwise.

If you are a practical person, like one of the finance majors in my freshman humanities class, you might conclude, along with T. S. Eliot, that efforts to comprehend existence are futile. You might urge friends majoring in philosophy to enjoy life rather than fretting over its meaning. You might summarize this advice with a catchy slogan: “Shut up and procreate!” But even those pragmatists must wonder now and then what our communal dream means.

The Quirky, Contingent, And Self-Referential Nature Of Biological Evolution Is Rare

inference-review |  Previous analyses have also looked at the emergence of life in conjunction with the emergence of human-like intelligence.⁹ Motivated by the assumption that four data points are better than two, Snyder-Beattie et al. have extended this earlier work with a Bayesian analysis of not only the timing of abiogenesis and the evolution of intelligence, but also the timing of two other major transitions: eukaryogenesis and the evolution of sexual reproduction. They conclude that intelligent life is rare in the universe because it took humans such a long time to evolve all four of the assumed prerequisites: abiogenesis, eukaryogenesis, sexual reproduction, and intelligence itself. Their Bayesian exploration of this result includes varying the timing of abiogenesis over a relatively wide range—between 4.3 and 3.5 billion years ago—and computing the effect of discovering that life emerged twice on earth.¹⁰ They found that their conclusion no longer holds if life emerged twice; or if abiogenesis occurred earlier, say, within ~10 million years of habitability; or if the habitable lifetime of the earth is 10 times longer than expected.¹¹

Recent exoplanet studies strongly suggest that every star has some kind of planetary system and that earth-like planets are likely common in such systems.¹² The earth may well be representative of a very large group of wet, rocky planets. But what about atmospheric composition, ocean volume, plate tectonics, spin period, orbital period, obliquity, the presence of a large moon, and the timing of large impacts? If the emergence and evolution of life are dependent on some of these additional details, the number of earth-like planets could be quite small.¹³

Once life has emerged from prebiotic chemistry, the strongest selection pressures on the evolution of a species come from other life forms: conspecifics, parasites, predators, diseases, viruses, and ecosystem variability. This self-referential nature of biology makes evolution a historical science characterized by the quirks of contingency. This characterization of evolution remains controversial.¹⁴ Our ability to extrapolate crow–puzzle experiments to crows on other planets depends on the existence of extraterrestrial crows. Similarly, the Snyder-Beattie et al. result depends on the assumption that “intelligent life elsewhere requires analogous evolutionary transitions.” The validity of the Snyder-Beattie et al. result, among others,¹⁵ is dependent on the assumption that the major transitions that characterize our evolution happen elsewhere.¹⁶

There is little evidence in the history of life on earth to support this assumption. Although abiogenesis is a transition shared by the lineages of all known life on earth, diverging lineages over the next four billion years are punctuated by their own evolutionary transitions. After diverging from other life forms, transitions within our own eukaryotic lineage include eukaryogenesis, sexual reproduction, and intelligence. A general feature of these transitions in the tree of life is that the closer a transition is to the end of a branch, the more recent, specific, and uncommon it is.¹⁷ In our lineage, eukaryogenesis occurred about two billion years ago and the transition to sexual reproduction about a billion years ago. The transition to intelligence is much more recent and its timing depends on how intelligence is defined. The transition to human-like intelligence or technological intelligence occurred only about 100,000 years ago and is species-specific. The latter trait is strong evidence we should not expect to find it elsewhere.¹⁸

Solution Of The Fundamental Problem Of Quantum Mechanics

The photon interaction, however, constitutes a time-differentiating operation imposed upon 4-dimensional Minkowskian reality (which is unperceived reality), producing three-dimensional, objective, determined, past reality. 

Photon absorption constitutes dimensional differentiation of reality, while photon emission constitutes dimensional integration. Objective concepts have been developed in correspondence to the photon interaction.

In the two-slit experiment, the electron is 4-dimensional, not 3-dimensional. When shielded against the photon interaction, it remains four-dimensional,  possessing its time dimension, and capable of interacting in a time-like manner. By wavelength one refers inversely to a time interval. 

Synchronization of time intervals between slit dimensions and electron wavelength results in time interaction between the electron’s time dimension and the time dimension of the two slits . Thus the electron interacts with both slits if shielded against the photon interaction, and time waves are propagated forward from both slits. If the slits are made much larger, time synchronization is destroyed and the classical effect reappears . If the photon interaction is imposed upon the electron, it is time-differentiated and becomes a classical object , having lost its time dimension.

When the electron encounters the screen, it meets a region of randomly varying time oscillations of the orbital electrons around the individual atoms comprising the screen . Thus the exact location of the orbital electron in the screen which will first precisely time-synchronize with the electron wavelength reciprocally is a random choice , and the “place” where the electron hits the screen is randomly selected along the screen, when the electron is four dimensional. The time pattern of the 4-d electron , however, had a distribution induced by its previous time interaction with the two slits . The pattern of this time distribution is wavelike, and is recovered when the distribution of the number of electron hits per screen length (which involves cumulation over time) is plotted .

Thus the two-slit experiment can be explained once the fourth law of logic is comprehended , and once the dimensionality of the electron and other parts of the experimental apparatus are taken into account.

The author points out that ordinary instruments and devices can be made to process entities in the unseparated state (multi-ocular state) , as demonstrated by the two-slit apparatus itself . Some consequences of this fact are mentioned, and the author refers to a basic mechanism he has proposed for the deliberate and controlled violation of objective reality .

What You Call "Your Conscious Mind" Is Fitted To The Photon Interaction

The Conscious Mind is Fitted to the Photon Interaction

What is normally referred to as the "conscious, thinking mind" is simply a functioning temporal (rigorously, chronotopological) mechanism that is painfully built up in the individual's awareness (his mind in the greater sense of both thought and awareness, whether monocular or multiocular) by training, conditioning and experience. Its functioning is largely conditioned by one's 90% or so attention to visual stimuli (to the partial reality remaining after photon interaction has been invoked, and to the memory-collated ordering of vast numbers of such photon interactions) and by one's cultural conditioning - which itself has been almost exclusively conditioned and shaped by the monocular photon interaction at base root.

Thus, since the beginning of man, (Bearden radically overstates the case here. It would be more accurate to say that since a time definite in the western epoch) his conscious, rational mind has been trained and constructed to function almost exclusively in basic correspondence with the photon interaction, and his experiential reality consists of the partial reality stripped from fundamental reality by photon interaction.

All "perceived differences," e.g., are created by this deep mind-set. As has been previously pointed out, ⁶ the solitary human problem responsible for all man's inhumanity to his fellow man is directly dependent upon man's almost exclusive detection, observation, perception, and conception of "difference" between humans, these "differences" being due exclusively and totally to the fitting of men's conscious minds to the photon interaction's monocular separation of spatial reality from nonspatial reality, i.e., to

∂/∂T (L³T) => L³

Such well-nigh total devotion to, and enslavement by, photon interaction also is responsible for the scientist's well-nigh total devotion to, and enslavement by, the present imperfect and incomplete three laws of logic, as presented by Aristotle. The depth of that devotion and enslavement is evidenced by the fact that the resolution of such paradoxes as Heraclitus's problem of change have eluded the best minds of humanity for several thousands of years. Indeed, these paradoxes cannot be resolved by the conscious, rational mind in its present state, for it has been most firmly constructed and fitted to function in accordance with the photon interaction.⁷ One cannot hope to resolve any logical paradox by using only those same logical methods that found the situation to be paradoxical in the first place!

RNA Is The Embodied Information That Sets Causal Boundary Conditions

axial  |  Schrödinger won the Nobel Prize in Physics in 1933 and was exiled from his native home Austria after the nation was annexed by Nazi Germany. He moved to Ireland after he was invited to set up the Dublin Institute of Advanced Studies. This follows the past history of Ireland acting as a storehouse of knowledge during the Dark Ages. After decades of work, biology was becoming more formalized around the 1940s. Better tools were emerging to perturb various organisms and samples and the increasing number of discoveries was building out the framework of life. With the rediscovery of Mendel’s work on genetics, scientists probably most importantly Thomas Hunt Morgan and his work on fruit flies (Drosophila) set up the rules of heredity - genes located on chromosomes with each cell containing a set of chromosomes. In 1927, a seminal discovery was made that irradiation by X-rays of fruits flies can induce mutations. Just the medium was not known where Schrödinger was thinking through his ideas on biology. At the same type, organic chemistry was improving and various macromolecules in the cell such as enzymes were being identified along with the various types of bonds made. For Schrödinger, there were no tools to characterized these macromolecules (i.e. proteins, nucleic acids) such as X-ray crystallography. Really the only tool useful at the time was centrifugation. At the time, many people expected proteins to be the store and transmitter of genetic information. Luckily, Oswald Avery published an incredible paper in 1944 that found DNA as probably the store instead of proteins.

With this knowledge base Schrödinger took a beginner’s mind to biology. In some ways his naivety was incredibly useful. Instead of being anchored to some widely-accepted premise that proteins transmitted genetic information (although he had a hunch some protein was responsible), the book thought from first principles and identified a few key concepts in biology that were not appreciated but became very important. Thankfully Schrödinger was curious - he enjoyed writing poetry and reading philosophy so jumped into biology somewhat fearlessly. At the beginning of the book, he sets the main question as:

“How can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?”

Information

In the first chapter, Schrödinger argues that because organisms have orderly behavior they must follow the laws of physics. Because physics relies on statistics, life was follow the same rules. He then argues that because biological properties have some level of permanence the material that stores this information then must be stable. This material must have the ability to change from one stable state to another (i.e. mutations). Classical physics is not very useful here, but for Schrödinger his expertise in quantum mechanics helped determine that these stable states must be held together through covalent bonds (a quantum phenomena) within a macromolecule. In the early chapters, the book argues that the gene must be a stable macromolecule.

Through discussion around the stability of the gene, the book makes its most important breakthrough - an analogy between a gene and an aperiodic crystal (DNA is aperiodic but Schrödinger amazingly didn’t know that at the time): “the germ of a solid.” Simply, a periodic crystal can store a small amount of information with an infinite number of atoms and an aperiodic crystal has the ability to store a near infinite amount of information in a small number of atoms. The latter was more in line with what the current data suggested what a gene was. Max Delbrück had similar ideas along with J.B.S. Haldane, but the book was the first to connect this idea to heredity. But readers at the time and maybe even still overextended this framework to believe that genetic code contains all of the information to build an organism. This isn’t true, development requires an environment with some level of randomness.

GOD Must Be Small In Size And Permanent In Time

wikipedia |  In chapter I, Schrödinger explains that most physical laws on a large scale are due to chaos on a small scale. He calls this principle "order-from-disorder." As an example he mentions diffusion, which can be modeled as a highly ordered process, but which is caused by random movement of atoms or molecules. If the number of atoms is reduced, the behaviour of a system becomes more and more random. He states that life greatly depends on order and that a naïve physicist may assume that the master code of a living organism has to consist of a large number of atoms.

In chapter II and III, he summarizes what was known at this time about the hereditary mechanism. Most importantly, he elaborates the important role mutations play in evolution. He concludes that the carrier of hereditary information has to be both small in size and permanent in time, contradicting the naïve physicist's expectation. This contradiction cannot be resolved by classical physics.

In chapter IV, Schrödinger presents molecules, which are indeed stable even if they consist of only a few atoms, as the solution. Even though molecules were known before, their stability could not be explained by classical physics, but is due to the discrete nature of quantum mechanics. Furthermore, mutations are directly linked to quantum leaps.

He continues to explain, in chapter V, that true solids, which are also permanent, are crystals. The stability of molecules and crystals is due to the same principles and a molecule might be called "the germ of a solid." On the other hand, an amorphous solid, without crystalline structure, should be regarded as a liquid with a very high viscosity. Schrödinger believes the heredity material to be a molecule, which unlike a crystal does not repeat itself. He calls this an aperiodic crystal. Its aperiodic nature allows it to encode an almost infinite number of possibilities with a small number of atoms. He finally compares this picture with the known facts and finds it in accordance with them.

In chapter VI Schrödinger states:

...living matter, while not eluding the "laws of physics" as established up to date, is likely to involve "other laws of physics" hitherto unknown, which however, once they have been revealed, will form just as integral a part of science as the former.

He knows that this statement is open to misconception and tries to clarify it. The main principle involved with "order-from-disorder" is the second law of thermodynamics, according to which entropy only increases in a closed system (such as the universe). Schrödinger explains that living matter evades the decay to thermodynamical equilibrium by homeostatically maintaining negative entropy in an open system.

In chapter VII, he maintains that "order-from-order" is not absolutely new to physics; in fact, it is even simpler and more plausible. But nature follows "order-from-disorder", with some exceptions as the movement of the celestial bodies and the behaviour of mechanical devices such as clocks. But even those are influenced by thermal and frictional forces. The degree to which a system functions mechanically or statistically depends on the temperature. If heated, a clock ceases to function, because it melts. Conversely, if the temperature approaches absolute zero, any system behaves more and more mechanically. Some systems approach this mechanical behaviour rather fast with room temperature already being practically equivalent to absolute zero.

Schrödinger concludes this chapter and the book with philosophical speculations on determinism, free will, and the mystery of human consciousness. He attempts to "see whether we cannot draw the correct non-contradictory conclusion from the following two premises: (1) My body functions as a pure mechanism according to Laws of Nature; and (2) Yet I know, by incontrovertible direct experience, that I am directing its motions, of which I foresee the effects, that may be fateful and all-important, in which case I feel and take full responsibility for them. The only possible inference from these two facts is, I think, that I – I in the widest meaning of the word, that is to say, every conscious mind that has ever said or felt 'I' – am the person, if any, who controls the 'motion of the atoms' according to the Laws of Nature". Schrödinger then states that this insight is not new and that Upanishads considered this insight of "ATHMAN = BRAHMAN" to "represent quintessence of deepest insights into the happenings of the world." Schrödinger rejects the idea that the source of consciousness should perish with the body because he finds the idea "distasteful". He also rejects the idea that there are multiple immortal souls that can exist without the body because he believes that consciousness is nevertheless highly dependent on the body. Schrödinger writes that, to reconcile the two premises,

The only possible alternative is simply to keep to the immediate experience that consciousness is a singular of which the plural is unknown; that there is only one thing and that what seems to be a plurality is merely a series of different aspects of this one thing…

Any intuitions that consciousness is plural, he says, are illusions. Schrödinger is sympathetic to the Hindu concept of Brahman, by which each individual's consciousness is only a manifestation of a unitary consciousness pervading the universe — which corresponds to the Hindu concept of God. Schrödinger concludes that "...'I' am the person, if any, who controls the 'motion of the atoms' according to the Laws of Nature." However, he also qualifies the conclusion as "necessarily subjective" in its "philosophical implications". In the final paragraph, he points out that what is meant by "I" is not the collection of experienced events but "namely the canvas upon which they are collected." If a hypnotist succeeds in blotting out all earlier reminiscences, he writes, there would be no loss of personal existence — "Nor will there ever be."^[8]

A LOOOOONG Ways To Go Sonny Boy, But At Least He's Barking In The Vicinity Of A Tree!

medium |  One of the clear indicators of non-equilibrium processes that scientists have studied in single celled organisms is a loss of what is called detailed balance. Detailed balance is simply the sense that time is neither running forwards or backwards. In other words, a process is just as likely to move from one state in phase space to another as back again.

Thus, the trajectories through phase space that exemplify non-equilibria are those that are distinctly future oriented. They have a memory of past, and they are irreversible or nearly so. And these are also what life depends upon.

Life is able to keep non-equilibrium processes in check however. When it gets out of control, you get cancer, unconstrained growth and out of control metabolic properties. It is as if life is trying to ride a bike down a steep path and cancer is when the bike starts to careen out of control down the slope. Because an out of control process will lead to complete disorder eventually, a tangled mess at the bottom where equilibrium, i.e., death, occurs, life must maintain itself at the brink between chaos and order, between a fast decent to one equilibrium and a stand still at another.

Despite all its vast array, perhaps this definition of life as non-equilibrium processes that maintain high probability trajectories in phase space while maintaining order for a long time will provide, if not a definition, at least a measure of how alive something is. Certainly passing on genetic encoding might be included for it is another measure of persistence.

Such an achievement might also have applications. It could provide us insight into how to build technology that is more “alive” and thus able to repair itself and stop from degrading in hostile environments. This could be useful for biotechnology including medical implants. It could also have applications for space based technologies, especially those that are designed to visit distant planets and act autonomously in unknown environments. The future may not be one of steel and glass and obviously artificial machines but one where biology meets technology and technology borrows the best of what it means to be alive in order to sustain itself. What a fascinating world that would be.

Fugg Around With Sheeple Quantum Biology, But You Not Gonna Phug With Mine...,

medical-net  |  Quantum biology is an emerging field of science, established in the 1920s, which looks at whether the subatomic world of quantum mechanics plays a role in living cells. Quantum mechanics is an interdisciplinary field by nature, bringing together nuclear physicists, biochemists and molecular biologists.

In a research paper published by the journal Physical Chemistry Chemical Physics, a team from Surrey's Leverhulme Quantum Biology Doctoral Training Centre used state-of-the-art computer simulations and quantum mechanical methods to determine the role proton tunneling, a purely quantum phenomenon, plays in spontaneous mutations inside DNA.

Proton tunneling involves the spontaneous disappearance of a proton from one location and the same proton's re-appearance nearby.

The research team found that atoms of hydrogen, which are very light, provide the bonds that hold the two strands of the DNA's double helix together and can, under certain conditions, behave like spread-out waves that can exist in multiple locations at once, thanks to proton tunneling. This leads to these atoms occasionally being found on the wrong strand of DNA, leading to mutations.

Although these mutations' lifetime is short, the team from Surrey has revealed that they can still survive the DNA replication mechanism inside cells and could potentially have health consequences.

Dr Marco Sacchi, the project lead and Royal Society University Research Fellow at the University of Surrey, said: "Many have long suspected that the quantum world - which is weird, counter-intuitive and wonderful - plays a role in life as we know it. While the idea that something can be present in two places at the same time might be absurd to many of us, this happens all the time in the quantum world, and our study confirms that quantum tunneling also happens in DNA at room temperature."

There is still a long and exciting road ahead of us to understand how biological processes work on the subatomic level, but our study - and countless others over the recent years - have confirmed quantum mechanics are at play. In the future, we are hoping to investigate how tautomers produced by quantum tunneling can propagate and generate genetic mutations."

Louie Slocombe, PhD Student, Leverhulme Quantum Biology Doctoral Training Centre and Study Co-Author

Jim Al-Khalili, a co-author of the study and Co-Director of the Leverhulme Quantum Biology Doctoral Training Centre at the University of Surrey, said: "It has been thrilling to work with this group of young, diverse and talented thinkers - made up of a broad coalition of the scientific world. This work cements quantum biology as the most exciting field of scientific research in the 21st century."

mRNA Neo-Vaccinoids Are An ABOMINATION To The Root Of Life Itself

discovermagazine |  With photosynthesis, scientists show for the first time that there are quantum effects in living systems. This could lead to better solar panels, energy storage or even quantum computers. (Credit: Shutterstock) We all probably learned about photosynthesis, how plants turn sunlight into energy, in school. It might seem, therefore, that we figured out this bit of the world. But scientists are still learning new things about even the most basic stuff (see also the sun and moon), and photosynthesis is no different. In particular, according to a study released Monday in Nature Chemistry, an international team of scientists showed that molecules involved in photosynthesis display quantum mechanical behavior. Even though we’d suspected as much before, this is the first time we’ve seen quantum effects in living systems. Not only will it help us better understand plants, sunlight and everything in between, but it could also mean cool new tech in the future.

The Quantum Conundrum

First, let’s back up. While photosynthesis may be taught in classrooms the world over, quantum mechanics is a bit less popular, in part because it’s so weird. Nobel Prize-winning quantum physicist Richard Feynman once said, "I think I can safely say that nobody understands quantum mechanics." It’s so impenetrable to non-experts that the same metaphors come up whenever someone tries to explain it. You might have heard of Schrödinger's Cat, which is both alive and dead at the same time thanks to quantum weirdness — in particular, because electrons can be in two states at the same time. It’s only when we observe the system that the weirdness collapses and reality “picks” one state: the cat’s actually alive (or dead), the electron’s actually at this end of the room (or that end). But quantum effects are typically limited to the very small, and only really observable in perfect, laboratory conditions. A living being, with its wet, messy systems, would be a tough place to find some quantum weirdness lurking — and yet we have. 

Molecular Madness

Scientists zoomed in on the Fenna-Matthews-Olson (FMO) complex, a key component of green sulfur bacteria's machinery for photosynthesis. It’s been a historical favorite for such research because we’ve long known its structure and it's fairly easy to work with. Previous experiments had seemed to show light-sensitive molecules in this area in two different states at the same time — that’s quantum weirdness — but the effect lasted more than 1 picosecond, which is much longer than expected. This new study shows that it was really just regular vibrations in the molecules, nothing quantum about it. But researchers have been excited about the possibilities of quantum biology for years, so having disproved the earlier experiments, the authors wanted to find some new evidence of their own. “We wondered if we might be able to observe that Schrödinger cat situation,” says co-author Thomas la Cour Jansen in a press release. And observe it they did! With a technique called two-dimensional electronic spectroscopy, researchers saw molecules in simultaneous excited states — quantum weirdness akin to a cat being alive and dead at the same time. What’s more, the effect lasted exactly as long as theories predicted it, suggesting this evidence of quantum biology will last. As the authors succinctly put it, “Thus, our measurements provide an unambiguous experimental observation of excited-state vibronic coherence in the FMO complex.” What could be simpler? The results shed light (haha) on how to harvest energy from light, and the team thinks they’re “generally applicable” to a variety of systems, living and non-living alike. This means it could result in engineering benefits such as better solar panels, energy storage or even quantum computers. And, of course, updated textbooks for tomorrow’s lessons on photosynthesis.

 

I Don't Think Of Quantum Biology As A Metaphor...,

quantamagazine  |   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.

 

 

Indefinite Causality

wired |  Over the last five years, a growing community of quantum physicists has been implementing the quantum switch in tabletop experiments and exploring the advantages that indefinite causal order offers for quantum computing and communication. It’s “really something that could be useful in everyday life,” said Giulia Rubino, a researcher at the University of Bristol who led the first experimental demonstration of the quantum switch in 2017.

But the practical uses of the phenomenon only make the deep implications more acute.

Physicists have long sensed that the usual picture of events unfolding as a sequence of causes and effects doesn’t capture the fundamental nature of things. They say this causal perspective probably has to go if we’re ever to figure out the quantum origin of gravity, space and time. But until recently, there weren’t many ideas about how post-causal physics might work. “Many people think that causality is so basic in our understanding of the world that if we weaken this notion we would not be able to make coherent, meaningful theories,” said Brukner, who is one of the leaders in the study of indefinite causality.

That’s changing as physicists contemplate the new quantum switch experiments, as well as related thought experiments in which Alice and Bob face causal indefiniteness created by the quantum nature of gravity. Accounting for these scenarios has forced researchers to develop new mathematical formalisms and ways of thinking. With the emerging frameworks, “we can make predictions without having well-defined causality,” Brukner said.

Progress has grown swifter recently, but many practitioners trace the origin of this line of attack on the quantum gravity problem to work 16 years ago by Lucien Hardy, a British-Canadian theoretical physicist at the Perimeter Institute for Theoretical Physics in Waterloo, Canada. “In my case,” said Brukner, “everything started with Lucien Hardy’s paper.”

Hardy was best known at the time for taking a conceptual approach made famous by Albert Einstein and applying it to quantum mechanics.

Einstein revolutionized physics not by thinking about what exists in the world, but by considering what individuals can possibly measure. In particular, he imagined people on moving trains making measurements with rulers and clocks. By using this “operational” approach, he was able to conclude that space and time must be relative.

In 2001, Hardy applied this same approach to quantum mechanics. He reconstructed all of quantum theory starting from five operational axioms.

He then set out to apply it to an even bigger problem: the 80-year-old problem of how to reconcile quantum mechanics and general relativity, Einstein’s epic theory of gravity. “I’m driven by this idea that perhaps the operational way of thinking about quantum theory may be applied to quantum gravity,” Hardy told me over Zoom this winter.

Curiously Satisfying...,

To return to Hebrews, the writer goes on to say: ' ... it is impossible to please God without faith' (xi.6). That is, it is impossible without the basis or foundation of faith, which makes it possible for a man to think beyond the evidence of his senses and realise the existence of invisible scale and understand psychological meaning. To realise scale means to realise that there are different levels of meaning. Literal meaning is one thing, psychological or spiritual meaning is another thing - although the words used are the same. For example, we saw that the word yeast used in the incident quoted indicated two levels of meaning. The disciples took it on the lower level and were told it was because their faith was little. Their thinking was sensual.

They had difficulty in thinking in a new way on another level. And their psychological thinking was so weak just because they were based on sense and not on faith. Thus sense and faith describe two ways of thinking, not opposites, not antagonistic, but on different levels. For without the perception of scale and levels, things are made to be opposite when they are not so, and Man's mind is split into 'either - or', which leads to endless confusions and mental wrangles and miseries. The writer goes on to say: 'Nobody reaches God's presence until he has learned to believe that God exists and that He rewards those that try to find Him' (xi.6). It is apparent that if scale is behind all things, if order is scale, and if to set in order is to set in scale then what is higher and what is lower must exist. To everything there must be an above and a below. A man who cannot perceive scale, visible and invisible, as did that centurion by means of his psychological understanding due to his great faith, will be shut to the intuitions that only faith opens out to every mind that hitherto has been asleep in the senses and the limited world revealed by them.

The chief preliminary voluntary act - and it needs to be lifelong in its voluntaryness - towards the inner spirit, the source and conveyor of meaning, is that of affirmation. Only by this act does all that is outward, external and dead become connected with what is internal and alive. This is the chief of all psychological acts. It is the preliminary and at the same time the continually renewable act whereby psychology, in the deepest sense - (that is, the science of personal evolution) begins. The final goal of it, far ahead, is the unity of oneself. Man becomes gradually united through himself with himself and not merely with what he accidentally has become and believes himself to be. Affirmation is not by argument but by understanding. Negation leads always to an inner deprivation and so to an increasing superficiality, impatience, loss of meaning, and violence. One can always deny. What is easier? One can always follow the path of negation, if one evades all acts of understand-
ing as sentimental or as scientifically and commercially valueless.

For St. Augustine and many more before and after him, the sick, the deaf, and the dead in the Gospels are the sick and deaf,  and the dead within. And in speaking of the two blind men who, sitting by the way side as Jesus was passing, cried out and asked that their eyes might be opened, he asks if we can really suppose that this is merely an account of a miraculous event concerning two physically blind men? Why does it say that the crowd try to restrain them, and that they fight against it and insist on attracting the attention of Jesus? 'They overcame the crowd, who kept them back, by the great perseverance of their cry, that their voice might reach the Lord's ears. . . . The Lord was passing by and they cried out. The Lord stood still and they were healed. For the Lord Jesus stood still and said, What will ye that I shall do unto you? They said unto him, That our eyes may be opened.' (Matthew xx.30-34) The blind here are those who cannot see but wish to see. Augustine says they are those who are blind in their hearts and realise it. Like the deaf, like the sick and the dead, the blind are a certain kind of people. They are, in this case, people in a certain inner state, knowing they are blind, and wishing to see clearly. 'Cry out among the very crowds', he says, 'and do not despair.' Who are these two blind men who know they cannot see but who recognise the spiritual meaning typified in the person of Jesus - what individual functions of the soul are shewn here that struggle with the crowd of commonplace meanings and thoughts and finally, by their own determination, receive their power of vision? 'If two or three are gathered together in my name . . . ' said Christ (Matthew xviii.20). What two sides of ourselves must first take part that our eyes may be opened - that is, our understanding? Why two, to make it effective?  Nicoll The Mark

DISC: Why Black Holes Instead Of Dark Energy Stars?

consciousnessanduniverse |  A recent study has suggested that dark energy stars may be an alternative to black holes. The term “dark energy star” was coined by George Chapline when he proposed that gravitational collapse of objects with masses greater than a few solar masses should lead to the formation of a compact object called dark energy star with a much larger vacuum energy. The study may be viewed in the context of another paper which states that the important question concerns whether dark energy is a completely new physical entity or one which we already know, namely a gravitational energy within the vacuum of a closed gravitating system that has long been known to be a negative energy. It remains to be seen whether scientists currently analyzing the data gathered by the Event Horizon Telescope (EHT) will provide evidence that dark energy stars exist. EHT is a virtual Earth-sized telescope aimed to measure the size of the emission regions of two supermassive black holes, Sagittarius A* at the center of the Milky Way and M87 in the center of the Virgo A galaxy.

 We know that dark energy is embedded in space, counteracting gravity. The way gravity and antigravity are interacting in my mind is somehow related to time. With the understanding that time’s arrow is perspectival,   I  picture the negative-energy particles of the dark sector traveling backwards from the future somehow meeting at the intersection of past and future those positive-energy particles traveling forward in time as if they both were traveling the same distance in their determination to meet. That is how I see a cosmic coincidence unfolding, with matter and dark energy densities being of precisely the same order in the present times. Lastly, I imagine a phantom energy to be something that appears to have no physical reality and still is ultimately real. Raising the concept of a divide begs the question of what lies on the other side and what circumstances enable its crossing. The modified gravity approach as an alternative to dark energy is the focus of research and may be the 

key to unifying both components of the dark sector, a path to solving the coincidence problem.

Consciousness Does Not Compute

nautil |  This past March, when I called Penrose in Oxford, he explained that his interest in consciousness goes back to his discovery of Gödel’s incompleteness theorem while he was a graduate student at Cambridge. Gödel’s theorem, you may recall, shows that certain claims in mathematics are true but cannot be proven. “This, to me, was an absolutely stunning revelation,” he said. “It told me that whatever is going on in our understanding is not computational.”

He was also jolted by a series of lectures on quantum mechanics by the great physicist Paul Dirac. Like many others, Penrose struggled with the weirdness of quantum theory. “As Schrödinger clearly pointed out with his poor cat, which was dead and alive at the same time, he made this point deliberately to show why his own equation can’t be the whole truth. He was more or less saying, ‘That’s nonsense.’ ” To Penrose, the takeaway was that something didn’t add up in quantum theory: “Schrödinger was very upset by this, as were Dirac and Einstein. Some of the major figures in quantum mechanics were probably more upset than I was.”

But what, I asked, does any of this have to do with consciousness? “You see, my argument is very roundabout. I think this is why people don’t tend to follow me. They’ll pick up on it later, or they reject it later, but they don’t follow argument.” Penrose then launched into his critique of why computers, for all their brute calculating power, lack any understanding of what they’re doing. “What I’m saying—and this is my leap of imagination which people boggle at—I’m saying what’s going on in the brain must be taking advantage not just of quantum mechanics, but where it goes wrong,” he said. “It’s where quantum mechanics needs to be superseded.” So we need a new science that doesn’t yet exist? “That’s right. Exactly.”

After we’d talked for 20 minutes, I pointed out that he still hadn’t mentioned biology or the widely held belief that consciousness is an emergent property of the brain. “I know, I know,” he chuckled, and then told me why he felt compelled to write his first book on consciousness, The Emperor’s New Mind, published in 1989. It was after he heard a BBC interview with Marvin Minsky, a founding father of artificial intelligence, who had famously pronounced that the human brain is “just a computer made of meat.” Minsky’s claims compelled Penrose to write The Emperor’s New Mind, arguing that human thinking will never be emulated by a machine. The book had the feel of an extended thought experiment on the non-algorithmic nature of consciousness and why it can only be understood in relation to Gödel’s theorem and quantum physics.

Minsky, who died last year, represents a striking contrast to Penrose’s quest to uncover the roots of consciousness. “I can understand exactly how a computer works, although I’m very fuzzy on how the transistors work,” Minsky told me during an interview years ago. Minsky called consciousness a “suitcase word” that lacks the rigor of a scientific concept. “We have to replace it by ‘reflection’ and ‘decisions’ and about a dozen other things,” he said. “So instead of talking about the mystery of consciousness, let’s talk about the 20 or 30 really important mental processes that are involved. And when you’re all done, somebody says, ‘Well, what about consciousness?’ and you say, ‘Oh, that’s what people wasted their time on in the 20th century.’ ”

Is Sir Roger Penrose's Science of Consciousness Spooky?

medium |  Thus could Roger Penrose’s position be entirely motivated by scientific anti-reductionism? Doctor Susan Blackmore certainly thinks that this is an important motivation. Or at least the programme maker in the following quote does. She writes:

“Finally they got to consciousness. With clever computer graphics and Horizonesque hype they explained that brave scientists, going against the reductionist grain, can now explain the power of the mind to transcend death. It all comes down to quantum coherence in the microtubules. And to make sure the viewer knows that this is ‘real science’ the ponderous voice-over declared ‘Their theory is based on a well established field of science; the laws of general relativity, as discovered by Einstein.’…”

Sure, Blackmore’s talking here about “near-death experiences” (NDEs). Yet those who believe in this — or at least some of them — have found succor in “quantum coherence in the microtubules”. Now don’t those things sound very scientific? Of course we’ll now need to know what quantum coherence is. (Or is it really a case of needing to know whether or not the believers in NDEs actually have any idea of what quantum coherence is?)

Of course Penrose and Stuart Hameroff can’t personally be blamed for spook-lovers quoting their work. However, a psychologist or philosopher may tell us that these two fellows — both scientists — are motivated by very similar things. After all, Hameroff himself has talked about NDEs.

Specifically, Hameroff has said that when the brain dies (or stops functioning), the information within that brain’s microtubules remains alive (as it were) or intact. Moreover, the information of the microtubules leaks out into the world (or, well, into the universe). Not only that: this microtubular information remains intact and bound together because of the power of quantum coherence.

Hameroff goes even further. He’s stated that this phenomenon explains why the subject can experience — see? — himself hovering over his own body. That is, Hameroff seems to endorse near-death experiences. Yet even if “information” (P.M.S. Hacker would have a field day with this word — see here) did leak out into the universe, how would that make it the case that the body which hovers above also has a body and sensory experiences? Microtubular information in the air doesn’t a physical person make. And without a physical body, there are no sensory experiences or anything else for that matter. Thus this is like claiming that if you turn the computer off and then smash it up so violently that its material structure shatters into dust, then the “information” inside would still be intact and would simply float in the air above it. In other words, the soul of the computer would still exist. Unless Hameroff is simply telling us about what he thinks people imagine (or hallucinate) when they’re having a NDE. Though if that’s the case, why all this stuff about microtubular information leaking into the air or even into the universe?

This spooky anti-reductionist motivation is further explained by the philosopher and materialist Patricia Churchland and also the philosopher Rick Grush. According to Blackmore,

“they suggest, it is because some people find the idea of explaining consciousness by neuronal activity somehow degrading or scary, whereas ‘explaining’ it by quantum effects retains some of the mystery”.

Churchland is even more dismissive when she says (as quoted by Blackmore):

“Quantum coherence in the microtubules is about as explanatorily powerful as pixie dust in the synapses.”

To put it more philosophically and simply, Penrose and Hameroff’s position appears to be a defence of traditional dualism. Or, at the very least, the belief in NDEs certainly backs up traditional dualism. And, as we’ve just seen, Hameroff has defended NDEs.

Dualism, Intuition and Free Will

Traditional philosophical dualism has just been mentioned. Here again we can tie Hameroff and Penrose to the concerns (or obsessions) of traditional philosophy. That is, Hameroff hints that his and Penrose’s positions may solve the traditional problems of free will, “the unitary sense of self” and the source and nature of intuition/insight. More specifically, all these philosophical conundrums can be explained by quantum coherence in the microtubules. In terms of simply-put examples, free will is down to quantum indeterminacy; non-locality is responsible for “the unity of consciousness”; and non-algorithmic processing is the baby of “quantum superposition”.

In the technical terms of mind-brain interaction, and as a result of accepting mind-body dualism, the brain and mind can be mutually involved in quantum “entanglement” which is “non-local”. Thus, put simply, we can have mind-to-brain causation. Though this would of course depend on seeing the mind as not being the brain or not even being physical (in a strict or even a non-strict sense). This would put both the mind and brain in the same holistic package and that would help all of us explain…. just about everything!

Quantum Consciousness: Orch-OR Is Better Supported Experimentally Than Any Other Theory Of Consciousness

oxford |  The Penrose-Hameroff ‘Orchestrated objective reduction’ (‘Orch OR’) theory suggests consciousness arises from ‘orchestrated’ quantum superpositioned oscillations in microtubules inside brain neurons. These evolve to reach threshold for Penrose ‘objective reduction’ (‘OR’) by E=h/t (E is the gravitational self-energy of the superposition/separation, h is the Planck-Dirac constant, and at the time at which Orch OR occurs) to give moments of conscious experience. Sequences, interference and resonance of entangled moments govern neurophysiology and provide our ‘stream’ of consciousness. Anesthetic gases selectively block consciousness, sparing non-conscious brain activities, binding by quantum coupling with aromatic amino acid rings inside brain proteins. Genomic, proteomic and optogenetic evidence indicate the microtubule protein tubulin as the site of anesthetic action. We (Craddock et al, Scientific Reports 7,9877, 2017) modelled couplings among all 86 aromatic amino acid rings in tubulin, and found a spectrum of terahertz (‘THz’) quantum oscillations including a common mode peak at 613 THz. Simulated presence of 8 different anesthetics each abolished the peak, and dampened the spectrum proportional to anesthetic potency. Non-anesthetic gases which bind in the same regions, but do not cause anesthesia, did not abolish or dampen the THz activity. Orch OR is better supported experimentally than any other theory of consciousness.

Elven Queen Plumbing The Abyssal Reaches Got Me Wanting To Live Forever...,

Quantamagazine |  Furey has gone further. In her most recent published paper, which appeared in May in The European Physical Journal C, she consolidated several findings to construct the full Standard Model symmetry group, SU(3) × SU(2) × U(1), for a single generation of particles, with the math producing the correct array of electric charges and other attributes for an electron, neutrino, three up quarks, three down quarks and their anti-particles. The math also suggests a reason why electric charge is quantized in discrete units — essentially, because whole numbers are.

However, in that model’s way of arranging particles, it’s unclear how to naturally extend the model to cover the full three particle generations that exist in nature. But in another new paper that’s now circulating among experts and under review by Physical Letters B, Furey uses C⊗O to construct the Standard Model’s two unbroken symmetries, SU(3) and U(1). (In nature, SU(2) × U(1) is broken down into U(1) by the Higgs mechanism, a process that imbues particles with mass.) In this case, the symmetries act on all three particle generations and also allow for the existence of particles called sterile neutrinos — candidates for dark matter that physicists are actively searching for now. “The three-generation model only has SU(3) × U(1), so it’s more rudimentary,” Furey told me, pen poised at a whiteboard. “The question is, is there an obvious way to go from the one-generation picture to the three-generation picture? I think there is.”

This is the main question she’s after now. The mathematical physicists Michel Dubois-Violette, Ivan Todorov and Svetla Drenska are also trying to model the three particle generations using a structure that incorporates octonions called the exceptional Jordan algebra. After years of working solo, Furey is beginning to collaborate with researchers who take different approaches, but she prefers to stick with the product of the four division algebras, R⊗C⊗H⊗O, acting on itself. It’s complicated enough and provides flexibility in the many ways it can be chopped up. Furey’s goal is to find the model that, in hindsight, feels inevitable and that includes mass, the Higgs mechanism, gravity and space-time.

Already, there’s a sense of space-time in the math. She finds that all multiplicative chains of elements of R⊗C⊗H⊗O can be generated by 10 matrices called “generators.” Nine of the generators act like spatial dimensions, and the 10th, which has the opposite sign, behaves like time. String theory also predicts 10 space-time dimensions — and the octonions are involved there as well. Whether or how Furey’s work connects to string theory remains to be puzzled out.

So does her future. She’s looking for a faculty job now, but failing that, there’s always the ski slopes or the accordion. “Accordions are the octonions of the music world,” she said — “tragically misunderstood.” She added, “Even if I pursued that, I would always be working on this project.”