Bacteriophages

30 years ago, I was working in a medical research lab near NIH and Navy Medical in Bethesda, MD. I was a lab technition. My job over the summer of 1986 was to grow bacteriophages to inject plasmid DNA into bacteria to reproduce and harvest to be used in gene splicing studies. I was so facinated by the existance and evolution of bacteriophages. I often thought they seem like a link between organic living organisms and crystaline structures of molecules and compounds that are considered non-living. Eitherway, these buggers are quite facinating and at times quite deadly.

Here is some more information from the Khan Academy – https://www.khanacademy.org

A bacteriophage is a virus that infects bacteria

bacteriophage, or phage for short, is a virus that infects bacteria. Like other types of viruses, bacteriophages vary a lot in their shape and genetic material.
  • Phage genomes can consist of either DNA or RNA, and can contain as few as four genes or as many as several hundred^{1,2,3}1,2,3start superscript, 1, comma, 2, comma, 3, end superscript.
  • The capsid of a bacteriophage can be icosahedral, filamentous, or head-tail in shape. The head-tail structure seems to be unique to phages and their close relatives (and is not found in eukaryotic viruses)^{4,5}4,5start superscript, 4, comma, 5, end superscript.

    Icosahedral phage, head-tail phage, and filamentous phage.
    Image modified from “Corticovirus,” “T7likevirus,” and “Inovirus, by ViralZone/Swiss Institute of Bioinformatics, CC BY-NC 4.0.

Bacteriophage infections

Bacteriophages, just like other viruses, must infect a host cell in order to reproduce. The steps that make up the infection process are collectively called the lifecycle of the phage.
Some phages can only reproduce via a lytic lifecycle, in which they burst and kill their host cells. Other phages can alternate between a lytic lifecycle and a lysogenic lifecycle, in which they don’t kill the host cell (and are instead copied along with the host DNA each time the cell divides).
Let’s take closer look at these two cycles. As an example, we’ll use a phage called lambda (\lambdaλlambda), which infects E. coli bacteria and can switch between the lytic and lysogenic cycles.

Lytic cycle

In the lytic cycle, a phage acts like a typical virus: it hijacks its host cell and uses the cell’s resources to make lots of new phages, causing the cell to lyse (burst) and die in the process.

  1. Attachment: Proteins in the “tail” of the phage bind to a specific receptor (in this case, a sugar transporter) on the surface of the bacterial cell.
  2. Entry: The phage injects its double-stranded DNA genome into the cytoplasm of the bacterium.
  3. DNA copying and protein synthesis: Phage DNA is copied, and phage genes are expressed to make proteins, such as capsid proteins.
  4. Assembly of new phage: Capsids assemble from the capsid proteins and are stuffed with DNA to make lots of new phage particles.
  5. Lysis: Late in the lytic cycle, the phage expresses genes for proteins that poke holes in the plasma membrane and cell wall. The holes let water flow in, making the cell expand and burst like an overfilled water balloon.
Cell bursting, or lysis, releases hundreds of new phages, which can find and infect other host cells nearby.
Image modified from “Conjugation,” by Adenosine (CC BY-SA 3.0). The modified image is licensed under a CC BY-SA 3.0 license. Based on similar diagram in Alberts et al.^66start superscript, 6, end superscript
The stages of the lytic cycle are:
  1. Attachment: Proteins in the “tail” of the phage bind to a specific receptor (in this case, a sugar transporter) on the surface of the bacterial cell.
  2. Entry: The phage injects its double-stranded DNA genome into the cytoplasm of the bacterium.
  3. DNA copying and protein synthesis: Phage DNA is copied, and phage genes are expressed to make proteins, such as capsid proteins.
  4. Assembly of new phage: Capsids assemble from the capsid proteins and are stuffed with DNA to make lots of new phage particles.
  5. Lysis: Late in the lytic cycle, the phage expresses genes for proteins that poke holes in the plasma membrane and cell wall. The holes let water flow in, making the cell expand and burst like an overfilled water balloon.
Cell bursting, or lysis, releases hundreds of new phages, which can find and infect other host cells nearby. In this way, a few cycles of lytic infection can let the phage spread like wildfire through a bacterial population.

Lysogenic cycle

The lysogenic cycle allows a phage to reproduce without killing its host. Some phages can only use the lytic cycle, but the phage we are following, lambda (\lambdaλlambda), can switch between the two cycles.

^{7,8}start superscript, 7, comma, 8, end superscript
In the lysogenic cycle, the first two steps (attachment and DNA injection) occur just as they do for the lytic cycle. However, once the phage DNA is inside the cell, it is not immediately copied or expressed to make proteins. Instead, it recombines with a particular region of the bacterial chromosome. This causes the phage DNA to be integrated into the chromosome.

^7start superscript, 7, end superscript

Lysogenic cycle:
  1. Attachment. Bacteriophage attaches to bacterial cell.
  2. Entry. Bacteriophage injects DNA into bacterial cell.
  3. Integration. Phage DNA recombines with bacterial chromosome and becomes integrated into the chromosome as a prophage.
  4. Cell division. Each time a cell containing a prophage divides, its daughter cells inherit the prophage.
Image modified from “Conjugation,” by Adenosine (CC BY-SA 3.0). The modified image is licensed under a CC BY-SA 3.0 license. Based on similar diagram in Alberts et al.^66start superscript, 6, end superscript
The integrated phage DNA, called a prophage, is not active: its genes aren’t expressed, and it doesn’t drive production of new phages. However, each time a host cell divides, the prophage is copied along with the host DNA, getting a free ride. The lysogenic cycle is less flashy (and less gory) than the lytic cycle, but at the end of the day, it’s just another way for the phage to reproduce.
Under the right conditions, the prophage can become active and come back out of the bacterial chromosome, triggering the remaining steps of the lytic cycle (DNA copying and protein synthesis, phage assembly, and lysis).

  1. Prophage exits chromosome and becomes its own circularized DNA molecule.
  2. Lytic cycle commences.
Image modified from “Conjugation,” by Adenosine (CC BY-SA 3.0). The modified image is licensed under a CC BY-SA 3.0 license.

To lyse or not to lyse?

How does a phage “decide” whether to enter the lytic or lysogenic cycle when it infects a bacterium? One important factor is the number of phages infecting the cell at once^99start superscript, 9, end superscript. Larger numbers of co-infecting phages make it more likely that the infection will use the lysogenic cycle. This strategy may help prevent the phages from wiping out their bacterial hosts (by toning down the attack if the phage-to-host ratio gets too high)^{10}10start superscript, 10, end superscript.

^3start superscript, 3, end superscript
^4start superscript, 4, end superscript
What triggers a prophage to pop back out of the chromosome and enter the lytic cycle? At least in the laboratory, DNA-damaging agents (like UV radiation and chemicals) will trigger most prophages in a population to re-activate. However, a small fraction of the prophages in a population spontaneously “go lytic” even without these external cues^{7,11}7,11start superscript, 7, comma, 11, end superscript.

Bacteriophage vs. antibiotics

Before antibiotics were discovered, there was considerable research on bacteriophages as a treatment for human bacterial diseases. Bacteriophages attack only their host bacteria, not human cells, so they are potentially good candidates to treat bacterial diseases in humans.
After antibiotics were discovered, the phage approach was largely abandoned in many parts of the world (particularly English-speaking countries). However, phages continued to be used for medical purposes in a number of countries, including Russia, Georgia, and Poland, where they remain in use today^{12,13}12,13start superscript, 12, comma, 13, end superscript.
There is increasing interest in bringing back the “phage approach” elsewhere, as antibiotic-resistant bacteria become more and more of a problem. Research is still needed to see how safe and effective phages are, but who knows? One day, your doctor might write you a prescription for phages instead of penicillin!
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Self -ness, the Etherial Quantum of Me and the Other Mes …infinitum

May 31st, 2016

The concept of a continuum of matter, time and energy has always taken on a spiritual and metaphysical theme for me. Ever since in high school when I learned of Bell’s theorem, Heisenberg’s uncertainty principle, Schrödinger’s cat, or the concept of spooky action at a distance – quantum entanglement, I have really questioned much of my self-ness as a unit of being. Dawkins with the Selfish Gene and the concept of the unit of selection also put a biological spin on the theoretical physics (pun intended).

So if I move away from thinking about the outside of me, which doesn’t really make sense, but move more toward a mindset of understanding via my subjective brain experience, brain thinking about the brain thinking about the brain…never ending self reflexive paradox..maybe I am more than just me, but a few of me or infinite me, hummmm

Here is another similar video that I like that questions more of the same…

Researchers say they can predict awareness and return to consciousness of comatose patients

Digital Trends – Dyllan Furness – 30 May 2016


Researchers have developed a new method to peer into a comatose patient’s brain. By measuring how much sugar a brain consumes, scientists are able to predict a patient’s current state of awareness and the chance that the patient will regain consciousness within a year, according to a study published in the journal Current Biology.

inbraininjurA research team from the University of Copenhagen in Denmark and the University of Liège in Belgium sought a more dependable laboratory analysis that would accompany clinical examinations to determine a patient’s current and future level of awareness. They administered, mapped, and measured sugar as a marker in 131 brain-injured patients, and found that the brain’s glucose metabolism strongly correlated with behavioral responsiveness. The researchers were able to predict consciousness or return to consciousness in 94 percent of cases.

Related3D-printed brain tumors may help scientists fight cancer

“In nearly all cases, whole-brain energy turnover directly predicted either the current level of awareness or its subsequent recovery,” Ron Kupers of the University of Copenhagen and Yale University said in a press release. “In short, our findings indicate that there is a minimal energetic requirement for sustained consciousness to arise after brain injury.”

Patients whose glucose metabolism measured under a threshold of 42 percent of normal appeared unconscious and failed to recover consciousness within the following year. Meanwhile, patients whose glucose metabolism measured above 42 percent the threshold had signs of initial responsiveness or recovered responsiveness within a year.

“The take-home message [for now] is that consciousness is a highly energy demanding process, involving the brain at large,” Kupers said. “This fundamental physiological trait can help clinicians determine the potential for recovery of awareness in patients suffering from severe brain injuries of any kind.”

Kupers and his team still insist that their findings need to be verified by an independent study. However, their research opens interest in further investigating how awareness relates to brain metabolism and how brain metabolism may change over time in brain-injured patients.

Neuroscience & Quantum Consciousness Videos

May 24th, 2016

Consciousness & Physiology I
https://youtu.be/-nrsfZjDiq0
Consciousness & Physiology II
https://youtu.be/Rw2YHdh5Gng
Entanglement, Space Time Wormholes, and the Brain
https://youtu.be/TKGAeVrdU6c
Neuroscience of Consciousness
https://youtu.be/k_ZTNmkIiBc
Consciousness is the Unified Field
https://youtu.be/qyPWvg9dxD4
God is in The Neurons
https://youtu.be/oPEdDcs_8ZQ
YouTube – Part 4 – Phantoms In The Brain (Episode 1)
http://www.youtube.com/watch?v=_1RPkp…
YouTube – Part 5 – Phantoms In The Brain (Episode 1)
http://www.youtube.com/watch?v=F0R0OC…
Where is consciousness?
http://discovermagazine.com/video/unl…
Joseph M. Carver, Ph.D. – Norepinephrine: From Arousal to Panic
http://www.enotalone.com/article/4117…
Dharol Tankersley, C Jill Stowe, and Scott A Huettel – Brain Scan Predicts Difference Between Altruistic And Selfish People
http://www.medicalnewstoday.com/artic…
New Scientist – Empathetic mirror neurons found in humans at last
http://www.newscientist.com/article/m…
Dr. Christopher Reist – Psychiatry And The Brain
http://www.videojug.com/interview/psy…
John McManamy – Dopamine – Serotonin’s Secret Weapon
http://www.mcmanweb.com/dopamine.html
Invalidation
http://eqi.org/invalid.htm
YouTube – The Neuroscience of Emotions
http://www.youtube.com/watch?v=tShDYA…
How Our Brains Make Memories
http://www.smithsonianmag.com/science…
Alpha, beta, gamma – The language of brainwaves – life – 12 July 2010 – New Scientist
http://www.newscientist.com/article/m…
TSN: Take the Neuron Express for a brief tour of consciousness
http://thesciencenetwork.org/programs…
LeDouxlab Web-AudioFearful_Brains
http://www.cns.nyu.edu/ledoux/slide_s…
Joseph LeDoux Can Memories Be Erased
http://www.huffingtonpost.com/joseph-…
Zócalo Public Square :: Full Video
http://zocalopublicsquare.org/full_vi…
When in doubt, shout — why shaking someone’s beliefs turns them into stronger advocates | Not Exactly Rocket Science | Discover Magazine
http://blogs.discovermagazine.com/not…
The Brain: How The Brain Rewires Itself – TIME
http://www.time.com/time/magazine/art…

 

Perovskite the New Silicon

May 21st, 2016

Perovskite (pronunciation: /pəˈrɒvskt/) is a calcium titanium oxide mineral composed of calcium titanate, with the chemical formula CaTiO3. The mineral was discovered in the Ural Mountains of Russia by Gustav Rose in 1839 and is named after Russian mineralogist Lev Perovski (1792–1856).[1]This stuff is may impact microelectronics,  telecommunication,  superconductivity,  magnetoresistance,  ionic conductivity, and a multitude of dielectric properties. Because of the flexibility of bond angles inherent in the perovskite structure there are many different types of distortions which can occur from the ideal structure.

CH3NH3PbI3_structure

From Wikipedia:  perovskite is any material with the same type of crystal structure as calcium titanium oxide (CaTiO3), known as the perovskite structure, or XIIA2+VIB4+X2−3 with the oxygen in the face centers.[2] Perovskites take their name from the mineral, which was first discovered in the Ural mountains of Russia by Gustav Rose in 1839 and is named after Russian mineralogist L. A. Perovski (1792–1856). The general chemical formula for perovskite compounds is ABX3, where ‘A’ and ‘B’ are twocations of very different sizes, and X is an anion that bonds to both. The ‘A’ atoms are larger than the ‘B’ atoms. The ideal cubic-symmetry structure has the Bcation in 6-fold coordination, surrounded by an octahedron of anions, and the A cation in 12-fold cuboctahedral coordination. The relative ion size requirements for stability of the cubic structure are quite stringent, so slight buckling and distortion can produce several lower-symmetry distorted versions, in which the coordination numbers of A cations, B cations or both are reduced.

Perovskites have a cubic structure with general formula of ABO
3
. In this structure, an A-site ion, on the corners of the lattice, is usually an alkaline earth orrare earth element. B site ions, on the center of the lattice, could be 3d, 4d, and 5d transition metal elements. A large number of metallic elements are stable in the perovskite structure, if the tolerance factor t is in the range of 0.75 – 1.0.[14]

 t = \frac{R_A + R_O}{\sqrt2(R_B+R_O)}

where RA, RB and RO are the ionic radii of A and B site elements and oxygen, respectively.

Perovskites have sub-metallic to metallic luster, colorless streak, cube like structure along with imperfect cleavage and brittle tenacity. Colors include black, brown, gray, orange to yellow. Crystals of perovskite appear as cubes, but are pseudocubic and crystallize in the orthorhombic system. Perovskite crystals have been mistaken for galena; however, galena has a better metallic luster, greater density, perfect cleavage and true cubic symmetry.[5]

Structure of a perovskite with a chemical formula ABX3. The red spheres are X atoms (usually oxygens), the blue spheres are B-atoms (a smaller metal cation, such as Ti4+), and the green spheres are the A-atoms (a larger metal cation, such as Ca2+). Pictured is the undistorted cubicstructure; the symmetry is lowered toorthorhombic, tetragonal or trigonal in many perovskites.[1]

A Perovskite mineral (calcium titanate) from Kusa, Russia. Taken at the Harvard Museum of Natural History.

Cheaper, longer-lasting perovskite solar cells could be on the way

February 2, 2016

Perovskite-based solar cells have been hampered by poor durability, but a new compound developed at EPFL could lead to cells that are cheaper, efficient and more durable than current devices (Credit: Sven M. Hein (EPFL))

Perovskite solar cells are one of the most exciting green energy technologies to emerge in recent years, combining low cost with high energy conversion rates. Now, researchers at the Swiss Federal Institute of Technology in Lausanne (EPFL) have found a way to cut their cost even further by developing a charge-carrying material that is much cheaper, highly efficient, and could even help address the technology’s current major weakness by significantly lengthening the lifespan of the panels.Record efficiencies for solar cells tend to grab all the headlines, but it is other less flashy metrics – such as price per watt – that provide a much fairer assessment of whether a new technology can produce clean energy on the global scale. Perovskite solar cells excel in this area by combining low cost with efficiencies that have already surpassed the 20 percent mark, rivaling standard silicon-based panels while also being, according to a recent study, easier on the environment than any of the best-known alternatives in the solar arena.

But before perovskite cells can make it to mass production, one big issue still remains to be addressed: the outer shell of the panel, the function of which is to conduct electric charge, is made from organic compounds that will quickly wither away in real-life conditions, cutting the life of the cell to a few short months.

Researchers led by Mohammad Nazeeruddin at EPFL have now developed a new inorganic conductive material for perovskite cells that is cheaper, still allows for high energy conversion rates and, more importantly, offers plenty of wiggle room for experimentation, paving the way for longer-lasting, cost-effective perovskite panels.

The new material, dissymmetric fluorene–dithiophene (FDT), is said to cost less than one fifth to synthesize than previous compounds (US$60 versus $500 per gram) while still retaining a very competitive energy conversion rate of 20.2 percent.

“The previous material (Spiro) was rather difficult to synthesise and purify in large scale, preventing perovskite solar cells market penetration,” Nazeeruddin told Gizmag. “It is also well known in the literature that the stability of Spiro is limited. We are doing stability measurements of the new material: if the stability is established, the economic benefits would be enormous.”

While no determination has yet been made on the stability of the compound used in the study, two considerations leave room for optimism. First, the inorganic nature of the compound is expected to make it more resistant to weather and biodegradation. And secondly, the FTD core material can be reportedly modified with ease, creating not one, but a family of compounds.

The hope is that this amount of wiggle room will be enough for researchers to engineer a material that is both cheap, long-lasting, and still allowing for efficiencies that are competitive with respect to the final price of the panel.

A paper describing the advance appears in the journal Nature Energy.

Source: EPFL

Semiconductor Potentials

To the growing list of two-dimensional semiconductors, such as graphene, boron nitride, and molybdenum disulfide, whose unique electronic properties make them potential successors to silicon in future devices, you can now add hybrid organic-inorganic perovskites. However, unlike the other contenders, which are covalent semiconductors, these 2D hybrid perovskites are ionic materials, which gives them special properties of their own.

Researchers at the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) have successfully grown atomically thin 2D sheets of organic-inorganic hybrid perovskites from solution. The ultrathin sheets are of high quality, large in area, and square-shaped. They also exhibited efficient photoluminescence, color-tunability, and a unique structural relaxation not found in covalent semiconductor sheets.

“We believe this is the first example of 2D atomically thin nanostructures made from ionic materials,” says Peidong Yang, a chemist with Berkeley Lab’s Materials Sciences Division and world authority on nanostructures, who first came up with the idea for this research some 20 years ago. “The results of our study open up opportunities for fundamental research on the synthesis and characterization of atomically thin 2D hybrid perovskites and introduces a new family of 2D solution-processed semiconductors for nanoscale optoelectronic devices, such as field effect transistors and photodetectors.”

(From left) Peidong Yang, Letian Dou, Andrew Wong and Yi Yu successfully followed up on research first proposed by Yang in 1994.

Yang, who also holds appointments with the University of California (UC) Berkeley and is a co-director of the Kavli Energy NanoScience Institute (Kavli-ENSI), is the corresponding author of a paper describing this research in the journal Science. The paper is titled “Atomically thin two-dimensional organic-inorganic hybrid perovskites.” The lead authors are Letian Dou, Andrew Wong and Yi Yu, all members of Yang’s research group. Other authors are Minliang Lai, Nikolay Kornienko, Samuel Eaton, Anthony Fu, Connor Bischak, Jie Ma, Tina Ding, Naomi Ginsberg, Lin-Wang Wang and Paul Alivisatos.

Traditional perovskites are typically metal-oxide materials that display a wide range of fascinating electromagnetic properties, including ferroelectricity and piezoelectricity, superconductivity and colossal magnetoresistance. In the past couple of years, organic-inorganic hybrid perovskites have been solution-processed into thin films or bulk crystals for photovoltaic devices that have reached a 20-percent power conversion efficiency. Separating these hybrid materials into individual, free-standing 2D sheets through such techniques as spin-coating, chemical vapor deposition, and mechanical exfoliation has met with limited success.

In 1994, while a PhD student at Harvard University, Yang proposed a method for preparing 2D hybrid perovskite nanostructures and tuning their electronic properties but never acted upon it. This past year, while preparing to move his office, he came upon the proposal and passed it on to co-lead author Dou, a post-doctoral student in his research group. Dou, working mainly with the other lead authors Wong and Yu, used Yang’s proposal to synthesize free-standing 2D sheets of CH3NH3PbI3, a hybrid perovskite made from a blend of lead, bromine, nitrogen, carbon and hydrogen atoms.

Structural illustration of a single layer of a 2D hybrid perovskite (C4H9NH3)2PbBr4), an ionic material with different properties than 2D covalent semiconductors.

“Unlike exfoliation and chemical vapor deposition methods, which normally produce relatively thick perovskite plates, we were able to grow uniform square-shaped 2D crystals on a flat substrate with high yield and excellent reproducibility,” says Dou. “We characterized the structure and composition of individual 2D crystals using a variety of techniques and found they have a slightly shifted band-edge emission that could be attributed to structural relaxation. A preliminary photoluminescence study indicates a band-edge emission at 453 nanometers, which is red-shifted slightly as compared to bulk crystals. This suggests that color-tuning could be achieved in these 2D hybrid perovskites by changing sheet thickness as well as composition via the synthesis of related materials.”

The well-defined geometry of these square-shaped 2D crystals is the mark of high quality crystallinity, and their large size should facilitate their integration into future devices.

“With our technique, vertical and lateral heterostructures can also be achieved,” Yang says. “This opens up new possibilities for the design of materials/devices on an atomic/molecular scale with distinctive new properties.”

This research was supported by DOE’s Office of Science. The characterization work was carried out at the Molecular Foundry’s National Center for Electron Microscopy, and at beamline 7.3.3 of the Advanced Light Source. Both the Molecular Foundry and the Advanced Light Source are DOE Office of Science User Facilities hosted at Berkeley Lab.

Chemists offer more evidence of RNA as the origin of life

Phys.org – latest science and technology news stories

Source: Chemists offer more evidence of RNA as the origin of life

Phys.org)—A team of chemists at Ludwig Maximilian University of Munich has shown how the purines adenine and guanine can be synthesized easily and in reasonable yields, offering more evidence that RNA could have served as the origin of life on Earth. In their paper published in the journal Science, the team describes the process they took in looking for evidence that RNA could have been the first self-replicating molecule that event

For several years many scientists have supported the idea that got its start on our planet due to a series of events that led to the creation of RNA molecules—it seems like a strong candidate because it is able to both store information and act as a catalyst. To bolster the theory, scientists have been trying to show under what conditions RNA might have come about based on the conditions that existed on early Earth. In the early going, researchers found it relatively easy to show how two of the four main building blocks in RNA, uracil and cytosine, could have come about, but showing how the other two, adenine and guanine, might have come about has been problematic. In this new effort the research team describes a scenario under with both might have come about given conditions at the time that life is believed to have got its start.The team started by extending prior research that had shown that a molecule called formamidopyrimidine can react under certain to form purines—they discovered that adding acid to an amine (which the team showed could have come about very easily from plentiful carbon, nitrogen and hydrogen) allowed for a reaction that led to the formation of a purine and that it would easily bond with , which recent research has shown is plentiful on comets—that means it could have met with existing purines if a comet crashed into the planet at the right place. Once that happened, the resultant reactions would have led to forging bonds with sugars which would have resulted in the creation of large amounts of purines, including adenine and guanine—thus all of the necessary ingredients would have been in place for the creation of RNA molecules, setting the stage for the development of living organisms.

More information: S. Becker et al. A high-yielding, strictly regioselective prebiotic purine nucleoside formation pathway, Science (2016). DOI: 10.1126/science.aad2808

Abstract
The origin of life is believed to have started with prebiotic molecules reacting along unidentified pathways to produce key molecules such as nucleosides. To date, a single prebiotic pathway to purine nucleosides had been proposed. It is considered to be inefficient due to missing regioselectivity and low yields. We report that the condensation of formamidopyrimidines (FaPys) with sugars provides the natural N-9 nucleosides with extreme regioselectivity and in good yields (60%). The FaPys are available from formic acid and aminopyrimidines, which are in turn available from prebiotic molecules that were also detected during the Rosetta comet mission. This nucleoside formation pathway can be fused to sugar-forming reactions to produce pentosides, providing a plausible scenario of how purine nucleosides may have formed under prebiotic conditions.

© 2016 Phys.org

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Continuum of Life to Death

How did matter in the universe get to conscious life stuff. Is being alive just complex organization of matter. I have often thought about these issues when I think about patterns in organic molecules and biochemical systems in life.

What Makes You You?

When you say the word “me,” you probably feel pretty clear about what that means. It’s one of the things you’re clearest on in the whole world—something you’ve understood since you were a year old. You might be working on the question, “Who am I?” but what you’re figuring out is the who am part of the question—the part is obvious. It’s just you. Easy.

But when you stop and actually think about it for a minute—about what “me” really boils down to at its core—things start to get pretty weird. Let’s give it a try.

The Body Theory

We’ll start with the first thing most people equate with what a person is—the physical body itself. The Body Theory says that that’s what makes you you. And that would make sense. It doesn’t matter what’s happening in your life—if your body stops working, you die. If Mark goes through something traumatic and his family says, CH“It really changed him—he’s just not the same person anymore,” they don’t literally mean Mark isn’t the same person—he’s changed, but he’s still Mark, because Mark’s body is Mark, no matter what he’s acting like. Humans believe they’re so much more than a hunk of flesh and bone, but in the end, a physical ant is the ant, a squirrel’s body is the squirrel, and a human is its body. This is the Body Theory—let’s test it:

So what happens when you cut your fingernails? You’re changing your body, severing some of its atoms from the whole. Does that mean you’re not you anymore? Definitely not—you’re still you.

How about if you get a liver transplant? Bigger deal, but definitely still you, right?

What if you get a terrible disease and need to replace your liver, kidney, heart, lungs, blood, and facial tissue with synthetic parts, but after all the surgery, you’re fine and can live your life normally. Would your family say that you had died, because most of your physical body was gone? No, they wouldn’t. You’d still be you. None of that is needed for you to be you.

Well maybe it’s your DNA? Maybe that’s the core thing that makes you you, and none of these organ transplants matter because your remaining cells all still contain your DNA, and they’re what maintains “you.” One major problem—identical twins have identical DNA, and they’re not the same person. You are you, and your identical twin is most certainly not you. DNA isn’t the answer.

So far, the Body Theory isn’t looking too good. We keep changing major parts of the body, and you keep being you.

But how about your brain?

The Brain Theory

Let’s say a mad scientist captures both you and Bill Clinton and locks the two of you up in a room.

CH

The scientist then performs an operation on both of you, whereby he safely removes each of your brains and switches them into the other’s head. Then he seals up your skulls and wakes you both up. You look down and you’re in a totally different body—Bill Clinton’s body. And across the room, you see your body—with Bill Clinton’s personality.

CFO

Now, are you still you? Well, my intuition says that you’re you—you still have your exact personality and all your memories—you’re just in Bill Clinton’s body now. You’d go find your family to explain what happened:

CF1

CF2

So unlike your other organs, which could be transplanted without changing your identity, when you swapped brains, it wasn’t a brain transplant—it was a body transplant. You’d still feel like you, just with a different body. Meanwhile, your old body would not be you—it would be Bill Clinton. So what makes you you must be your brain. The Brain Theory says that wherever the brain goes, you go—even if it goes into someone else’s skull.

The Data Theory

Consider this—

What if the mad scientist, after capturing you and Bill Clinton, instead of swapping your physical brains, just hooks up a computer to each of your brains, copies every single bit of data in each one, then wipes both of your brains completely clean, and then copies each of your brain data onto the other person’s physical brain? So you both wake up, both with your own physical brains in your head, but you’re not in your body—you’re in Bill Clinton’s body. After all, Bill Clinton’s brain now has all of your thoughts, memories, fears, hopes, dreams, emotions, and personality. The body and brain of Bill Clinton would still run out and go freak out about this to your family. And again, after a significant amount of convincing, they would indeed accept that you were alive, just in Bill Clinton’s body.

Philosopher John Locke’s memory theory of personal identity suggests that what makes you you is your memory of your experiences. Under Locke’s definition of you, the new Bill Clinton in this latest example is you, despite not containing any part of your physical body, not even your brain. 

This suggests a new theory we’ll call The Data Theory, which says that you’re not your physical body at all. Maybe what makes you you is your brain’s data—your memories and your personality.

We seem to be honing in on something, but the best way to get to concrete answers is by testing these theories in hypothetical scenarios. Here’s an interesting one, conceived by British philosopher Bernard Williams:

The Torture Test

Situation 1: The mad scientist kidnaps you and Clinton, switches your brain data with Clinton’s, as in the latest example, wakes you both up, and then walks over to the body of Clinton, where you supposedly reside, and says, “I’m now going to horribly torture one of you—which one should I torture?”

What’s your instinct? Mine is to point at my old body, where I no longer reside, and say, “Him.” And if I believe in the Data Theory, then I’ve made a good choice. My brain data is in Clinton’s body, so I’m now in Clinton’s body, so who cares about my body anymore? Sure, it sucks for anyone to be tortured, but if it’s between me and Bill Clinton, I’m choosing him.

Situation 2: The mad scientist captures you and Clinton, except he doesn’t do anything to your brains yet. He comes over to you—normal you with your normal brain and body—and asks you a series of questions. Here’s how I think it would play out:

Mad Scientist: Okay so here’s what’s happening. I’m gonna torture one of you. Who should I torture?

You: [pointing at Clinton] Him.

MS: Okay but there’s something else—before I torture whoever I torture, I’m going to wipe both of your brains of all memories, so when the torture is happening, neither of you will remember who you were before this. Does that change your choice?

You: Nope. Torture him.

MS: One more thing—before the torture happens, not only am I going to wipe your brains clean, I’m going to build new circuitry into your brain that will convince you that you’re Bill Clinton. By the time I’m done, you’ll think you’re Bill Clinton and you’ll have all of his memories and his full personality and anything else that he thinks or feels or knows. I’ll do the same thing to him, convincing him he’s you. Does that change your choice?

You: Um, no. Regardless of any delusion I’m going through and no matter who I think I am, I don’t want to go through the horrible pain of being tortured. Insane people still feel pain. Torture him.

So in the first situation, I think you’d choose to have your own body tortured. But in the second, I think you’d choose Bill Clinton’s body—at least I would. But the thing is—they’re the exact same example. In both cases, before any torture happens, Clinton’s brain ends up with all of your data and your brain has his—the difference is just at which point in the process you were asked to decide. In both cases, your goal is for you to not be tortured, but in the first situation, you felt that after the brain data swap,you were in Clinton’s body, with all of your personality and memories there with you—while in the second situation, if you’re like me, you didn’t care what was going to happen with the two brains’ data, you believed that you would remain with your physical brain, and body, either way.

Choosing your body to be the one tortured in the first situation is an argument for the Data Theory—you believe that where your data goes, you go. Choosing Clinton’s body to be tortured in the second situation is an argument for the Brain Theory, because you believe that regardless of what he does with your brain’s data, you will continue to be in your own body, because that’s where your physical brain is. Some might even take it a step further, and if the mad scientist told you he was even going to switch your physical brains, you’d still choose Clinton’s body, with your brain in it, to be tortured. Those that would torture a body with their own brain in it over torturing their own body believe in the Body Theory.

Not sure about you, but I’m finishing this experiment still divided. Let’s try another. Here’s my version of modern philosopher Derek Parfit’s teletransporter thought experiment, which he first described in his book Reasons and Persons

The Teletransporter Thought Experiment

It’s the year 2700. The human race has invented all kinds of technology unimaginable in  today’s world. One of these technologies is teleportation—the ability to transport yourself to distant places at the speed of light. Here’s how it works—

You go into a Departure Chamber—a little room the size of a small cubicle.

cube stand

You set your location—let’s say you’re in Boston and your destination is London—and when you’re ready to go, you press the button on the wall. The chamber walls then scan your entire body, uploading the exact molecular makeup of your body—every atom that makes up every part of you and its precise location—and as it scans, it destroys, so every cell in your body is destroyed by the scanner as it goes.

cube beam

When it’s finished (the Departure Chamber is now empty after destroying all of your cells), it beams your body’s information to an Arrival Chamber in London, which has all the necessary atoms waiting there ready to go. The Arrival Chamber uses the data to re-form your entire body with its storage of atoms, and when it’s finished you walk out of the chamber in London looking and feeling exactly how you did back in Boston—you’re in the same mood, you’re hungry just like you were before, you even have the same paper cut on your thumb you got that morning.

The whole process, from the time you hit the button in the Departure Chamber to when you walk out of the Arrival Chamber in London, takes five minutes—but to you it feels instantaneous. You hit the button, things go black for a blink, and now you’re standing in London. Cool, right?

In 2700, this is common technology. Everyone you know travels by teleportation. In addition to the convenience of speed, it’s incredibly safe—no one has ever gotten hurt doing it.

But then one day, you head into the Departure Chamber in Boston for your normal morning commute to your job in London, you press the big button on the wall, and you hear the scanner turn on, but it doesn’t work.

cubicle broken

The normal split-second blackout never happens, and when you walk out of the chamber, sure enough, you’re still in Boston. You head to the check-in counter and tell the woman working there that the Departure Chamber is broken, and you ask her if there’s another one you can use, since you have an early meeting and don’t want to be late.

She looks down at her records and says, “Hm—it looks like the scanner worked and collected its data just fine, but the cell destroyer that usually works in conjunction with the scanner has malfunctioned.”

“No,” you explain, “it couldn’t have worked, because I’m still here. And I’m late for this meeting—can you please set me up with a new Departure Chamber?”

She pulls up a video screen and says, “No, it did work—see? There you are in London—it looks like you’re gonna be right on time for your meeting.” She shows you the screen, and you see yourself walking on the street in London.

“But that can’t be me,” you say, “because I’m still here.”

At that point, her supervisor comes into the room and explains that she’s correct—the scanner worked as normal and you’re in London as planned. The only thing that didn’t work was the cell destroyer in the Departure Chamber here in Boston. “It’s not a problem, though,” he tells you, “we can just set you up in another chamber and activate its cell destroyer and finish the job.”

And even though this isn’t anything that wasn’t going to happen before—in fact, you have your cells destroyed twice every day—suddenly, you’re horrified at the prospect.

“Wait—no—I don’t want to do that—I’ll die.”

The supervisor explains, “You won’t die sir. You just saw yourself in London—you’re alive and well.”

“But that’s not me. That’s a replica of me—an imposterI’m the real me—you can’t destroy my cells!”

The supervisor and the woman glance awkwardly at each other. “I’m really sorry sir—but we’re obligated by law to destroy your cells. We’re not allowed to form the body of a person in an Arrival Chamber without destroying the body’s cells in a Departure Chamber.”

You stare at them in disbelief and then run for the door. Two security guards come out and grab you. They drag you toward a chamber that will destroy your cells, as you kick and scream…

__________

If you’re like me, in the first part of that story, you were pretty into the idea of teletransportation, and by the end, you were not.

The question the story poses is, “Is teletransportation, as described in this experiment, a form of traveling? Or a form of dying?

This question might have been ambiguous when I first described it—it might have even felt like a perfectly safe way of traveling—but by the end, it felt much more like a form of dying. Which means that every day when you commute to work from Boston to London, you’re killed by the cell destroyer, and a replica of you is created.1 To the people who know you, you survive teletransportation just fine, the same way your wife seems just fine when she arrives home to you after her own teletransportation, talking about her day and discussing plans for next week. But is it possible that your wife was actually killed that day, and the person you’re kissing now was just created a few minutes ago?

Well again, it depends on what you are. Someone who believes in the Data Theory would posit that London you is you as much as Boston you, and that teletransportation is perfectly survivable. But we all related to Boston you’s terror at the end there—could anyone really believe that he should be fine with being obliterated just because his data is safe and alive over in London? Further, if the teletransporter could beam your data to London for reassembly, couldn’t it also beam it to 50 other cities and create 50 new versions of you? You’d be hard-pressed to argue that those were all you. To me, the teletransporter experiment is a big strike against the Data Theory.

Similarly, if there were an Ego Theory that suggests that you are simply your ego, the teletransporter does away nicely with that. Thinking about London Tim, I realize that “Tim Urban” surviving means nothing to me. The fact that my replica in London will stay friends with my friends, keep Wait But Why going with his Tuesday-ish posts, and live out the whole life I was planning for myself—the fact that no one will miss me or even realize that I’m dead, the same way in the story you never felt like you lost your wife—does almost nothing for me. I don’t care about Tim Urban surviving. I care about me surviving.

All of this seems like very good news for Body Theory and Brain Theory. But let’s not judge things yet. Here’s another experiment:

The Split Brain Experiment

A cool fact about the human brain is that the left and right hemispheres function as their own little worlds, each with their own things to worry about, but if you remove one half of someone’s brain, they can sometimes not only survive, but their remaining brain half can learn to do many of the other half’s previous jobs, allowing the person to live a normal life. That’s right—you could lose half of your brain and potentially function normally.

So say you have an identical twin sibling named Bob who developes a fatal brain defect. You decide to save him by giving him half of your brain. Doctors operate on both of you, discarding his brain and replacing it with half of yours. When you wake up, you feel normal and like yourself. Your twin (who already has your identical DNA because you’re twins) wakes up with your exact personality and memories.

twins

When you realize this, you panic for a minute that your twin now knows all of your innermost thoughts and feelings on absolutely everything, and you’re about to make him promise not to tell anyone, when it hits you that you of course don’t have to tell him. He’s not your twin—he’s you. He’s just as intent on your privacy as you are, because it’s his privacy too.

As you look over at the guy who used to be Bob and watch him freak out that he’s in Bob’s body now instead of his own, you wonder, “Why did I stay in my body and not wake up in Bob’s? Both brain halves are me, so why am I distinctly in my body and not seeing and thinking in dual split-screen right now, from both of our points of view? And whatever part of me is in Bob’s head, why did I lose touch with it? Who is the me in Bob’s head, and how did he end up over there while I stayed here?”

Brain Theory is shitting his pants right now—it makes no sense. If people are supposed to go wherever their brains go, what happens when a brain is in two places at once? Data Theory, who was badly embarrassed by the teletransporter experiment, is doing no better in this one.

But Body Theory—who was shot down at the very beginning of the post—is suddenly all smug and thrilled with himself. Body Theory says “Of course you woke up in your own body—your body is what makes you you. Your brain is just the tool your body uses to think. Bob isn’t you—he’s Bob. He’s just now a Bob who has your thoughts and personality. There’s nothing Bob’s body can ever do to not be Bob.” This would help explain why you stayed in your body.

So a nice boost for Body Theory, but let’s take a look at a couple more things—

What we learned in the teletransporter experiment is that if your brain data is transferred to someone else’s brain, even if that person is molecularly identical to you, all it does is create a replica of you—a total stranger who happens to be just like you. There’s something distinct about Boston you that was important. When you were recreated out of different atoms in London, something critical was lost—something that made you you.

Body Theory (and Brain Theory) would point out that the only difference between Boston you and London you was that London you was made out of different atoms. London you’s body was like your body, but it was still made of different material. So is that it? Could Body Theory explain this too?

Let’s put it through two tests:

The Cell Replacement Test

Imagine I replace a cell in your arm with an identical, but foreign, replica cell. Are you not you anymore? Of course you are. But how about if, one at a time, I replace 1% of your cells with replicas? How about 10%? 30%? 60%? The London you was composed of 100% replacement cells, and we decided that that was not you—so when does the “crossover” happen? How many of your cells do we need to swap out for replicas before you “die” and what’s remaining becomes your replica?

Something feels off with this, right? Considering that the cells we’re replacing are molecularly identical to those we’re removing, and someone watching this all happen wouldn’t even notice anything change about you, it seem implausible that you’d ever die during this process, even if we eventually replaced 100% of your cells with replicas. But if your cells are eventually all replicas, how are you any different from London you?

The Body Scattering Test 

Imagine going into an Atom Scattering Chamber that completely disassembles your body’s atoms so that all that’s left in the room is a light gas of floating atoms—and then a few minutes later, it perfectly reassembles the atoms into you, and you walk out feeling totally normal.

disassemble

Is that still you? Or did you die when you were disassembled and what has been reassembled is a replica of you? It doesn’t really make sense that this reassembled you would be the real you and London you would be a replica, when the only difference between the two cases is that the scattering room preserves your exact atoms and the London chamber assembles you out of different atoms. At their most basic level, atoms are identical—a hydrogen atom from your body is identical in every way to a hydrogen atom in London. Given that, I’d say that if we’re deciding London you is not you, then reassembled you is probably not you either.

The first thing these two tests illustrate is that the key distinction between Boston you and London you isn’t about the presence or absence of your actual, physical cells. The Cell Replacement Test suggests that you can gradually replace much or all of your body with replica material and still be you, and the Body Scattering Test suggests that you can go through a scatter and a reassembly, even with all of your original physical material, and be no more you than the you in London. Not looking great for Body Theory anymore.

The second thing these tests reveal is that the difference between Boston and London you might not be the nature of the particular atoms or cells involved, but about continuity. The Cell Replacement Test might have left you intact because it changed you gradually, one cell at a time. And if the Body Scattering Test were the end of you, maybe it’s because it happened all at the same time, breaking thecontinuity of you. This could also explain why the teletransporter might be a murder machine—London you has no continuity with your previous life.

So could it be that we’ve been off the whole time pitting the brain, the body, and the personality and memories against each other? Could it be that anytime you relocate your brain, or disassemble your atoms all at once, transfer your brain data onto a new brain, etc., you lose you because maybe, you’re not defined by any of these things on their own, but rather by a long and unbroken string of continuous existence?

Continuity

A few years ago, my late grandfather, in his 90s and suffering from dementia, pointed at a picture on the wall of himself as a six-year-old. “That’s me!” he explained.

He was right. But come on. It seems ridiculous that the six-year-old in the picture and the extremely old man standing next to me could be the same person. Those two people had nothing in common. Physically, they were vastly different—almost every cell in the six-year-old’s body died decades ago. As far as their personalities—we can agree that they wouldn’t have been friends. And they shared almost no common brain data at all. Any 90-year-old man on the street is much more similar to my grandfather than that six-year-old.

But remember—maybe it’s not about similarity, but about continuity. If similarity were enough to define you, Boston you and London you, who are identical, would be the same person. The thing that my grandfather shared with the six-year-old in the picture is something he shared with no one else on Earth—they were connected to each other by a long, unbroken string of continuous existence. As an old man, he may not know anything about that six-year-old boy, but he knows something about himself as an 89-year-old, and that 89-year-old might know a bunch about himself as an 85-year-old. As a 50-year-old, he knew a ton about him as a 43-year-old, and when he was seven, he was a pro on himself as a 6-year-old. It’s a long chain of overlapping memories, personality traits, and physical characteristics.

It’s like having an old wooden boat. You may have repaired it hundreds of times over the years, replacing wood chip after wood chip, until one day, you realize that not one piece of material from the original boat is still part of it. So is that still your boat? If you named your boat Polly the day you bought it, would you change the name now? It would still be Polly, right?

In this way, what you are is not really a thing as much as a story, or a progression, or one particulartheme of person. You’re a bit like a room with a bunch of things in it—some old, some new, some you’re aware of, some you aren’t—but the room is always changing, never exactly the same from week to week.

Likewise, you’re not a set of brain data, you’re a particular database whose contents are constantly changing, growing, and being updated. And you’re not a physical body of atoms, you’re a set of instructions on how to deal with and organize the atoms that bump into you.

People always say the word soul and I never really know what they’re talking about. To me, the word soul has always seemed like a poetic euphemism for a part of the brain that feels very inner to us; or an attempt to give humans more dignity than just being primal biological organisms; or a way to declare that we’re eternal. But maybe when people say the word soul what they’re talking about is whatever it is that connects my 90-year-old grandfather to the boy in the picture. As his cells and memories come and go, as every wood chip in his canoe changes again and again, maybe the single common thread that ties it all together is his soul. After examining a human from every physical and mental angle throughout the post, maybe the answer this whole time has been the much less tangible Soul Theory.

______

It would have been pleasant to end the post there, but I just can’t do it, because I can’t quite believe in souls.

The way I actually feel right now is completely off-balance. Spending a week thinking about clones of yourself, imagining sharing your brain or merging yours with someone else’s, and wondering whether you secretly die every time you sleep and wake up as a replica will do that to you. If you’re looking for a satisfying conclusion, I’ll direct you to the sources below since I don’t even know who I am right now.

The only thing I’ll say is that I told someone about the topic I was posting on for this week, and their question was, “That’s cool, but what’s the point of trying to figure this out?” While researching, I came across this quote by Parfit: “The early Buddhist view is that much or most of the misery of human life resulted from the false view of self.” I think that’s probably very true, and that’s the point of thinking about this topic.

___________

Related Wait But Why Posts
– Here’s how I’m working on this false view of self thing.
– And things could get even more confusing soon when we have to figure out if Artificial Superintelligence is conscious or not.

Sources
Very few of the ideas or thought experiments in this post are my original thinking. I read and listened to a bunch of personal identity philosophy this week and gathered my favorite parts together for the post. The two sources I drew from the most were philosopher Derek Parfit’s book Reasons and Persons and Yale professor Shelly Kagan’s fascinating philosophy course on death—the lectures are all watchableonline for free.

Other Sources:
David Hume: Hume on Identity Over Time and Persons
Derek Parfit: We Are Not Human Beings
Peter Van Inwagen: Materialism and the Psychological-Continuity Account of Personal Identity
Bernard Williams: The Self and the Future
John Locke: An Essay Concerning Human Understanding (Chapter: Of Identity and Diversity)
Douglas Hofstadter: Gödel, Escher, Bach
Patrick Bailey: Concerning Theories of Personal Identity

And a fascinating and related video
For a while now, my favorite YouTube channel has been Kurzgesagt. They make one amazing five-minute animated video a month on the exact kinds of topics I love to write about. I highly recommend subscribing. Anyway, I’ve spoken to them and we liked the idea of tag-teaming a similar topic at the same time, and since this one was on both of our lists, we did that this week. I focused on what the self is, they explored what life itself is. Check it out: