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A random.random() Joseph Wilbrand Weblog

Tag: Schrodinger: What is Life?

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What is Life? (Chapter 7) – Schrodinger

What is Life? (Chapter 7) - Schrodinger

Summary

Life cannot be reduced to ordinary laws of physics.  This is because the construction of living beings is different than anything we have tested in the physical laboratory. 

Life is controlled by well ordered groups of atoms. 

Small numbers of atoms behave unpredictably: a healthy sparrow will live with more certainty than a single radioactive atom.  

Life and genetics is beyond mere statistical physics and probability mechanisms.  

Life utilizes two systems: order from disorder, and order from order.

Genetics relies upon a solid “aperiodic structure” (later revealed to be DNA) which Schrodinger says is “the finest masterpiece ever achieved along the lines of the Lord’s quantum mechanics. 

Two Premises: body is a pure mechanism, the individual has free choice through consciousness.  Consciousness is never experienced in the plural, only in the singular.  Consciousness finds itself constrained to the physical state and region of matter.  Each person has the impression they are the sum total of their experience and memory forming an “I” – The “I” being the ground stuff from which experience is collected.  

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What is Life? (Chapter 6) – Schrodinger

What is Life? (Chapter 6) - Schrodinger, Order, Disorder, and Entropy

Terms

entelechy – the supposed vital principle that guides the development and functioning of an organism or other system or organization.

metabolism – the chemical processes that occur within a living organism in order to maintain life.

absolute zero – (-)273 degrees C

death – thermodynamical equilibrium

Summary

Schrodinger’s reason for writing this book: living matter, while not eluding the “laws of physics” is likely to involve other “laws of physics” hitherto unknown, which, once revealed, will form just as integral part of this science as the former.

The laws of physics are statistical laws.  They have a lot to do with the tendency toward disorder.

To reconcile the durability of heredity with tendency toward disorder, the genetic molecule has to be a “masterpiece of highly differentiated order” safeguarded by quantum theory.  Life seems to follow order which is “kept up.”

Question: What is the characteristic feature of life?

When it goes on to “do something” – moving and exchanging material with its environment, and for a longer period than should be expected.

Systems are usually subject to friction, equalization of chemical potential, and tendency toward uniform temperature.  This is when a uniform state is achieved and and no observable events occur.  

Living beings remain alive by drawing from its environment negative entropy.  The essential thing in metabolism is that the organism succeeds in freeing itself from all the entropy it cannot help producing while alive.  

Life continually sucks orderliness from its environment. 

 

 

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What is Life? (Chapter 5) – Schrodinger

What is Life? (Chapter 5) - Schrodinger

Persons

Max Ludwig Henning Delbrück – was a German–American biophysicist who participated in launching the molecular biology research program in the late 1930s. He stimulated physical scientists’ interest into biology, especially as to basic research to physically explain genes, mysterious at the time. 

Definitions

amorphous – lacking a clear structure or focus.

Summary

Question: are these structures (molecules) composed of comparatively few atoms capable of withstanding for long periods the disturbing influence of heat motion to which the hereditary substance is continually exposed?

Energy thresholds required to create isomers must be high to make changes (mutations) a rare event.

The assumption at the time of writing (1944) was that genes were molecules.

Genes and possibly chromosome fibers are likely aperiodic solids (structure consisting of large aggregate without repetition)

**Note: Just nine years later, it was clear that DNA is indeed an aperiodic crystal and that genetic information is conveyed through this irregular pattern.

A well ordered association of atoms, endowed with sufficient resistivity to keep its order permanently appears to be the only conceivable material structure that offers a variety of possible arrangements sufficiently large to embody a complicated system of determinations within a small spatial boundary.  Additionally the number of atoms in such a structure need not be large to produce an almost unlimited number of possible arrangements (example morse code).  

This system can account for high degrees of permanence with high thresholds for spontaneous mutation.

 

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What is Life? (Chapter 4) – Schrodinger

What is Life? (Chapter 4) - Schrodinger, "The Quantum-Mechanical Evidence

Persons

Max Planck – was a German theoretical physicist whose discovery of energy quanta won him the Nobel Prize in Physics in 1918.

Fritz Wolfgang London – was a German born physicist and professor at Duke University. His fundamental contributions to the theories of chemical bonding and of intermolecular forces are today considered classic and are discussed in standard textbooks of physical chemistry. 

Walter Heinrich Heitler – was a German physicist who made contributions to quantum electrodynamics and quantum field theory. He brought chemistry under quantum mechanics through his theory of valence bonding.

Terms

Isomer – In chemistry, isomers are molecules or polyatomic ions with identical molecular formulae – that is, same number of atoms of each element – but distinct arrangements of atoms in space. Isomerism is existence or possibility of isomers. Isomers do not necessarily share similar chemical or physical properties. 

Summary

Question: how can we from the point of statistical physics reconcile the facts that the gene structure seems to involve only a comparatively small number of atoms (of the order of 1,000 and possibly less), and that nevertheless displays a regular and lawful activity (with a durability and permanence that borders upon the miraculous)?

The answer lies in the fact that the genetic material structure are molecules.  That being said, what causes the molecular stability?

Heredity is founded on quantum theory.  

Changes in energy levels at the atomic level are called “quantum jumps.”  

When atomic nuclei are within close proximity to each other in “a system” (molecule) they are unable by their nature to adopt arbitrary configurations.  Rather the configurations are set in limited “states” (including energy levels).  A transformation from one state to another is a quantum jump.  An increase in energy requires the acquisition of energy from the outside, and a decrease in energy can result in spending or radiating energy.

Molecules have a certain stability.  Different configurations require temperature changes.  The measurement of chance for change given a temperature is described as the “time of expectation.”

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What is Life? (Chapter 3) – Schrodinger

What is Life? (Chapter 3) - Schrodinger, "Mutations"

Persons

Hugo Marie de Vries – was a Dutch botanist and one of the first geneticists. He is known chiefly for suggesting the concept of genes, rediscovering the laws of heredity in the 1890s while apparently unaware of Gregor Mendel’s work, for introducing the term “mutation”, and for developing a mutation theory of evolution.

Gregor Mendel – was a biologist, meteorologist, mathematician, Augustinian friar and abbot of St. Thomas’ Abbey in Brünn (Brno), Margraviate of Moravia.

Definitions

allele – one of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome.

homozygous – having two identical alleles of a particular gene or genes.

heterozygous – having two different alleles of a particular gene or genes.

phenotype – the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.

genotype – the genetic constitution of an individual organism.

Survival of the Fittest and Natural Seleciton

Darwin’s theory of sequential, continuous, and small variations is incorrect when it comes to how natural selection works.  If you plot variation in crops you will see variance in the form of a statistical bell curve with deviations from the mean on either side.  If you take a sample of above average size corn from a pure-bread strain and make a new crop, it will create a statistical curve identical to the original.  

Small continuous variations are not inherited.

Occasionally a “jump-like” change, or mutation, occurs.  In this instance there are no intermediate forms.  This is similar to quantum theory in which no intermediate energies occur between two neighboring energy levels.  These mutations are inherited. 

**note: a rule in quantum theory states small systems can only possess specific amounts of energy.  For this system to increase energy it must make a “quantum” jump to the next level without passing through an intermediate quantity of energy in between.   

**note: a quantum leap is a discontinuous transition between quantum states. What this means is that an electron in one energy level in an atom jumps instantly into another energy level, emitting or absorbing energy as it does so. There is no in-between state, and it doesn’t take any time for the leap to occur.

For Schrodinger, mutation can substitute Darwin’s slight variation to support natural selection.  In light of this, it would be wrong to say that the original version is orthodox and the mutant version is a heretic.  

Because two organisms look alike (phenotype) does not mean they differ in inheritance (genotype).

**A recessive allele influences the phenotype only when the genotype is homozygous.

Because some mutations are recessive, even detrimental mutations may not manifest because they are latent.  In this sense close breeding has harmful effects.

In order for mutations to be suitable for the work of natural selection, they must be rare events – else injurious mutations would dominate suitable ones negating natural selection.  (Example: in a manufacturing plant, improvements should be tried one at a time while keeping everything else constant to determine if the change is in fact an improvement or not).

 

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What is Life? (Chapter 2) – Schrodinger 

What is Life? (Chapter 2) - Schrodinger

Summary

Whereas organisms contain large quantities of atoms which can follow statistical rules which prevent the influence of random behavior of single atoms, reproductive processes involve systems of small numbers of atoms which can not operate merely according to statistical physical laws.  Despite this, genes are responsible for transmitting unchanged data across centuries of generations.

Persons

John Burdon Sanderson Haldane FRS – nicknamed “Jack” or “JBS”, was a British-Indian scientist who worked in physiology, genetics, evolutionary biology, and mathematics. With innovative use of statistics in biology, he was one of the founders of neo-Darwinism.

Cyril Dean Darlington FRS – an English biologist, cytologist, geneticist and eugenicist, who discovered the mechanics of chromosomal crossover, its role in inheritance, and therefore its importance to evolution. He was Sherardian Professor of Botany at the University of Oxford from 1953 to 1971.

Terms

dilettante – amateur

ontogeny – the structure and function an organism will develop throughout its entire life, from its beginnings as a fertilized egg cell to the state of maturity when it begins to reproduce.

prolixity – use of excessive words

Notes

Although biological structures have “many atomic” structures which can protect against haphazard “single atomic” events, small groups of atoms play a dominating role in “the very orderly and lawful events within a living organism.”  These events involving small amounts of atoms follow strict biological laws.  

Of interest, all cells contain a complete (double) copy of the code-script (chromosomes) which is the equivalent of a general giving every soldier copies of campaign battle plans.  The only exception to this are gametes which are reproductive cells. 

**Schrodinger mentions that humans have 48 chromosomes, which was the belief in 1944.  The correct determination of the human diploid chromosome number as 46, by J-H Tjio and A Levan, at the University of Lund, Sweden, occurred 50 years ago, in December 1955; the finding was published in April 1956, ending a period of more than 30 years when the number had been thought to be 48.

Biologists describe organisms as “four dimensional patterns” – a pattern which includes time

Mitosis vs Meiosis

Mitosis produces two diploid (2n) somatic cells that are genetically identical to each other and the original parent cell, whereas meiosis produces four haploid (n) gametes that are genetically unique from each other and the original parent (germ) cell.

Haploid Individuals

Some male bees and plants are haploid – they have no father, and are the result of multiple divisions from unfertilized eggs, which indicates a complete code-script pattern exists in every set of chromosomes.  

Genes

Genes are the locus of what causes properties such as eye color.  The space of a gene is approximately 300 angstrom – approximately a few million atoms.  That quantity is too small to follow “orderly and lawful” behavior based on statistical physics.  Unlike a drop of liquid, genes likely require each atom to play an individual role.  

Genetics transmit information without appreciable change for generations – permanent within centuries.  All this occurs in the beginning with the transmission by the material structure of the nuclei of the two cells which unite to form the fertilized egg cell. 

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What is Life? (Chapter 1) – Schrodinger

What is Life? The Physical Aspect of the Living Cell

Well, here we go—Great Books of the Western World, a ten-year reading plan. Aside from a yearly plan, I didn’t see that Adler wanted books to be read in any particular order within the year. So, I wanted my first read to be Schrodinger – What is Life? I am sure my commentary and interaction with each work will evolve; however, part of the enjoyment (I predict) of participating in the “great conversation” is adaptation and maturation over time.  

 

Chapter 1 Summary

Individual atoms and particles act in unpredictable ways; however, large groups of atoms and particles follow statistical laws which can be predicted and viewed as orderly. Examples of this phenomenon include the paramagnetism of oxygen gas, sinking fog and Brownian movement, and diffusion. In short small scale chaos can have an order or follow statistical laws on a larger scale, which can be described as “order from disorder.” Life depends on order, which require large numbers of atoms.  

 

Notes:

 

Persons

Ludwig Boltzmann – Austrian physicist and philosopher. His greatest achievements were the development of statistical mechanics and the statistical explanation of the second law of thermodynamics.

 

Willard Gibbs – was an American scientist who made significant theoretical contributions to physics, chemistry, and mathematics. His work on the applications of thermodynamics was instrumental in transforming physical chemistry into a rigorous inductive science.

 

Definition

Angstrom – a unit of length equal to one hundred-millionth (10^-10th) of a centimeter, and is used to express wavelengths and interatomic distances

 

paramagnetism – a form of magnetism whereby some materials are weakly attracted by an externally applied magnetic field, and form internal, induced magnetic fields in the direction of the applied magnetic field.

 

predilection – a preference or special liking for something; a bias in favor of something

 

Chapter 1 (The Classical Physicist’s Approach to the Subject)

This book was written from a series of lectures, which were determined to be challenging to understand at the outset despite not using mathematical deduction. The main question this book seeks to answer is:

 

Primary Question: How can the events in space and time that occur within a living organism’s boundary be accounted for by physics and chemistry?

 

The conclusion (up front) was: present-day physics and chemistry cannot account for such events; however, there is no reason to think that these sciences couldn’t eventually account for it. The inability to explain is accounted for, which is an accomplishment in itself. 

 

Non-physicists aren’t expected to understand or appreciate the difference in statistical structure.  

 

The essential part of living cells is chromosome fiber which can be called aperiodic crystals. Aperiodic crystals are one of the most fascinating and complex material structures.

 

Question: How do aperiodic crystals compare to periodic crystals?

 

Whereas periodic crystals can be described as having a repeating pattern, aperiodic crystals show no repetition while maintaining an elaborate, meaningful design.

 

The Line of Attack

Develop a “naive physicist’s (what Shrodinger calls himself) idea about organisms.”

Investigate whether a Physicist can contribute to ideas about life and organisms.

When a theory is made, compare this theory to biological facts.

 

Question: Why are the atoms so small?

 

Lord Kelvin described this: if you could mark the molecules in a glass of water, then pour the contents into the ocean and evenly distribute them throughout the seven seas, and if then you took a class of water anywhere in the ocean, you would find in it about a hundred of these marked molecules.  

 

This question is more aimed at comparing the size of an atom and the size of our bodily selves, or why our bodies are so large compared with the atom.

 

The most interesting aspect of humans is their ability to feel, think, and perceive; however, we cannot perceive single atoms, which is a good thing because if we could, we would likely be unable to form ideas.  

 

Thought is orderly, which means our physical organization is well-ordered and follows physical laws. The interaction between our “system” and other “systems” is orderly.  

 

Individual atoms are disorderly, but large numbers allow for statistical laws to apply. The accuracy of these statistical laws increases with the number of atoms. All physical and chemical laws that play an essential role in organisms are statistical – large numbers to create order.  

 

An example was given where oxygen particles become magnetized in a magnetic field; however, the strength decreases with increased heat. The quality of paramagnetism depends on large quantities of oxygen particles; otherwise, there is no consistency but rather fluctuation.  

 

A second example is sinking fog, in which defined velocities depend on statistics of large quantities of minute droplets, whereas single droplets are subject to “Brownian movement.”

 

A third example is diffusion which is compared with “that of a blindfolded person on a large surface imbued with a certain desire of walking but without any preference for any particular direction and so changing his line continuously.”  

 

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