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Background thoughts before this question: is it feasible to simulate a complete bacterium, atom by atom, in a computer simulation? On modern systems, either in an upcoming exascale computer?
In current research they've simulated an organella with 100M atoms but I don't know on which infrastructure.
On Quora, there is an estimation of E.coli to have about 9x1010 atoms. With 4m base pairs it is though still quite big and possibly would produce too high computational workload in a simulation.
See also: https://scicomp.stackexchange.com/questions/33941/is-a-complete-bacteria-simulation-with-an-exascale-supercomputer-possible
If they have simulated an organella with 100M atoms atom by atom, possibly you could already completely simulate some viruses, but they are not independent organisms.
So there has been an atom by atom simulation of the polio virus capsid in 2014 on the K computer with 10 petaflops. To include enough water molecules to fill and surround the capsid, Okazaki and colleagues needed to model the dynamics of nearly 6.5 million atoms, which they did for a simulated 200 ns.
Question - which order of magnitude would a small bacterium count on atoms? What about the smallest known bacterium Nasuia deltocephalinicola with its 112K base pairs? How many atoms has it got?
Let's take the example of the model bacterium E. coli, for which one can find the numbers for a wet cell of a dry mass of 0.28pg. If you have a feeling for how much smaller the smallest known bacterium is compared to E. coli, you can ballpark things.
The number of carbon atoms in a single E. coli cell is approx. 7x10^9 carbon atoms.
The ratio of elements in E. coli is C : H(1.77) : O(0.49) : N(0.24) .
More simply, if you multiply the ratios by 4, you get the ratios of approximately 4 carbons, 7 hydrogen, and 2 oxygen atoms for each nitrogen atom.
Taken together, there are approximately the following number of atoms in an E. coli cell:
C: 7 x 10^9
H: 1.23 x 10^10
O: 3.5 x 10^9
N: 1.75 x 10^9
That is around 2.4 x 10^10 individual atoms. As you may have noticed, these numbers do not have any bearing on the complexity of the system whatsoever. They also do not provide any insight into the intrinsic biological plasticity and dynamics of the system.
"Schrödinger's Bacterium" Could Be a Quantum Biology Milestone
The quantum world is a weird one. In theory and to some extent in practice its tenets demand that a particle can appear to be in two places at once&mdasha paradoxical phenomenon known as superposition&mdashand that two particles can become &ldquoentangled,&rdquo sharing information across arbitrarily large distances through some still-unknown mechanism.
Perhaps the most famous example of quantum weirdness is Schrödinger&rsquos cat, a thought experiment devised by Erwin Schrödinger in 1935. The Austrian physicist imagined how a cat placed in a box with a potentially lethal radioactive substance could, per the odd laws of quantum mechanics, exist in a superposition of being both dead and alive&mdashat least until the box is opened and its contents observed.
As far-out as that seems, the concept has been experimentally validated countless times on quantum scales. Scaled up to our seemingly simpler and certainly more intuitive macroscopic world, however, things change. No one has ever witnessed a star, a planet or a cat in superposition or a state of quantum entanglement. But ever since quantum theory&rsquos initial formulation in the early 20th century, scientists have wondered where exactly the microscopic and macroscopic worlds cross over. Just how big can the quantum realm be, and could it ever be big enough for its weirdest aspects to intimately, clearly influence living things? Across the past two decades the emergent field of quantum biology has sought answers for such questions, proposing and performing experiments on living organisms that could probe the limits of quantum theory.
Those experiments have already yielded tantalizing but inconclusive results. Earlier this year, for example, researchers showed the process of photosynthesis&mdashwhereby organisms make food using light&mdashmay involve some quantum effects. How birds navigate or how we smell also suggest quantum effects may take place in unusual ways within living things. But these only dip a toe into the quantum world. So far, no one has ever managed to coax an entire living organism&mdashnot even a single-celled bacterium&mdashinto displaying quantum effects such as entanglement or superposition.
So a new paper from a group at the University of Oxford is now raising some eyebrows for its claims of the successful entanglement of bacteria with photons&mdashparticles of light. Led by the quantum physicist Chiara Marletto and published in October in the Journal of Physics Communications, the study is an analysis of an experiment conducted in 2016 by David Coles from the University of Sheffield and his colleagues. In that experiment Coles and company sequestered several hundred photosynthetic green sulfur bacteria between two mirrors, progressively shrinking the gap between the mirrors down to a few hundred nanometers&mdashless than the width of a human hair. By bouncing white light between the mirrors, the researchers hoped to cause the photosynthetic molecules within the bacteria to couple&mdashor interact&mdashwith the cavity, essentially meaning the bacteria would continuously absorb, emit and reabsorb the bouncing photons. The experiment was successful up to six bacteria did appear to couple in this manner.
Marletto and her colleagues argue the bacteria did more than just couple with the cavity, though. In their analysis they demonstrate the energy signature produced in the experiment could be consistent with the bacteria&rsquos photosynthetic systems becoming entangled with the light inside the cavity. In essence, it appears certain photons were simultaneously hitting and missing photosynthetic molecules within the bacteria&mdasha hallmark of entanglement. &ldquoOur models show that this phenomenon being recorded is a signature of entanglement between light and certain degrees of freedom inside the bacteria,&rdquo she says.
According to study co-author Tristan Farrow, also of Oxford, this is the first time such an effect has been glimpsed in a living organism. &ldquoIt certainly is key to demonstrating that we are some way toward the idea of a &lsquoSchrödinger&rsquos bacterium,&rsquo if you will,&rdquo he says. And it hints at another potential instance of naturally emerging quantum biology: Green sulfur bacteria reside in the deep ocean where the scarcity of life-giving light might even spur quantum-mechanical evolutionary adaptations to boost photosynthesis.
There are many caveats to such controversial claims, however. First and foremost, the evidence for entanglement in this experiment is circumstantial, dependent on how one chooses to interpret the light trickling through and out of the cavity-confined bacteria. Marletto and her colleagues acknowledge a classical model free of quantum effects could also account for the experiment&rsquos results. But, of course, photons are not classical at all&mdashthey are quantum. And yet a more realistic &ldquosemiclassical&rdquo model using Newton&rsquos laws for the bacteria and quantum ones for photons fails to reproduce the actual outcome Coles and his colleagues observed in their laboratory. This hints that quantum effects were at play in both the light and the bacteria. &ldquoIt&rsquos a little bit indirect, but I think it&rsquos because they&rsquore only trying to be so rigorous in ruling out things and claiming anything too much,&rdquo says James Wootton, a quantum computing researcher at IBM Zurich Research Laboratory who was not involved in either paper.
The other caveat: the energies of the bacteria and the photon were measured collectively, not independently. This, according to Simon Gröblacher of Delft University of Technology in the Netherlands who was not part of this research, is somewhat of a limitation. &ldquoThere seems to be something quantum going on,&rdquo he says. &ldquoBut&hellipusually if we demonstrate entanglement, you have to measure the two systems independently&rdquo to confirm any quantum correlation between them is genuine.
Despite these uncertainties, for many experts, quantum biology&rsquos transition from theoretical dream to tangible reality is a question of when, not if. In isolation and collectively, molecules outside of biological systems have already exhibited quantum effects in decades&rsquo worth of laboratory experiments, so seeking out these effects for similar molecules inside a bacterium or even our own bodies would seem sensible enough. In humans and other large multicellular organisms, however, such molecular quantum effects should be averaged out to insignificance&mdashbut their meaningful manifestation within far smaller bacteria would not be too shocking. &ldquoI&rsquom a little torn about how surprising [this finding] is,&rdquo Gröblacher says. &ldquoBut it&rsquos obviously exciting if you can show this in a real biological system.&rdquo
Several research groups, including those led by Gröblacher and Farrow, are hoping to take these ideas even further. Gröblacher has designed an experiment that could place a tiny aquatic animal called a tardigrade in superposition&mdasha proposition much more difficult than entangling bacteria with light owing to a tardigrade&rsquos hundreds-fold&ndashlarger size. Farrow is looking at ways to improve on the bacterial experiment in 2019 he and his colleagues hope to entangle two bacteria together, rather than independently with light. &ldquoThe long-term goals are foundational and fundamental,&rdquo Farrow says. &ldquoThis is about understanding the nature of reality, and whether quantum effects have a utility in biological functions. At the root of things, everything is quantum,&rdquo he adds, with the big question being whether quantum effects play a role in how living things work.
It might be, for example, that &ldquonatural selection has come up with ways for living systems to naturally exploit quantum phenomena,&rdquo Marletto notes, such as the aforementioned example of bacteria photosynthesizing in the light-starved deep sea. But getting to the bottom of this requires starting small. The research has steadily been climbing toward macrolevel experiments, with one recent experiment successfully entangling millions of atoms. Proving the molecules that make up living things exhibit meaningful quantum effects&mdasheven if for trivial purposes&mdashwould be a key next step. By exploring this quantum&ndashclassical boundary, scientists could get closer to understanding what it would mean to be macroscopically quantum, if such an idea is true.
Jonathan O'Callaghan is a freelance space and science journalist based in London. You can follow him on Twitter @Astro_Jonny.
Many bacteria are long but narrow. Some of the larger species are Schaudinnum bütschlii, 50 to 60 micrometers long and 4 to 5 μm thick and Spirochaeta plicatilis, 250 μm long by 0.75 μm thick. A typical very large rounded bacterium, Achromatium oxaliferium is about 100 μm by 45 μm.
In 1993 , DNA testing revealed that Epulopiscium fishelsoni, an organism that only lives in the guts of a brown surgeonfish found in the Red Sea, is an extraordinary kind of bacteria.¹ Individual specimens have been measured at 80 mm thick and more than 600 μm long (more than half a millimeter, making them visible to the naked eye). Similar species are found in the guts of surgeonfish on Australia's Great Barrier Reef. It had previously been assumed that prokaryotes were bound to be small because the materials could only travel through the cell by diffusion. (Eukaryotes have ways of actively transporting materials within the cell.) On this assumption, microfossils had been classified as eukaryotes solely because of their size.
A sulfur bacteria found in sediments off the coast of Namibia in 1997 , Thiomargarita namibiensis, is typically 0.1 to 0.3 millimeters in diameter, but some are almost half a millimeter wide and visible to the naked eye. Most of the cell volume is a vacuole of sulfur. The bacteria are frequently found in loosely bound chains.
(× 10 6 cubic micrometers)
|Epulopiscium fishelsoni||average||250 × 40||0.3|
|big one||600 x 80||3|
1. Esther R. Angert, Kendall D. Clements and Norman R. Pace.
“The largest bacterium.”
Nature, volume 362, pages 239-241 ( 18 March 18 1993 ).
2. H. N. Schulz, T. Brinkhoff, T. G. Ferdelman, M. Hernández Mariné, A. Teske, B. B. Jørgensen.
Dense populations of a giant sulfur bacterium in Namibian shelf sediments.
Science, vol. 284, no. 5413, pages 493-495 ( 16 April 1999 ).
As you can see from the list below, life on Earth is built from increasingly more complex building blocks. At the widest view you have all living and non-living things - Earth. Soon you learn that each building block seems to be made of smaller building blocks - until you reach the smallest building blocks with the funny name - quarks.
The list below deals with living things and how each building block is made from yet a smaller set of building blocks.
Biosphere - Our Earth is made up of all living and non-living things. The interaction of all these building blocks make up the biosphere.
Biomes - The different environments on Earth are all unique, but there is a way for us to group areas by habitat type, such as tropical rainforest, desert, or marine environment. These are called biomes. You can think of biomes as specific areas on Earth that are defined by the plants and animals that live in that geographic region. Within a biome it is possible to have many ecosystems.
Ecosystems - All living things interact with non-living things around them. All the animals and plants in an area, plus the non-living things around them (air, earth, water, etc.) make up an ecosystem. Ecosystems can be various sizes, from an entire desert to a small pond.
Communities - All animals and plants that live in one place are considered a community. This can be tricky when you include humans, because they can move from community to community. There are also other animals, such as birds and butterflies that migrate from community to community. Communities do not include the non-living things in that place or area.
Populations - All the individuals of one species that live in an area are called a population. In this way, individuals become the building blocks for a species. For example, the entire human population is made of billions of people, who interact with each other to make up this world we live in. We can also specifically talk about the human population of one country, one city, or one neighborhood.
Individuals - Individual people make up the population. Each person has their own individual characteristics that cause diversity within a population.
Organs and Tissues - The human body, like all plants and animals, is made up of organs. In humans, these are the brain, heart, kidneys, liver, etc. Each organ is made of different tissues. These tissues have their own characteristics and functions. Did you know the largest organ in the body is the skin and that you are not wearing the same skin that you were born with?
Cells - Tissues are made of cells. The cell is the smallest unit of life. What does that mean? It means that the cell is the smallest living thing capable of replicating.
Organelles - Cells are also made up of individual parts. The interior of any cell has many types of little organs called organelles, such as the nucleus, mitochondria, Golgi complex, etc. All these organelles have their own functions to perform within the cell.
Proteins - Fats - Carbohydrates - Nucleic Acids- What are organelles made of? All the cellular organelles are made of macromolecules like carbohydrates, Lipids, Proteins, and Nucleic acids (DNA, RNA).
Atoms - To make macromolecules involves even smaller building blocks. You may have heard of atoms before and their parts: neutrons, protons, and electrons. There are 92 naturally occurring atoms (also called elements) but only 11 of these atoms are found in a significant amount in living things. It takes only two atoms to make a molecule.
Quarks - For many years it was thought that the smallest building blocks were atoms, but now we know that is not true. Scientists have found even smaller building blocks than atoms. These subatomic particles have a funny name - quarks. There are many "flavors" of quarks. Their names are up, down, top, bottom, charm, and strange.
Building Pig illustration by L. Leslie Brooke, from The Golden Goose Book, Frederick Warne & Co., Ltd. 1905. From Project Gutenberg.
The Nature And Function Of Cells
A cell is enclosed by a plasma membrane, which forms a selective barrier that allows nutrients to enter and waste products to leave. The interior of the cell is organized into many specialized compartments, or organelles, each surrounded by a separate membrane. One major organelle, the nucleus, contains the genetic information necessary for cell growth and reproduction. Each cell contains only one nucleus, whereas other types of organelles are present in multiple copies in the cellular contents, or cytoplasm. Organelles include mitochondria, which are responsible for the energy transactions necessary for cell survival lysosomes, which digest unwanted materials within the cell and the endoplasmic reticulum and the Golgi apparatus, which play important roles in the internal organization of the cell by synthesizing selected molecules and then processing, sorting, and directing them to their proper locations. In addition, plant cells contain chloroplasts, which are responsible for photosynthesis, whereby the energy of sunlight is used to convert molecules of carbon dioxide (CO2) and water(H2O) into carbohydrates. Between all these organelles is the space in the cytoplasm called the cytosol. The cytosol contains an organized framework of fibrous molecules that constitutethe cytoskeleton, which gives a cell its shape, enables organelles to move within the cell, and provides a mechanism by which the cell itself can move. The cytosol also contains more than 10,000 different kinds of molecules that are involved in cellular biosynthesis, the process of making large biological molecules from small ones.
Solving Biology's Mysteries Using Quantum Mechanics
There’s a fine line between being hailed as a visionary and being denounced as a crank, as Iraq-born physicist Jim Al-Khalili is only too aware. Seated in his office at the University of Surrey in the U.K. on a sunny day, he recalls a less tranquil time in his career, almost 15 years ago. Back then, he and his Surrey colleague, biologist Johnjoe McFadden, explored a strange mechanism to explain how DNA — the molecule that carries our genetic code — may mutate.
Their theory caused a stir because it invoked quantum mechanics, the branch of physics that describes the behavior of particles in the subatomic realm. Their idea gave some insight into the origins of genetic mutations, which over the centuries have given rise to the variety of species in the biological kingdom, and in the short term can lead to the development of diseases like cancer. The proposal was scoffed at, however, sparking incredulity from both biologists and physicists because quantum effects supposedly hold sway only on the smallest scales and cannot govern large biological molecules.
“Senior colleagues in physics warned me off this line of research, saying, ‘This isn’t just speculative, it’s wacky,’ ” Al-Khalili says. “I have since realized that some of the best ideas come out of seemingly crazy thoughts, because otherwise they wouldn’t be new.”
Though Al-Khalili and McFadden did not label it as such at the time, their paper was one of the first in the now burgeoning field of quantum biology. The strange rules that control the subatomic world might be unintuitive, but they have been verified through many experiments for the better part of a century. Yet it is only in the past decade or so that a small but dedicated band of physicists and biologists has found hints that nature may also use these rules to enhance the efficiency of biological tasks.
If true, then physicists struggling to innovate in the lab could take a quantum leaf out of nature’s book and learn how to devise better machines. Even more ambitiously — and controversially — some argue that quantum biology could be a game-changer in treating serious diseases. “The holy grail is to find that quantum effects stimulate biological processes that are relevant to medicine,” says Al-Khalili. “Looking to the long term, if these effects underlie the mechanism of DNA mutations, that could allow for real progress in the treatment of cancer.”
The seeds for Al-Khalili’s interest in biology were sown in 1960s Baghdad, when his parents gave him a microscope for Christmas. At the time, biology was all the rage: In 1953, Cambridge University biophysicists Francis Crick and James Watson had discovered that DNA takes the form of a double helix, or a twisted ladder. Al-Khalili’s parents hoped that their son would develop an interest in this exciting new science, but to their despair, he was far too preoccupied with football and music.
A few years later, however, at the age of 13, he fell in love — not with biology, but with physics, when he realized that mathematics could predict the outcome of high school experiments. “I suddenly understood that common sense was the route to answering deep questions about the way things worked,” he says. Ironically, this love of logic was severely tested when he later embarked on an undergraduate degree in physics at the University of Surrey and learned that, at the fundamental level where quantum laws take over, everyday rules fly out the window.
Now in his 50s, Al-Khalili’s face lights up and he becomes as animated as a teenager, waving his hands in frustration when he recalls his first encounters with quantum mechanics. For instance, the phenomenon of superposition states that before you look, a particle has no definite location. Only when the position of the particle is measured does it randomly settle into one spot. “We were told things like this very dryly,” says Al-Khalili. “The lecturers didn’t like me asking what it actually means to say that something can be in two places at the same time.”
Another perplexing oddity is known as quantum tunneling: In the microscopic realm, particles can travel across barriers that, in theory, they should not have the energy to get through. Al-Khalili remembers his lecturer trying to illuminate the topic by explaining, “It’s as if I were able to take a run up at this wall, and instead of crashing into it, I would suddenly appear, intact, on the other side.” He says the weirdness of the quantum world still frustrates him.
As strange as they are, these quantum characteristics have been demonstrated time and again in the lab, as Al-Khalili discovered when he later specialized in nuclear physics, the study of particles within the atom. By the mid-’80s, as he was establishing his early career, physicists had become so comfortable with the bizarre behavior of quantum objects that they began to ponder exploiting them to build powerful machines.
Whereas modern computers process information encoded in binary digits (or bits) that take the value of either 0 or 1, physicists realized that so-called quantum computers could store information in “qubits” that can exist in superposition, simultaneously both 0 and 1. If multiple qubits could be strung together, they reasoned, it should be possible to construct a quantum processor that performs calculations at speeds that are unimaginably quicker than standard devices. For instance, while current computers search through databases by examining each entry separately, a quantum computer would be able to look at all entries simultaneously.
The idea that plants and animals may already be carrying out such superfast quantum operations within their own cells, however, did not seriously cross the minds of either physicists or biologists, even though cells are made up of atoms and, at a basic level, all atoms obey quantum mechanics. The main reason was that, as the would-be builders of quantum computers discovered, quantum effects are extremely fragile. To maintain superposition in the lab, physicists need to cool their systems down to almost absolute zero, the lowest temperature possible, because heat can destroy quantum features. So there seemed little chance that these quantum properties could survive in the balmy temperatures within living cells.
But in the late 1990s, Al-Khalili realized that this assumption may have been too hasty when he first met McFadden, who introduced him to a biological mystery whose solution might require quantum help.
At the time, McFadden, a member of Surrey’s biology department, wanted to ask physicists for advice about how to handle a puzzle regarding DNA mutations. He and his colleagues had been investigating the genetic makeup of a nonlethal cousin of M. tuberculosis, the bacterium that causes tuberculosis, and they found that under special circumstances — when held in conditions nearly devoid of oxygen — the bacteria mutated in a way that made it especially virulent. What surprised the team was that this particular mutation seemed to occur at a more frequent rate than other mutations.
McFadden, like all good biologists, had learned that no such enhancement should occur. The central dogma since the 19th century, when Charles Darwin formulated the idea that mutations create the genetic variety needed for species to evolve, has been that all mutations should happen at random. No single type of mutation should occur more often than another, no matter what the environment. Certain mutations may prove useful, but the environmental conditions themselves should not play a role in the rate of any particular genetic mutation: Evolution is blind. McFadden’s team, however, seemed to have found a case that defied standard evolutionary theory, since the lack of oxygen in the experiment’s environment appeared to be triggering one type of mutation over others.
This was not the first time he had heard about such controversial findings. A decade earlier, in 1988, a group of molecular biologists led by John Cairns at the Harvard School of Public Health published startling results showing similar adaptive mutations. When they spread a strain of E. coli that could not digest lactose onto an agar plate whose only food source was lactose, they found that the bacteria developed the mutation required to digest the sugar at a far faster rate than expected if that mutation occurred at random. It looked like this adaptation had somehow resulted from the environment. “The study was absolutely heretical in the Darwinian sense,” says McFadden. Nonetheless, the experiments were respected enough to be published in the prestigious journal Nature.
In search of a possible mechanism that could explain just how the environment might do this, McFadden’s mind turned to popular accounts he had read about quantum computing that explained how superposition could significantly speed up otherwise slow processes. With that vague thought, McFadden asked his university’s physics department if quantum processes might explain the TB adaptations. His audience did not welcome the idea. “Most of my physicist colleagues thought he was naïve, and the idea that quantum effects might play a role in adaptive mutations was ridiculous,” recalls Al-Khalili.
Yet Al-Khalili — no stranger to potentially embarrassing questions — was intrigued enough to discuss the problem. “Don’t imagine that we sat there with some grand vision that we were pioneering quantum biology,” laughs Al-Khalili. “Really we just enjoyed meeting up once a week at Starbucks to chat through things we both found fascinating.” It paid off. Over the course of a year, they hashed out a theory using quantum mechanisms to explain how adaptive mutations occur.
DNA’s twisted ladder structure requires rungs of hydrogen bonds to hold it together each bond is essentially made up of a single hydrogen atom that unites two molecules. This means sometimes a single atom can determine whether a gene mutates. And single atoms are vulnerable to quantum weirdness. Usually the single atom sits closer to a molecule on one side of the DNA ladder than the other. Al-Khalili and McFadden dug out a long-forgotten proposal made back in 1963 that suggested DNA mutates when this hydrogen atom tunnels, quantum-mechanically, to the “wrong” half of its rung. The pair built on this by arguing that, thanks to the property of superposition, before it is observed, the atom will simultaneously exist in both a mutated and non-mutated state — that is, it would sit on both sides of the rung at the same time.
In the case of the fast-adapting E. coli, that would correspond to its DNA being primed to both enable the bacteria to eat lactose and also not be able to eat lactose. Al-Khalili and McFadden mathematically analyzed the interactions between the single hydrogen atom in the germ’s DNA and its surrounding lactose molecules. The presence of the sugar molecules jostling the atom have the effect of “observing” it, they argue, forcing the hydrogen to snap into one position, just as measuring the state of any quantum particle will fix it to one set location. What’s more, their calculations showed that the mutation that would enable E. coli to digest lactose would occur at a faster rate than in the absence of sugar. “It was hand-waving, but we had an inkling that something quantum was happening at the level of DNA,” says Al-Khalili. He and McFadden had joined a small group of mavericks who dared to link biology and quantum physics.
Not everyone was convinced. Many of Al-Khalili’s colleagues advised him to drop this fool’s errand, arguing that no experiments had definitively shown that quantum effects play a role in biological molecules. Given the state of biological imaging at the time, verifying the pair’s theory directly seemed impossible. In the meantime, Cairns’ original E. coli study had also come under close scrutiny. The increased rate of lactose-digesting mutations was independently reproduced a number of times, says McFadden, but there were suggestions that other non-beneficial mutations might also be enhanced, too — possibly obviating the need to invoke quantum mechanics. “It was around then that we lost interest in the subject,” says McFadden. Both he and Al-Khalili forgot their lofty ambitions and returned to their day jobs.
Looking back, Al-Khalili admits they were too easily swayed. In the following years, a host of experimental results sprang up hinting that quantum effects may be at work in many different corners of the biological world. The most significant appeared in 2007 and involved photosynthesis, the process by which chlorophyll molecules in plants convert water, carbon dioxide and sunlight into energy, oxygen and carbohydrates.
Photosynthesis achieves a whopping 95 percent energy transfer efficiency rate, “more efficient than any other energy transfer process known to man,” says McFadden. Within chlorophyll, so-called antenna pigments guide energy from light-collecting molecules to nearby reaction-center proteins along a choice of possible pathways. Biologists had assumed that the energy hopped from molecule to molecule along a single pathway. But calculations showed that this could account only for about a 50 percent efficiency rate. To explain the near-perfect performance of plants, biophysicists reasoned, the energy must exist in a quantum superposition state, traveling along all molecular pathways at the same time — similar to the quantum computer that could simultaneously search all entries in a database. Once the quickest road is identified, the idea goes, the system snaps out of superposition and onto this route, allowing all the energy to take the best path every time.
In the 2007 experiment, University of California, Berkeley, chemist Graham Fleming and colleagues ran experiments on green sulfur bacteria that appeared to suggest this quantum approach. Fleming’s work took place at minus 321 degrees Fahrenheit, but similar effects appeared three years later in experiments with marine algae carried out at room temperature by a team led by Gregory Scholes, a chemist at the University of Toronto in Ontario. “These were jaw-dropping experiments,” says McFadden. “Physicists had been battling for years to build a quantum computer — and now it seemed that all that time they may have been eating quantum computers for lunch, in the leaves in their salad!”
Vlatko Vedral — a physicist who whimsically describes himself as being quantum superimposed at both the University of Oxford in the U.K. and the Centre for Quantum Technologies in Singapore — took notice. “Up to then, all these ideas in quantum biology sounded good, but they lacked experimental evidence,” he recalls. “The photosynthesis experiments changed people’s minds.” Although, he adds, critics have pointed out that the tests use artificial light from lasers, rather than natural sunlight. It remains unclear whether the same quantum effects observed in tightly controlled lab conditions really do occur outdoors in our gardens.
The experiments were enough to set Vedral wondering if he and his colleagues could find quantum effects within the animal equivalent of photosynthesis. The energy factory in animal cells like our own is the mitochondrion, a repository for channeling energy from glucose harvested from food into electrons. These high-energy electrons are then shuffled through a cascade of reactions to make adenosine triphosphate (ATP), the molecule that fuels most cellular work. Conventional biological models described the electrons as hopping from molecule to molecule within mitochondria, but — once again — this simple picture cannot account for the speed at which ATP is spit out.
Vedral’s team has come up with a model in which, rather than hopping, the electrons exist in a quantum superposition, smeared out at once across all the molecules in the ATP production line. Their calculations predicted a boosted ATP production rate, as seen in experiments. Once again, it was a quantum solution to a biological mystery. Uncertain Future
Though still tentative, the possible health ramifications of these theories have not gone unnoticed. Vedral notes that failure in electron transfer in mitochondria has been linked to Parkinson’s disease and to some cancers. The connection is still speculative, he admits, because the precise cause-and-effect relationship between the two is murky. “Does the failure of electron transfer lead to the disease, or does the disease cause the breakdown of electron transfer?” Vedral asks. “That’s something biologists don’t know, and we have to look to them for an answer.”
Nonetheless, because the payoff could be so high, the conjecture has attracted the first major research grant enabling the Oxford group, led by Oxford physicist Tristan Farrow, to run their own experiments into quantum biology. The grant stands as one of the biggest stamps of approval for this controversial discipline, which until now has largely been a topic for researchers’ spare time. As Farrow walks me around the darkened lab where these tests will take place, he explains that it’s arduous work, and it can take up to five years to prepare.
The first task, says Farrow, will be to verify the 2007 photosynthesis results after this, the team will study the larger and more complex molecules involved in mitochondrial energy transfer. Farrow explains that he personally is driven not so much by the potential medical benefits that helped lead to the grant — which will come many years down the road, if at all — but by the hope that nature could teach us how to build better machines.
“If we can show that quantum effects survive for a long time in biological molecules and work out how that happens, then we can use that information to design better quantum computers in the lab,” he says. McFadden agrees: “If we could understand how photosynthesis is so efficient at transforming sunlight into energy and re-create that artificially, then today’s poorly performing solar cells would be a thing of the past.”
Physicists struggling to string together more than a handful of qubits at ultracold temperatures in the lab are also keen to discover just how biomolecules can apparently shield fragile quantum effects so that they can be exploited by living systems without disruption. “A benefit of studying quantum effects in biological systems is to learn if and how nature protects them, so that we may copy the architecture of the natural building blocks,” says Farrow. Quantum computers must operate at room temperature if they are ever to be used in mainstream applications. “Such blocks could then be used as the basic units in ‘biological’ quantum computers,” Farrow adds.
A decade ago, such experiments would have been impossible because the technology to manipulate single biological molecules did not exist. These improvements in experimental techniques, combined with the advances made by others in quantum biology, have inspired McFadden and Al-Khalili to leave the sidelines and rejoin the game. “We started to think, ‘Hang on, maybe we were onto something all those years ago,’ ” Al-Khalili laughs. As a mark of just how much the tide has turned, in January 2013, Al-Khalili gave a talk about his ideas on quantum tunneling and DNA mutations at the Royal Institution, London’s prestigious scientific establishment.
Al-Khalili and McFadden are also about to embark on the first set of tests of their mutation theory. Their proposed experiments compare the behavior of normal DNA molecules with specially modified DNA molecules whose hydrogen atoms have been replaced with deuterium atoms (also known as heavy hydrogen because the atoms have the same chemical properties as hydrogen, but double the mass). If they’re right that mutations are caused when a hydrogen atom tunnels quantum-mechanically to the wrong side of DNA’s ladder, then they predict that the rate of mutations will be significantly lower in the modified DNA molecules, since heavier deuterium is less likely to tunnel across the ladder.
But all of these tests will take a few years to design and carry out. Surveying the lasers and mirrors laid out on Farrow’s laboratory table in Oxford, he notes that the road to definitive experimental proof of quantum biology will be a long one — and there is a very real chance they will never prove quantum effects lurk within living beings.
“There is a huge risk that we may be heading in the wrong direction,” Farrow says ruefully. “But my hunch tells me this is worth it because if we succeed, the payoff will be massive: We will have pioneered a new discipline.”
[This article originally appeared in print as "This Quantum Life."]
100 Biology Trivia Questions None Should Miss
Biology is a topic that explains life around us with many interesting trivia questions for the learners. From microscopic organisms to large mammoths, the dwelling world is residence to a number of animals and crops. Even our human body is a treasure trove of educational information and insights of biology trivia questions.
As an illustration, do you know that the human lung can float on water? Or the truth that our liver has the superb capacity to regenerate with biology trivia questions?
One can discover all these fascinating biology trivia questions and improve one’s information.
Most of our physique capabilities appear fairly uninteresting, however, these similar capabilities and roles in different organisms are eye-openers to us. It’s because most of them are actually fascinating and mind-bending biology trivia questions.
The best vertical bounce ever carried out by a human measured at simply over 7 toes. That is insignificant once we have a look at different organisms from the animal kingdom found in these biology trivia questions.
As an illustration, fleas can bounce 150 occasions increased than their very own physique peak.
When that is scaled as much as our proportions, it’s just like a human leaping over 800 toes, which is near twice as excessive because of the Pyramids of Egypt as well as these biology trivia questions.
Basic Biology test!
Back in school, you might have liked chemistry better. Or maybe physics. But do those sciences allow you to, you know, breathe? We didn't think so!
Biology, as you probably know, is the very science of life. It's the base of more specific scientific fields like botany, animal behavior, nutrition and more. And, of course, it underlies all fields of medicine. So perhaps it's time you took a second look at this classic element of middle-school and high-school curricula, and find out how much you remember from those long-ago classes.
How much, for example, do you know about the cell? From the Latin for "small room," the cell is to biology what the atom is to chemistry, its most basic part. (Although, as with atoms, there are things in biology smaller than cells). Also, if you want to be a biology whiz, you'd better learn how things are classified. A large part of basic biology is sorting things into groups and subgroups, based on their size, how they reproduce, and more. Which reminds us -- do you remember the name of the Swedish botanist/zoologist who is known as the father of modern taxonomy? For that matter, did you know that classification in biology is *called* taxonomy? We really hope so, or this quiz might not go so well!
Life and information
One of the most compelling evidences in support of the instantaneous creation worldview is the daily observation that information does not come about by chance and, if left to itself, disorder usually soon results. Archeologists are normally easily able to discern if an object found in their field research digs was produced by humans or by natural events such as wind or rain. The criteria they use to do this is the degree of information the object contains (Yockey, 1992). Complexity and information are compelling evidence that some outside intelligent agency (which in the case of an archeologist’s findings was another human) has applied design skills and intelligence to the natural world, adding a higher level of information and order on top of that which naturally exists in the nonliving world such as rocks.
Both plant and animal kingdoms manifest enormous complexity and information in their genetic codes, but this order and information preexists in the animal or plant and was inherited and passed on through reproduction. Except for the living world and the “world” made by humans, the natural world operates according to preexisting physical laws and previous events. The living world, which scientists are only now beginning to understand, represents a level of design complexity based on information existing in the genetic code which is not found anywhere in the nonliving world except that created by humans. Hence the rationale for the belief that the living world could not come from the nonliving world. As Nobel laureate research molecular biologist Komfield stated in a now-famous interview that occurred over 36 years ago:
While laboring among the intricacies and definitely minute particles in a laboratory, I frequently have been overwhelmed by a sense of the infinite wisdom of God … one is rather amazed that a mechanism of such intricacy could ever function properly at all … the simplest man-made mechanism requires a planner and a maker how a mechanism ten times more involved and intricate can be conceived as self-constructed and self-developed is completely beyond me (Komfield, p. 16, 1962).
In other words, the enormous amount of genetic information that is translated into the complexity that is evident everywhere in the living world is far beyond that found in both the nonliving and human-manufactured world. Products produced by the nonliving world (such as smooth stones polished by moving water) could never produce either plant or animal life because all life is based on information, and the parts produced by that information must be assembled according to a designed plan in an environment such as a certain ecosystem that supports life.
Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized following a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere. Evolution is the source of the tremendous biological diversity on Earth today. A diagram called a phylogenetic tree can be used to show evolutionary relationships among organisms. Biology is very broad and includes many branches and sub disciplines. Examples include molecular biology, microbiology, neurobiology, zoology, and botany, among others.