The Quantum Future Of Biology

royalsocietypublishing |  Biological systems are dynamical, constantly exchanging energy and matter with the environment in order to maintain the non-equilibrium state synonymous with living. Developments in observational techniques have allowed us to study biological dynamics on increasingly small scales. Such studies have revealed evidence of quantum mechanical effects, which cannot be accounted for by classical physics, in a range of biological processes. Quantum biology is the study of such processes, and here we provide an outline of the current state of the field, as well as insights into future directions.

1. Introduction

Quantum mechanics is the fundamental theory that describes the properties of subatomic particles, atoms, molecules, molecular assemblies and possibly beyond. Quantum mechanics operates on the nanometre and sub-nanometre scales and is at the basis of fundamental life processes such as photosynthesis, respiration and vision. In quantum mechanics, all objects have wave-like properties, and when they interact, quantum coherence describes the correlations between the physical quantities describing such objects due to this wave-like nature.

In photosynthesis, respiration and vision, the models that have been developed in the past are fundamentally quantum mechanical. They describe energy transfer and electron transfer in a framework based on surface hopping. The dynamics described by these models are often ‘exponential’ and follow from the application of Fermi’s Golden Rule [1,2]. As a consequence of averaging the rate of transfer over a large and quasi-continuous distribution of final states the calculated dynamics no longer display coherences and interference phenomena. In photosynthetic reaction centres and light-harvesting complexes, oscillatory phenomena were observed in numerous studies performed in the 1990s and were typically ascribed to the formation of vibrational or mixed electronic–vibrational wavepackets. The reported detection of the remarkably long-lived (660 fs and longer) electronic quantum coherence during excitation energy transfer in a photosynthetic system revived interest in the role of ‘non-trivial’ quantum mechanics to explain the fundamental life processes of living organisms [3]. However, the idea that quantum phenomena—like coherence—may play a functional role in macroscopic living systems is not new. In 1932, 10 years after quantum physicist Niels Bohr was awarded the Nobel Prize for his work on the atomic structure, he delivered a lecture entitled ‘Light and Life’ at the International Congress on Light Therapy in Copenhagen [4]. This raised the question of whether quantum theory could contribute to a scientific understanding of living systems. In attendance was an intrigued Max Delbrück, a young physicist who later helped to establish the field of molecular biology and won a Nobel Prize in 1969 for his discoveries in genetics [5].

All living systems are made up of molecules, and fundamentally all molecules are described by quantum mechanics. Traditionally, however, the vast separation of scales between systems described by quantum mechanics and those studied in biology, as well as the seemingly different properties of inanimate and animate matter, has maintained some separation between the two bodies of knowledge. Recently, developments in experimental techniques such as ultrafast spectroscopy [6], single molecule spectroscopy [7–11], time-resolved microscopy [12–14] and single particle imaging [15–18] have enabled us to study biological dynamics on increasingly small length and time scales, revealing a variety of processes necessary for the function of the living system that depend on a delicate interplay between quantum and classical physical effects.

Quantum biology is the application of quantum theory to aspects of biology for which classical physics fails to give an accurate description. In spite of this simple definition, there remains debate over the aims and role of the field in the scientific community. This article offers a perspective on where quantum biology stands today, and identifies potential avenues for further progress in the field.

2. What is quantum biology?

Biology, in its current paradigm, has had wide success in applying classical models to living systems. In most cases, subtle quantum effects on (inter)molecular scales do not play a determining role in overall biological function. Here, ‘function’ is a broad concept. For example: How do vision and photosynthesis work on a molecular level and on an ultrafast time scale? How does DNA, with stacked nucleotides separated by about 0.3 nm, deal with UV photons? How does an enzyme catalyse an essential biochemical reaction? How does our brain with neurons organized on a sub-nanometre scale deal with such an amazing amount of information? How do DNA replication and expression work? All these biological functions should, of course, be considered in the context of evolutionary fitness. The differences between a classical approximation and a quantum-mechanical model are generally thought to be negligible in these cases, even though at the basis every process is entirely governed by the laws of quantum mechanics. What happens at the ill-defined border between the quantum and classical regimes? More importantly, are there essential biological functions that ‘appear’ classical but in reality are not? The role of quantum biology is precisely to expose and unravel this connection.

Fundamentally, all matter—animate or inanimate—is quantum mechanical, being constituted of ions, atoms and/or molecules whose equilibrium properties are accurately determined by quantum theory. As a result, it could be claimed that all of biology is quantum mechanical. However, this definition does not address the dynamical nature of biological processes, or the fact that a classical description of intermolecular dynamics seems often sufficient. Quantum biology should, therefore, be defined in terms of the physical ‘correctness’ of the models used and the consistency in the explanatory capabilities of classical versus quantum mechanical models of a particular biological process.

As we investigate biological systems on nanoscales and larger, we find that there exist processes in biological organisms, detailed in this article, for which it is currently thought that a quantum mechanical description is necessary to fully characterize the behaviour of the relevant subsystem. While quantum effects are difficult to observe on macroscopic time and length scales, processes necessary for the overall function and therefore survival of the organism seem to rely on dynamical quantum-mechanical effects at the intermolecular scale. It is precisely the interplay between these time and length scales that quantum biology investigates with the aim to build a consistent physical picture.

Grand hopes for quantum biology may include a contribution to a definition and understanding of life, or to an understanding of the brain and consciousness. However, these problems are as old as science itself, and a better approach is to ask whether quantum biology can contribute to a framework in which we can repose these questions in such a way as to get new answers. The study of biological processes operating efficiently at the boundary between the realms of quantum and classical physics is already contributing to improved physical descriptions of this quantum-to-classical transition.

More immediately, quantum biology promises to give rise to design principles for biologically inspired quantum nanotechnologies, with the ability to perform efficiently at a fundamental level in noisy environments at room temperature and even make use of these ‘noisy environments’ to preserve or even enhance the quantum properties [19,20]. Through engineering such systems, it may be possible to test and quantify the extent to which quantum effects can enhance processes and functions found in biology, and ultimately answer whether these quantum effects may have been purposefully selected in the design of the systems. Importantly, however, quantum bioinspired technologies can also be intrinsically useful independently from the organisms that inspired them.

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

Is An Ancient Virus The Physical Substrate For Memory Formation?

royalsocietyofbiology |  Understanding how memories are formed and stored is one of the great enigmas in neuroscience. After more than a century of research, detailed knowledge of the mechanisms of memory formation remain elusive.

In the past decade, memory research has been advanced by the study of neuronal engrams, or networks of neurons that are incorporated into a memory. In particular brain regions associated with memory, a neuronal engram is theorised to consist of a subset of neurons within that brain region that is uniquely activated by a behaviour that leads to memory formation.

For example, when mice are trained on a simple, initial behavioural task, a certain subset of neurons within a specific brain region will become activated. Genetic techniques can be used to ‘tag’ this network of neurons.

If the mouse is then placed in a different behavioural or environmental context, and the network of neurons from the initial behavioural task is artificially activated, the mouse will display behaviour that it learned in the initial task[1]. The initial behavioural task triggered the incorporation of a subset of neurons into an engram, which encoded the memory for that task.

Given the vast number of neurons in the brain, the potential combination of neurons that could make up separate memory engrams is virtually limitless. So the question that is key to our understanding of the mechanisms of memory formation is: what causes the incorporation of one neuron, but not another, into memory engrams?

Research has demonstrated that certain proteins can ‘prime’ neurons for incorporation into an engram[2]. Neurons that naturally express more of these proteins are frequently found in memory engrams for a behaviour. Artificially inducing more of these substances to be expressed can encourage neurons to become part of an engram.

One substance in particular that was found to be important for priming neurons for engram incorporation is known as Arc[3]. This protein is induced rapidly by neuronal activity and regulates levels of receptors at synapses that are critical for synaptic function and neuronal communication.

Mice that genetically lack Arc protein are unable to form memories that last longer than the course of a behavioural training session (known as long-term memories), although they can learn normally at short-term time scales. Although these experimental findings suggest that Arc is an important piece of the memory puzzle, the mechanisms that regulate Arc at the cellular and molecular level remain unclear.

Recently, research I conducted in the laboratory of Dr Jason Shepherd at the University of Utah[4] revealed something very surprising: Arc structurally and functionally resembles a retrovirus such as HIV. This is the first time a neuronal protein, much less one underlying a process as crucial as memory formation, has been shown to have a viral structure. Evolutionary analysis from our laboratory showed that Arc protein is distantly related to a class of retrotransposons that also gave rise to retroviruses such as HIV.

The Fungus Among Us...,

scientificamerican |  We are likely to think of fungi, if we think of them at all, as minor nuisances: mold on cheese, mildew on shoes shoved to the back of the closet, mushrooms springing up in the garden after hard rains. We notice them, and then we scrape them off or dust them away, never perceiving that we are engaging with the fragile fringes of a web that knits the planet together. Fungi constitute their own biological kingdom of about six million diverse species, ranging from common companions such as baking yeast to wild exotics. They differ from the other kingdoms in complex ways. Unlike animals, they have cell walls, not membranes; unlike plants, they cannot make their own food; unlike bacteria, they hold their DNA within a nucleus and pack cells with organelles—features that make them, at the cellular level, weirdly similar to us. Fungi break rocks, nourish plants, seed clouds, cloak our skin and pack our guts, a mostly hidden and unrecorded world living alongside us and within us.

That mutual coexistence is now tipping out of balance. Fungi are surging beyond the climate zones they long lived in, adapting to environments that would once have been inimical, learning new behaviors that let them leap between species in novel ways. While executing those maneuvers, they are becoming more successful pathogens, threatening human health in ways—and numbers—they could not achieve before.

Surveillance that identifies serious fungal infections is patchy, and so any number is probably an undercount. But one widely shared estimate proposes that there are possibly 300 million people infected with fungal diseases worldwide and 1.6 million deaths every year—more than malaria, as many as tuberculosis. Just in the U.S., the CDC estimates that more than 75,000 people are hospitalized annually for a fungal infection, and another 8.9 million people seek an outpatient visit, costing about $7.2 billion a year.

For physicians and epidemiologists, this is surprising and unnerving. Long-standing medical doctrine holds that we are protected from fungi not just by layered immune defenses but because we are mammals, with core temperatures higher than fungi prefer. The cooler outer surfaces of our bodies are at risk of minor assaults—think of athlete's foot, yeast infections, ringworm—but in people with healthy immune systems, invasive infections have been rare.

That may have left us overconfident. “We have an enormous blind spot,” says Arturo Casadevall, a physician and molecular microbiologist at the Johns Hopkins Bloomberg School of Public Health. “Walk into the street and ask people what are they afraid of, and they'll tell you they're afraid of bacteria, they're afraid of viruses, but they don't fear dying of fungi.”

Ironically, it is our successes that made us vulnerable. Fungi exploit damaged immune systems, but before the mid-20th century people with impaired immunity didn't live very long. Since then, medicine has gotten very good at keeping such people alive, even though their immune systems are compromised by illness or cancer treatment or age. It has also developed an array of therapies that deliberately suppress immunity, to keep transplant recipients healthy and treat autoimmune disorders such as lupus and rheumatoid arthritis. So vast numbers of people are living now who are especially vulnerable to fungi. (It was a fungal infection, Pneumocystis carinii pneumonia, that alerted doctors to the first known cases of HIV 40 years ago this June.)

Not all of our vulnerability is the fault of medicine preserving life so successfully. Other human actions have opened more doors between the fungal world and our own. We clear land for crops and settlement and perturb what were stable balances between fungi and their hosts. We carry goods and animals across the world, and fungi hitchhike on them. We drench crops in fungicides and enhance the resistance of organisms residing nearby. We take actions that warm the climate, and fungi adapt, narrowing the gap between their preferred temperature and ours that protected us for so long.

But fungi did not rampage onto our turf from some foreign place. They were always with us, woven through our lives and our environments and even our bodies: every day, every person on the planet inhales at least 1,000 fungal spores. It is not possible to close ourselves off from the fungal kingdom. But scientists are urgently trying to understand the myriad ways in which we dismantled our defenses against the microbes, to figure out better approaches to rebuild them.

 

 

 

Politics Restructured So Corporations CanTreat Citizens As Natural Resources To Be Used For Profit

TCH |  The people behind the JoeBama administration do not need to step on the hot-button issue of ‘vaccine passports’ because they already have ideological allies working on the issue.  Remember that phone call with 100 multinational corporations a few days ago?  Why would a Marxist government need to engage in an issue highly charged with politics, when they can just farm-out the same outcome to their Marxist corporate allies?

Hopefully people can see what is happening here.

There are trillions at stake.  Those trillions need to engage in control mechanisms to retain their position.  The multinational corporations know how financially lucrative COVID compliance is.  Those same multinationals are setting up the parameters for control in the exact same manner the U.S. government would.  The ideological multinationals and the ideological JoeBama administration are working in concert.

Multinationals do not like capitalism because within the process of capitalism they do not have control over the financial outcomes.  Capitalism breeds competition; multinationals abhor competition, they are totalitarian in ideology and want the entire pie under their control.  Multinational corporations do not like capitalism; underline it, emphasize it, do not forget it.

Capitalism is based on the principles of a free market.  Multinationals do not want a free market, they want a controlled market.  Their efforts toward a vaccine passport are an example of yet another control they can manipulate for maximum financial benefit.  It really is that simple…..

…. Meanwhile the crew of totalitarians behind JoeBama know they can benefit from their corporate allies.  The multinationals will pay the politicians for control and the politicians will construct defensive legislative outcomes that protect the multinationals.  That is what is happening in exponentially increasing sunlight.

Unfortunately the multinationals are also the funding mechanism for the UniParty.  Democrats and Republicans both benefit from the financial process of payments by the multinationals for control of legislative outcomes.   This is the entire purpose of K-Street.   In third-world countries we call bribery of elected officials “corruption”; however, in the United States we call bribery of elected officials “lobbying”, the process is exactly the same.

In a slightly nuanced outline of the same type of Government and Multinational merging, Glenn Greenwald has a solid article explaining why and how the corporate world is using “false wokeness” as a tool for expanded financial benefit.

In Bourne Legacy A 1.5% Gain Of Mitochondrial Function Yielded Super Soldiers

thescientist |  Since the 1970s, when researchers turned up similarities between DNA in eukaryotes’ mitochondria and bacterial genomes, scientists have suspected that the organelles descended from symbionts that took up residence within larger cells. A diverse class of bacteria called Alphaproteobacteria soon emerged as a likely candidate for the evolutionary origins of mitochondria. 

But a new analysis, published today (April 25) in Nature, suggests that mitochondria are at best distant cousins to known alphaproteobacteria lineages, and not descendents as previously thought.

“We are still left hungry for the ancestor of mitochondria,” says Puri Lopez-Garcia, a biologist at the University of Paris-South who was not involved in the study.

While it’s generally agreed that Alphaproteobacteria includes the closest bacterial relatives of mitochondria, that relationship doesn’t reveal much about how mitochondrial ancestors made a living or how they made the jump to acting as organelles. That’s because “Alphaproteobacteria is a particularly diverse group of organisms in terms of kinds of metabolism,” Lopez-Garcia explains. 

“You find more or less everything in there.” Some studies have found genetic similarities between mitochondria and an order of alphaproteobacterial symbionts known as Rickettsiales, but other, free-living candidates have also emerged.

The question of where on the alphaproteobacteria family tree the mitochondrial ancestor fell has pestered study coauthor Thijs Ettema throughout his scientific career. “Now, with all the available data from all these new lineages in all sorts of environments, we thought we should just do one bold approach and see where this ends up,” says Ettema, an evolutionary biologist at Uppsala University in Sweden.

Much of the genomic data he and colleagues used in their analysis came from the Tara Oceans dataset, which includes metagenomic sequences from microbes in ocean waters sampled from various depths. “For reasons that are not extremely clear . . . it seems that oceanic waters are extremely enriched for Alphaproteobacteria, and not just one species—it seems to be a whole array,” Ettema explains. The datasets were “good and deep enough to make an effort to reconstruct near-complete genomes.”

Elon Musk Thinks Humans Must Merge with Machines

libertyblitzkrieg |  To start, let’s examine some recent comments made by Elon Musk at the World Government Summit in the UAE.

ArsTechnica reports:

Humans must become cyborgs and develop a direct high-bandwidth connection with machines or risk irrelevance and obsolescence, says Tesla and SpaceX founder Elon Musk.

Musk’s latest cheery thoughts were imparted at the World Government Summit in the UAE. “Over time I think we will probably see a closer merger of biological intelligence and digital intelligence,” Musk said, according to CNBC.

The main thrust of Musk’s argument seems to hinge on the limited bandwidth and processing power of a single human being. Computers can ingest, transfer, and process gigabytes of data per second, every second, forever. Meatbags, however, are severely limited by an input/output rate—talking, typing, listening—that’s best measured in bits per second. Thus, avoid replacement by robot or artificial intelligence, we need to become machines.

By way of example, Musk spoke about self-driving cars, which will very soon start displacing jobs—lots and lots of jobs. “The most near term impact from a technology standpoint is autonomous cars … There are many people whose jobs are to drive. In fact I think it might be the single largest employer of people … We need to figure out new roles for what do those people do, but it will be very disruptive and very quick.”
Autonomous vehicles are perhaps the most visible prominence when it comes to recent developments in AI, but rest assured (or not) that we aren’t even close to AI’s capability ceiling. Current deployments of AI are quite limited in that they can only perform one or two tasks adequately—drive a car, lift a piece of steel, flip a burger—but AI research is slowly bubbling towards artificial general intelligence (AGI), which can ostensibly perform every task that a human is capable of.

Once that happens, it’s fairly safe to assume that AGI will continue to improve until, in the words of Elon Musk, it is “smarter than the smartest human on earth.”

As for how humans might achieve silicon symbiosis, the jury’s still out. Musk, according to CNBC, proposed a brain-attached high-bandwidth computer link, perhaps via neural lace. Low-speed and low-resolution EEG-based brain-computer interfaces already exist, of course, but I doubt that’s what Musk has in mind. In all likelihood, we will need to massively improve our understanding of the human brain before any such interface can be created.

Musk has been one of the individuals at the forefront of warning about the threats of artificial intelligence (AI) for a very long time, but it appears the thrust of his most recent comments center around concerns that a rapid increase in technology applied to the economy will result in a massive wave of job losses. This seems plausible to me, and I’ve called attention to it in the past. For example, in the 2015 post, Chinese Company Moves to Replace 90% of its Workforce with Robots,

Living Together: The Symbiosis of Host-Microbial Interactions

ibiology |  Advances in rRNA sequencing and other techniques have allowed scientists to characterize novel symbiotic partnerships.  In her first lecture, Dr. Margaret McFall-Ngai provides an overview of the three main types of symbiosis: mutualism (both partners benefit), commensalism (only one partner benefits), and parasitism (one partner benefits, but the other partner is harmed).  McFall-Ngai’s research is currently focused on understanding the establishment and maintenance of symbiotic relationships, and the molecular effects that these relationships have on development, health, and disease.

In her second talk, McFall-Ngai tells the story of a symbiosis between the Hawaiian bobtail squid and Vibrio fischeri (V. fischeri), a type of luminescent bacteria that enables the squid to hunt at night. McFall-Ngai and collaborators have identified the molecular mechanism by which nascent Hawaiian bobtail squid select V. fischeri from the thousands of other bacteria in their habitat.  V. fischeri induces developmental changes in the squid that drive daily rhythms of gene expression, which are necessary to control bacterial growth, a crucial cycle in this symbiotic partnership.

Atlas of the RNA Universe

phys.org |  As the floor plan of the living world, DNA guides the composition of animals ranging from unicellular organisms to humans. DNA not only helps shepherd every organism from birth through death, it also plays an essential role in the development of many human diseases.

But it wasn't always so. Long before DNA emerged as the molecule of life, its closely related cousin, RNA (ribonucleic acid), held center stage.

The RNA world refers to a time in earth's distant past when primitive forms used RNA rather than DNA to archive genetic information, pass it along using RNA-based copying machinery and perform biological reactions.

With the emergence of DNA, RNA came to play an intermediary role, copying DNA messages known as genes and translating them into proteins. This pathway from DNA to RNA to protein has become so engrained in the field of biology it is often referred to as "the central dogma."

Recently, however, RNA's strict subservience to DNA has been called into question. New discoveries have prompted an explosion in RNA research, with vital implications for both the foundations of biology and the practice of medicine. (Sidney Altman, who won the Nobel Prize for establishing that RNA can act independently and perform chemical reactions on its own, providing powerful evidence for the RNA world hypothesis, has recently joined ASU's School of Life Sciences).

Planets Will Either Be Lush or Dead

nautilus |  A “living worlds” perspective implies that after billions of years, life will either be absent from a planet or, as on Earth, have thoroughly taken over and become an integral part of all global processes. Signs of life will be everywhere. Once life has taken hold of a planet, once it has become a planetary‐scale entity (a global organism, if you will), it may be very hard to kill. Certainly life has seen Earth through many huge changes, some quite traumatic. Life here is remarkably robust and persistent. It seems to have a kind of immortality. Call it quasi‐immortality, because the planet won’t be around forever, and it may not be habitable for its entire lifetime. Individuals are here for but an instant. Whole species come and go, usually in timescales barely long enough to get the planet’s attention. Yet life as a whole persists. This gives us a different way to think about ourselves. The scientific revolution has revealed us, as individuals, to be incredibly tiny and ephemeral, and our entire existence, not just as individuals but even as a species, to be brief and insubstantial against the larger temporal backdrop of cosmic evolution. If, however, we choose to identify with the biosphere, then we, Gaia, have been here for quite some time, for perhaps 3 billion years in a universe that seems to be about 13 billion years old. We’ve been alive for a quarter of all time. That’s something.

The origin of life on Earth was not just the beginning of the evolution of species, the fount of diversity that eventually begat algae blooms, aspen groves, barrier reefs, walrus huddles, and gorilla troops. From a planetary evolution perspective, this development was a major branching point that opened up a gateway to a fundamentally different future. Then, when life went global, and went deep, planet Earth headed irreversibly down the path not taken by its siblings.

Now, very recently, out of this biologically altered Earth, another kind of change has suddenly emerged and is rewriting the rules of planetary evolution. On the nightside of Earth, the lights are switching on, indicating that something new is happening and someone new is home. Has another gateway opened? Could the planet be at a new branching point?

The view from space sheds light on the multitude of rapid changes inscribed on our planet by our industrial society. The orbital technology enabling this observation is itself one of the strange and striking aspects of the transition now gripping Earth. If up to now the defining characteristic of Earth has been planetary‐scale life, then what about these planetary‐scale lights? Might this spreading, luminous net be part of a new defining characteristic?

inconceivable that humans are the most intelligent animals on the planet

upliftconnect |  Mammals like us, who have been on the planet a whole lot longer than us, who also have larger brains than us, is interesting to reflect on. We humans pride ourselves on technology, on creating tools, gadgets and machines. Of course it is easy to consider that intelligence is based on technology. Then there is the idea of emotional intelligence which acknowledges a form of intelligence which is internal, can not be easily measured empirically but plays a major role in the success of an individual. Intuition, compassion, empathy are usually considered feelings, but these are skills, non-physical tools that we can use to ascend the social ladder. Meditation could also be considered a non-physical tool that changes our biology, reduces stress and opens the mind. We may be at the very beginning of understanding that tools do not need to be physical or easily measurable by traditional science in order to be valuable.

We willingly accept the idea of intelligence in a life-form only if the intelligence displayed is on the same evolutionary wavelength as our own. Technology automatically indicates intelligence. An absence of technology translates into an absence of intelligence.Dolphins and whales do not display intelligence in a fashion recognizable to this conditioned perception of what intelligence is, and thus for the most part, we are blind to a broader definition of what intelligence can be.Evolution molds our projection of intelligence. Humans evolved as tool-makers, obsessed with danger and group aggression. This makes it very difficult for us to comprehend intelligent non-manipulative beings whose evolutionary history featured ample food supplies and an absence of fear from external dangers.  – Paul Watson

Again it is important to recognize how this attitude has not only been applied to animals, but also to indigenous people historically. How we define intelligence is restricted to our definition of intelligence. Are we willing to broaden our definition of intelligence?

Intelligence can also be measured by the ability to live within the bounds of the laws of ecology — to live in harmony with one’s own ecology and to recognize the limitations placed on each species by the needs of an ecosystem. Is the species that dwells peacefully within its habitat with respect for the rights of other species the one that is inferior? Or is it the species that wages a holy war against its habitat, destroying all species that irritate it? What can be said of a species that reproduces beyond the ability of its habitat to support it? What do we make of a species that destroys the diversity that sustains the ecosystem that nourishes it? How is a species to be judged that fouls its water and poisons its own food? On the other hand, how is a species that has lived harmoniously within the boundaries of its ecology to be judged?  – Paul Watson

Watson gets very in-depth and cites the research which compares cranial capacity, and brain complexity between humans and sea mammals. At the very least this information is humbling. Paul Watson has given us a lot to think about, but probably the greatest gift in his essay can be summarized by this quote:

It’s not enough to understand the natural world, the point is to defend and preserve it. – Edward Abbey

Watson is not merely a philosopher, he puts his words and beliefs into action. For 35 years, Captain Paul Watson has been at the helm of the world’s most active marine non-profit organization – the Sea Shepherd Conservation Society. I highly recommend reading the entire essay which is available here.

ubiquitous indestructible cryptobiotic tards....,

theatlantic |  The toughest animals in the world aren't bulky elephants, or cold-tolerant penguins, or even the famously durable cockroach. Instead, the champions of durability are endearing microscopic creatures called tardigrades, or water bears.

They live everywhere, from the tallest mountains to the deepest oceans, and from hot springs to Antarctic ice. They can even tolerate New York. They cope with these inhospitable environments by transforming into a nigh-indestructible state. Their adorable shuffling gaits cease. Their eight legs curl inwards. Their rotund bodies shrivel up, expelling almost all of their water and becoming a dried barrel called a “tun.” Their metabolism dwindles to near-nothingness—they are practically dead. And in skirting the edge of death, they become incredibly hard to kill.

In the tun state, tardigrades don't need food or water. They can shrug off temperatures close to absolute zero and as high as 151 degrees Celsius. They can withstand the intense pressures of the deep ocean, doses of radiation that would kill other animals, and baths of toxic solvents. And they are, to date, the only animals that have been exposed to the naked vacuum of space and lived to tell the tale—or, at least, lay viable eggs. (Their only weakness, as a researcher once told me, is “vulnerability to mechanical damage;” in other words, you can squish ‘em.)

Scientists have known for centuries about the tardigrades’ ability to dry themselves out. But a new study suggests that this ability might have contributed to their superlative endurance in a strange and roundabout way. It makes them uniquely suited to absorbing foreign genes from bacteria and other organisms—genes that now pepper their genomes to a degree unheard of for animals.

Thomas Boothby from the University of North Carolina at Chapel Hill made this discovery after sequencing the first ever tardigrade genome, to better understand how they have evolved. Of the 700 species, his team focused on Hypsibius dujardini, one of the few tardigrades that’s easy to grow and breed in a lab.

At first, Boothby thought his team had done a poor job of assembling the tardigrade’s genome. The resulting data was full of genes that seemed to belong to bacteria and other organisms, not animals. “All of us thought that these were contaminants,” he says. Perhaps microbes had snuck into the samples and their DNA was intermingled with the tardigrade’s own.

But the team soon realized that these sequences are bona fide parts of the tardigrade’s genome.

can we understand evolution without symbiogenesis?

academia |  This work is a contribution to the literature and knowledge on evolution that takes into account the biological data obtained on symbiosis and sym-biogenesis. Evolution is traditionally considered a gradual process essentially consisting of natural selection, conducted on minimal phenotypical variations that are the result of mutations and genetic recombinations to form new spe-cies. However, the biological world presents and involves symbiotic associations between different organisms to form consortia, a new structural life dimension and a symbiont-induced speciation. The acknowledgment of this reality implies a new understanding of the natural world, in which symbiogenesis plays an important role as an evolutive mechanism. Within this understanding, symbiosis is the key to the acquisition of new genomes and new metabolic capacities, driving living forms’ evolution and the establishment of biodiversity and complexity on Earth. This chapter provides information on some of the key figures and their major works on symbiosis and symbiogenesis and reinforces the importance of these concepts in our understanding of the natural world and the role they play in the establishing of the evolutionary complexity of living systems. In this context, the concept of the symbiogenic superorganism is also discussed.

the transhuman jump will not be wearable or reversible...,

MIT |  Sturdy, wearable skins that transform hostile environments into friendlier ones are among the projects developed by Media Lab’s Mediated Matter group, headed by Associate Professor Neri Oxman PhD ’10.

Oxman, who earned her PhD in design computation, leads her Mediated Matter group through explorations of “Nature-inspired Design and Design-inspired Nature” using the tools of computational design, digital fabrication, materials science, and synthetic biology. Many projects rely on advanced 3D printing technologies.

Four artifacts that represent this intersection of 3D printing and synthetic biology were unveiled in Germany last fall in an exhibit of Wanderers: An Astrobiological Exploration, a collaboration with German designers Christoph Bader and Dominik Kolb.

The wearables, printed with Stratasys multi-material 3D printing technology, are designed to create the necessities of human life in space environments. Capillaries are expected to hold synthetically engineered microorganisms that could produce oxygen, light, food, and biofuels. Mediated Matter members led by Will Patrick and Sunanda Sharma are working on embedding living matter in the form of engineered bacteria inside the 3D structures.

“The future of wearables lies in designing augmented extensions to our own bodies, that will blur the boundary between the environment and ourselves,”

transhumans about the bidnis of enginnering biomes, as well...,

MIT |  No matter where you are, you are surrounded by your microbiome—the complex biological system of more than 100 trillion microorganisms on the human body, in airwaves, and in every environment.

“You may not know it, but you’re walking around with two pounds of microbes on you,” says Bernat Olle SM ’05, MBA ’07, PhD ’07. “But only recently have scientists discovered how important and how useful they can be.”

Research in the field of the microbiome is still in its early stages, but it has already shown that microbes play important roles in metabolism, digestion, and even mood. And Olle is one of a growing group of engineers focusing on this area.

“Modern habits have been to clean up and sterilize everything—make it clean as possible,” he says. “But we’re starting to find out this might not be a good idea—and we’re abusing anti-microbial chemicals. These microbial exposures can help develop key human functions.”

Olle is co-founder and COO of Vedanta Biosciences, a Boston-based startup that researches interactions between the human microbiome and the immune system. He spoke to Slice of MIT at the 2015 South by Southwest (SXSW) Interactive, where he was part of a three-person panel that discussed the benefits of microbes and the impact they could have on medicine in the future.

viral proteins regulate human embryonic development

phys.org |  A fertilized human egg may seem like the ultimate blank slate. But within days of fertilization, the growing mass of cells activates not only human genes but also viral DNA lingering in the human genome from ancient infections.

Now researchers at the Stanford University School of Medicine have found that the early human cells produce viral proteins, and even become crowded with what appear to be assembled viral particles. These viral proteins could manipulate some of the earliest steps in human development, affecting gene expression and even possibly protecting the cells from further viral infection.

The finding raises questions as to who, or what, is really pulling the strings during human embryogenesis.

"It's both fascinating and a little creepy," said Joanna Wysocka, PhD, associate professor of developmental biology and of chemical and systems biology. "We've discovered that a specific class of viruses that invaded the human genome during recent evolution becomes reactivated in the early development of the human embryo, leading to the presence of viral-like particles and proteins in the human cells."

A paper describing the findings was published online April 20 in Nature. Wysocka is the senior author, and graduate student Edward Grow is the lead author.

Viral particles in the embryo

Retroviruses are a class of virus that insert their DNA into the genome of the host cell for later reactivation. In this stealth mode, the virus bides its time, taking advantage of cellular DNA replication to spread to each of an infected cell's progeny every time the cell divides. HIV is one well-known example of a retrovirus that infects humans.

When a retrovirus infects a germ cell, which makes sperm and eggs, or infects a very early-stage embryo before the germ cells have arisen, the viral DNA is passed along to future generations. Over evolutionary time, however, these viral genomes often become mutated and inactivated. About 8 percent of the human genome is made up of viral sequences left behind during past infections. One retrovirus, HERVK, however, infected humans repeatedly until relatively recently—within about 200,000 years. Much of HERVK's genome is still snuggled, intact, in each of our cells.

Most of these sequences are inactive in mature cells, but recent research has shown that they can spring to life in tumor cells or in human embryonic stem cells. A study published in February in Cell Stem Cell by researchers from Singapore's Genome Institute showed that sequences from a primate virus called HERVH are also activated in early human development.

Now the Stanford researchers have shown for the first time that viral proteins are abundantly present in the developing human embryo and assemble into what appear to be viral particles in electron microscopy images. By following up with additional studies in human embryonic cells grown in vitro, scientists showed that these viral proteins affect gene expression in the developing embryo and may protect the cells from infection by other viruses.

sociogenomics...,

thescientist |  Eusocial insects are among the most successful living creatures on Earth. Found in terrestrial ecosystems across the globe (on every continent except Antarctica), the world’s ants alone weigh more than all vertebrates put together. Bees are key pollinators of major crops as well as many other ecologically important plants. Termites construct thermoregulating homes that can dominate the landscape, and that are inspiring new energy-efficient skyscraper designs. The organization and collective decision making of eusocial insects is even yielding new insights into human behavior and what it means to be part of a society. But one of the biggest unanswered questions in our understanding of these complex insect groups is how a single genome can produce such diverse and contrasting physical and behavioral forms, from egg layers, provisioners, and caretakers to soldiers.

In a eusocial colony, reproduction is dominated by one or a few individuals adapted to egg laying, 

while their offspring—colony workers—display physical and behavioral adaptations that help them perform their subordinate roles. These phenotypic adaptations can be extreme. A leafcutter ant queen is 10 times larger than her smallest workers, for example.  (See photograph below.) And some carpenter ant species have evolved a “kamikaze” caste, born with a self-destruct button that causes the insect to explode upon colony attack, killing itself and covering the invading animals in toxic chemicals. Remarkably, differences in the behavior and morphology of insect castes are usually generated through differences in the expression of identical sets of genes. (There are a few cases of genetically determined castes, but this is the exception, not the rule.)

We are now entering a new era of research into eusocial insects. For the first time, scientists are investigating the molecules that underlie eusocial behavior at a depth that was previously unimaginable. New, affordable sequencing technologies enable scientists to examine how genes across the entire genome are regulated to generate different caste phenotypes, the roles of DNA methylation and microRNAs in this differential expression, and what proteins are synthesized as a result. This burgeoning area of research, dubbed “sociogenomics” in 2005 by Gene E. Robinson,¹ is revolutionizing our understanding of the evolution of eusociality from a solitary wasp-like ancestor to the million-strong colonies we see today. New work is yielding insights into how genomes interact dynamically with the physical and social environment to produce highly adapted, specialized castes with remarkable phenotypic innovations. These findings are, in turn, illuminating the importance of gene regulation and epigenetics in controlling behavioral plasticity across the animal kingdom.

gene-centrism vs. multi-level selection

guardian |  A disagreement between the twin giants of genetic theory, Richard Dawkins and EO Wilson, is now being fought out by rival academic camps in an effort to understand how species evolve.

The learned spat was prompted by the publication of a searingly critical review of Wilson's new book, The Social Conquest of Earth, in Prospect magazine this month. The review, written by Dawkins, author of the popular and influential books The Selfish Gene, The Blind Watchmaker and The God Delusion, has prompted more letters and on-line comment than any other article in the recent history of the magazine and attacks Wilson's theory "as implausible and as unsupported by evidence".

"I am not being funny when I say of Edward Wilson's latest book that there are interesting and informative chapters on human evolution, and on the ways of social insects (which he knows better than any man alive), and it was a good idea to write a book comparing these two pinnacles of social evolution, but unfortunately one is obliged to wade through many pages of erroneous and downright perverse misunderstandings of evolutionary theory," Dawkins writes.

The Oxford evolutionary biologist, 71, has also infuriated many readers by listing other established academics who, he says, are on his side when it comes to accurately representing the mechanism by which species evolve. Wilson, in a short piece penned promptly in response to Dawkins's negative review, was also clearly annoyed by this attempt to outflank him.

"In any case," Wilson writes, "making such lists is futile. If science depended on rhetoric and polls, we would still be burning objects with phlogiston [a mythical fire-like element] and navigating with geocentric maps."

Wilson, 83, is a Harvard professor of evolutionary biology who became famous in the early 1970s with his study of social species in his books The Insect Societiesand Sociobiology. He is internationally acknowledged as "the father of sociobiology" and is the world's leading authority on ants.

For lay spectators, the row is a symptom of the long and controversial evolution of the very idea of evolution. At root it is a dispute about whether natural selection, the theory of "the survival of the fittest" first put forward by Charles Darwin in 1859, occurs only to preserve the single gene. Wilson is an advocate of "multi-level selection theory", a development of the idea of "kin selection", which holds that other biological, social and even environmental priorities may be behind the process.