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Monday, March 30, 2020

Book Reviewed: Entropy Principle for the Development of Complex Biotic Systems: Organisms, Ecosystems, the Earth, by Ichiro Aoki

Entropy and the flow of nature

The title of this book is a little puzzling, since I thought the author would be discussing about the application of the second law of thermodynamics; the concept of entropy, the operation of the biological equivalent of Maxwell’s Demon (the perpetual motion machines), information theory (Shannon’s entropy) and statistical mechanics to explain the high-degree of order in biological processes of a living cell. But this is not what you find in this book. This book is about the energy budget equation applied to macroscopic systems like animals, plants and the ecosystems. The energy budget equation has been used in meteorology and global climatology, which is based on both first and second laws of thermodynamics. In this book, the author describes the results of his calculation for the entropy production for a plant, human, lizard, deer, hog, earth, solar system and an ecosystem.

Thermodynamics is robust science because it is non-reductionistic. This means that the general scheme of systems does not depend on the detailed chemical properties of constituent subsystems and sub-subsystems but only to micro configurations (particles), thermodynamic parameters (pressure, temperature, volume, entropy, etc.) and statistics. For example, entropy is a measure of the quality (usefulness) of energy: the higher the entropy, the lower the quality (less useful) of energy. Also, it is a measure of the randomness or disorder. In a closed system such as this universe, entropy cannot decrease, but in an open system like a living cell, planets, stars, and galaxies, irreversible reactions dominate. The second law states that the change of entropy production for an irreversible process is always larger than the corresponding reversible process. And in the latter, change in entropy production is always zero. Entropy production is a measure of the strength and magnitude of the irreversibility of a processes and pertains to process of energy flow and the transportation of matter.

For example for earth-sun system, of the ~340 W/m² of solar radiation received by the earth (fixed by Earth-Sun distance), an average of ~77 W/m² is reflected back to space by clouds and atmosphere, and ~23 W/m² is reflected by earth’s surface albedo, leaving ~240 W/m² of solar energy input to the Earth's energy budget. But earth’s surface radiates about 17 percent of incoming solar energy as thermal infrared energy; 12 percent of it escapes to outer space, and the rest 5% become trapped by greenhouse gases like water vapor, carbon dioxide, methane raising the planets’ temperature.

Thursday, March 26, 2020

Book Reviewed: Hinduism: Hinduism for Beginners: Guide to Understanding Hinduism and the Hindu Religion by Shalu Sharma

Seeking the power of God for salvation: A Hindu way of living

In this book on Hinduism, author Shalu Sharma interprets the beliefs, traditions and teachings sacred scriptures of Hindu faith. The apparent polytheistic nature of Hinduism and the unique style of deity worship are inherent in Indian traditions since Vedic times. The sacred scriptures of Vedas, the Upanishads, the Gita, the Epics and the Puranas, with six schools of Hindu philosophy offers a solid foundation for a belief system that is significantly different, and more ancient than the Abrahamic religions. An understanding of ancient Indian history and the birth and evolution of Hindu belief systems are necessary to comprehend an Indian faith. In this regard, the author’s efforts to explain the deity worship and apparent polytheistic nature is commendable. Hinduism is the worship of One God in many forms, and the monotheistic nature of the faith is found in the concept of "Brahman," in the holy scriptures of Gita and Upanishads. This idea is enumerated extensively in the Vedanta school of Hindu philosophy. The gods of Hinduism are eternal, they are described in Vedas and the Epics and Puranas. The Vedic god represent a force of nature, Agni for fire; Varuna for water (ocean); Vayu for wind; Soma for plants; and Indra for thunder, power, and strength. The prayers (hymns) offer the highest attributes to Vedic gods; but there is One Supreme Godhead. Lord Krishna in BhagavadGita 4:11 and 7:21, says that He, the Supreme Lord, will respond to the devotees in whichever form they worship Him and in whichever way they approach Him. In Rigveda 1.164.46, we find, "ekam sat viprah bhaudha vadanti," translation; The Truth is One; Sages call it by different names. This sets the tone for very early metaphysical ideas that were later developed in Upanishads. The scribe of this hymn suggests that deities appear in different forms but there is only One God. The ancient traditions of Vedic beliefs and the monotheistic system of Upanishads and the six philosophical systems for the core of Hindu belief system.

The scared text of BhagavadGita, the holy book of Hinduism teaches the institution of dharma, and to practice the principles of bhakti and the yogic ideals for attaining moksha. Atman finding unification with Brahman is the goal of mortal sinners. We can free ourselves from the bondage of cycle of birth and death through the unification with Supreme Soul. The setting of the Gita in a battlefield has been interpreted as an allegory for the ethical and moral struggles of material life that is dominated by three human qualities, sattva, rajas or tamas. These gunas are part of Prakriti that cause our ignorance, delusion, bondage and suffering in a material world.

Book Reviewed: The Meaning of the Wave Function: In Search of the Ontology of Quantum Mechanics by Shan Gao

Physics & Philosophy: Quantum reality and the nature of wave function

This is about the physics and philosophy of the wave function that holds key to understanding quantum reality. But the discussions are narrowly focused, and reckless in blatant disregard for a balanced discussion. The author is on a mission to promote his ideas instead of an all-around discussion of wave functions. On the brighter side, there are very few equations and little mathematics. So, the reading is straightforward and easy to assimilate the discussions and the subject matter. This is intended for general readers interested in physics and philosophy of quantum reality, and the author’s writing skills makes reading easy.

In quantum physics, a wave function is a variable quantity that mathematically describes the wave characteristics of a particle. The value of the wave function of this particle, at a given point of space and time is related to the likelihood (probability) of that particle’s being there at a time. But it is the square of the wave function, Ψ2 that acquires the physical significance of existence.

The author argues that the wave function in quantum mechanics is real, and it represents the state of random discontinuous motion (RDM) of particles in three-dimensional space. He posits a picture of quantum ontology that accounts for our definite experience, but that requires that the quantum dynamics be revised to include a stochastic nonlinear evolution term resulting from the RDM of particles. Therefore, it follows that the wave function is real, and it represents a physical property of a single quantum system. This new interpretation represents an alternative to wave function realism interpretations.

Shan Gao ignores other approaches to wave functions except Realism, where the wave function represents something objective and mind independent reality. The realism approach may be grouped into three categories: ontological interpretations (analysis of being), nomological interpretations (on par with laws of nature), and the sui generis interpretation; here the wave function is neither ontological nor nomological, but it is distinct and unique. But Gao considers only the ontological interpretation in which the wave function is interpreted as part a of the fundamental material ontology, on par with particles, fields, space-time events or properties, which are the kind of microscopic/subatomic materials that make up macroscopic/molecular materials such as books and rocks. For a wave function to be nomological, it must be to be like a fundamental law in which one might expect it to be time independent.

In quantum mechanics, the fundamental physical space is high-dimensional. In configuration space fundamentalism, it is ((10exp80) dimensions. But it is possibly infinite in Hilbert space fundamentalism. Considering just three-dimensional space in the author’s interpretation calls for some discussions. For a clearheaded discussion of wave function physics, I recommend reading a recent paper by Eddy Chen. This is a lucid and easy to understand presentation of the topic (Realism about the Wave Function, Forthcoming in Philosophy Compass, June 12, 2019; arXiv:1810.07010 [quant-ph].

Tuesday, March 24, 2020

Book Reviewed: Astrobiology - Understanding Life in the Universe by Charles S. Cockell

Looking for life elsewhere in the universe

Does anyone think that planet Earth is unique in Milky Way galaxy? Or do we believe that human beings are peculiar in this universe? If there are planets elsewhere in the universe, are they habitable, and do they sustain millions of years of species evolution?

The author considers several aspects of astrobiology: planetary science, life’s Structure, building the biomolecules, especially, the CHNOPS (Carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur), energy for life, limits of the bio-space, and the ancient history of early earth. One of the fundamental questions in search for extra-terrestrial life is do they have similar geological conditions as we have? The bio-space gives us a basis for a first-order assessment of the habitability. If we find a planetary environment that has physical and chemical conditions suitable for life, we are motivated to explore it and see if it has liquid water, energy supplies and basic elements that build life. Other forms of planetary life could exist that uses other elements and biomolecules and perhaps different biochemistry!

Many environments on the Earth are of interest in astrobiology, extreme temperatures, extreme pH, high salt, toxic-chemical environments and deep oceans. Currently, we have more than 4,000 extrasolar planets discovered. The distribution of extrasolar planets is diverse, different sizes, different physical and chemical characteristics. TRAPPIST-1 star system looks like our solar system and hosts seven planets that are potentially Earth-like. It is about 40 light years from us. Another exoplanet is K2-18b that is 124 light years from us contains water vapor in its atmosphere and exists in the habitable part of its star system. In our solar system, Jovian moons like Europa, Ganymede, and Callisto are known to have oceans beneath the surface. It is also reported that the moons of Saturn such as Enceladus, Titan and possibly Dione are also known to have liquid water oceans. Enceladus is among NASA’s top targets in the search for life beyond Earth because it appears to have three of life’s most important ingredients: the right chemical ingredients (such as carbon or hydrogen), available energy and liquid water. Current evidence suggests that there is microbial life below the surface of Mars in deeply buried oceans.

The author systematically explores various pathways that led to the complex biosphere on Earth. This work is a tour de force that offers a unique perspective on the question that puzzled human beings for centuries. Are we alone? Based on our current understanding, we are still not sure, but there are helpful biosignatures elsewhere, and the list of habitable planets are growing.

Sunday, March 22, 2020

Book Reviewed: Life in the Universe by Jeffrey O. Bennett and Seth Shostak

Looking for life elsewhere

This book is an introduction to astrobiology, and it is designed to convey some of the major conceptual foundations in astrobiology that cut across traditional fields such as chemistry, biology, geology, physics and astronomy. The study of astrobiology received a great impetus in 2019 when astronomers Michel Mayor and Didier Queloz were awarded the 2019 Nobel Prize in Physics for the discovery of extrasolar planet 51 Pegasi b orbiting a Sun-like star. It is a gas giant, a type that astronomers had expected would orbit the outer reaches of a solar system. But it was orbiting much closer to its star than Mercury is to the Sun. This was an early sign that other planetary systems might not be like our own. Since then more than 4,000 exoplanets have been known to exist and most of them are gas giants like Jupiter. The 2016 revised edition of this book includes several new discoveries of extrasolar planets, since then there have been new and exciting detection of habitable extrasolar planets. Methods and tools used to detect these planets uses biosignatures such as planetary temperatures, evidence for water, carbon-based compounds and other indications of atmospheric systems.

The exoplanet K2-18b, which is 124 light-years away, is 2.6 times the radius of Earth, and orbits its star within the habitable zone. Two teams of scientists announced recently that they've found water vapor in this world's atmosphere, which is a big milestone in the search for alien life. Outer planets in the TRAPPIST-1 star system is also conducive to life. It is relatively close to our solar system and hosts seven planets that are potentially Earth-like. Their cores are stretched by its star’s gravity, which generates heat. And the two furthest away from their star could be warm, wet and perhaps even have living systems.

In solar system life is known to exist in deep underground on Mars, and in the sub-surface oceans of moons of Jupiter and Saturn. Jovian moons like Europa, Ganymede, and Callisto are known to have oceans beneath the surface. The moons of Saturn such as Enceladus, Titan and possibly Dione are also known to have liquid water oceans. Enceladus is among NASA’s top targets in the search for life beyond Earth because it appears to have three of life’s most important ingredients: the right chemical ingredients (such as carbon or hydrogen), available energy and liquid water. Plume of water erupting from Enceladus contain molecular hydrogen. This helped strengthen the case for habitability on Enceladus, because hydrogen is an important food source to critters that thrive near hydrothermal vents on Earth. Titan, which is half the size of Earth, is intriguing not only for its internal ocean, but also for its dense, nitrogen-rich atmosphere and complex carbon chemistry. Whether it's inhabited or not, Titan is a fantastic natural laboratory for the chemistry of life.

This is a college textbook for astrobiology courses. I like the depth and the level of discussion. The authors themselves are leading astronomers in the detection of alien-planets. Seth Shostak is a senior astronomer at the SETI Institute, a not-for-profit research organization whose mission is to explore, understand, and explain the origin and nature of life in the universe.

Thursday, March 19, 2020

Book Reviewed: Worlds Hidden in Plain Sight - Thirty Years of Complexity Thinking at the Santa Fe Institute by David C. Krakauer

Explaining the complexity of evolution in biological and non-biological systems

This is an edited book that discusses the evolutionary science of complex systems that includes diverse subjects as, matter (non-life) to life transitions, and evolution, which includes biological evolution, and evolution of, economics and technologies, educational system, rural and urban structures, political structures, and banking systems. There are 37 chapters from various teams active in complex science research, and many are from the Santa Fe Institute in New Mexico. The editor of this book is a leading researcher in the field, and I found many chapters very illuminating. This new and emerging area of science finds commonality in the birth and evolution in biology, economics and technology, and other systems.

The take-home message from this book is as follows: Biological and non-biological systems seem to be unrelated. However, when we consider concepts such as non-equilibrium thermodynamics, entropy, Shannon’s information theory and statistical mechanics, they yield surprisingly similar results for the evolution of life and non-life systems alike. From one perspective, dynamical systems can be viewed as obeying the laws of physics (and chemistry for biological systems). From another perspective, they can be viewed as processing information and the operation of non-linear statistical mechanics. This is how complex adaptive systems come into existence and solve problems to control its own environment. This is illustrated by an example of a robot that is trying to catch an irregularly bouncing ball. It must decide what information is relevant, and the best way to use that in a model of task, and how can it learn to perform that task in real time? Similar challenges are relevant to biological systems undergoing natural selection or to any system that processes information in order to adapt. The fact that the total information contains both order and disorder information. We must identify where order increased at the expense of disorder. A system that controls its environment successfully adapts by constructing models that allow it to decide what information is necessary and how to act on it.

Thermodynamics is not a dynamical theory, it offers no explanation for the mechanistic origins of its macroscopic variables, such as pressure, temperature, volume, entropy, etc. But statistical mechanics offers microscopic basis for these macroscopic variables. The statistical mechanics establishes the conditions for non-equilibrium states, that is for dynamical/irreversible processes for counting microscopic configurations of a system and then connecting to its macroscopic averages of thermodynamic/macroscopic variables. The evolution of pattern formation under these conditions becomes relevant in system learning. Then terms such as, ''individual species," the boundaries of "community," the functional scale at which to characterize the "ecosystems," and the interface between "natural selection and self-organization," becomes more meaningful.

It should also be emphasized that the methods of dynamical systems theory are derived from deterministic classical mechanics. In contrast, the methods of information theory are non-deterministic which are based on probabilities. An example should serve as a useful exercise; In some monkey societies, it has been observed and reported that individuals estimate the future cost of social interaction by encoding the average outcome of past interactions in special signals and then summing over these signals that help them to take next steps in social interactions!

The authors in the edited book help us take a closer view of the world we live in. The physical reality we see, and experience is not just a product of the laws of physics and chemistry but also information dynamics, statistical mechanics and thermodynamics of systems. The non-deterministic probability component of statistical mechanics is ever present. No body could have modelled the path of biological evolution if there were intelligent beings studying planet Earth 65 million years ago! Highly recommended to readers interested in understanding the parallels in biological and non-biological evolution.

Monday, March 16, 2020

Book Reviewed: The Next Billion Users: Digital Life Beyond the West by Payal Arora

Choosing the Digital Life in a Chaotic World

There are numerous books in literature about the perils and promises of the digital and social-media revolution. Twitter, Facebook, Instagram, Snap Chat, weblogs, smartphones and distance-learning have impacted the culture of global youth, especially those from developing countries. Some of these changes are regarded as breakthroughs in education, information gathering, and human progress. But authors like Arora argue that the digital divide has helped create a climate of false sense of reality. Declining reading habits, no time for schoolwork, withering attention spans, and unhealthy effects of peer pressure on young people of poorer countries have caused insecurities. Addiction to games, entertainment, and pornography appears to make them happy. Digital social networks like Facebook have enabled low-income youths to break free of traditional social norms to pursue their passions. On the other side of the spectrum, users of social media have drawn the attention of the corporate companies who seduce them with advertising just like they do with users in the West. Facebook has become an equalizer between the rich and the poor in online corporate marketing.

The author believes that the poor do not need more innovation if it is a proxy for pilot projects. They are better off without them, and without motivated communities, technology will not succeed, says author Arora! Liberal professors like Arora believe that corporations must get more involved in societal issues facing developing countries. Her motivations and beliefs are less helpful to countries like India and Brazil. She frequently refers to the so-called slums of India and Brazil, but slums also exist in Europe and North America. She is familiar with slums of San Francisco and must have seen the Skid Row district of Los Angeles. Her solutions to the problems of technology for poor is like Nike’s “Just Do It” right campaign. She comes short on the measures social media must take to educate the poor kids of India and Brazil. But corporations also have responsibilities to its stockholders, and the community they serve. There should be a balance between the two strategies. One dictates the other!

Technology creates our world; it creates wealth, economy, and our way of living. Does technology, like biological life, evolve? Researchers at the Santa Fe Institute in New Mexico have concluded that the answer is, Yes! Pioneering technology thinker and economist W. Brian Arthur answers these questions in his book “The Nature of Technology: What It Is and How It Evolves.” Branching networks are found at every level in biology from a single cell to the ecosystem. Human-made networks could share the same features; and if they don't, then it might be profitable to make them do so! That is how technology evolves! Nature's patterns tend to arise from economical solutions. Evolution propagates this flourishing organization. It creates new niches into existing organism or human technology. This respectively creates new creatures or new technology. There is a parallel in evolution in biology and economics, and Brian Arthur and Santa Fe Institute in New Mexico have been more convinced in this little idea that many of us overlook.

This book is very narrative about the negative impact of social media on third world. The author gets very preachy but little on solutions. Do not expect much from this book as it does not add anything new to the burgeoning literature that is already cluttered with unwanted gospels of hypocrisy.

Sunday, March 1, 2020

Book Reviewed: A World Beyond Physics: The Emergence and Evolution of Life by Stuart A. Kauffman

The Cosmic Song: Life, matter, energy, order and non-equilibrium thermodynamics

How did matter (non-life), a non-machine-like existence turned into a living cell (life) 3.8 billion years ago? Living cells are "machines" that construct and assemble their own working parts. The emergence of such systems, the origin of life was due to spontaneous phase transition that allowed self-organization in complex prebiotic systems. The protocells were capable of Darwin's heritable variation, hence open-ended evolution by natural selection. Evolution propagates this organization. Evolving living creatures, by existing, create new niches into which yet further new creatures can emerge. Biological evolution is un-predictable, and it has its own growing and subtends to economically possible solutions it is presented with by nature. In this respect living cell operates like the economic web, which is also un-predictable but grows with economic opportunities. There are parallels between biological evolution and evolution of the economy. There are no mathematical models for a predictable evolution, and reductionism which is at the heart of modern science fails to explain the “wholeness” of structure and organization of a biological cell that no one can build. It turns out that life’ is not an objective property of creation, but it’s a very special case made on this planet!

Economics creates our world; it creates wealth, technology and our way of living. Researchers at the Santa Fe Institute in New Mexico where the author is affiliated with have been pursuing a revolution in science and economics. Ignoring the boundaries of disciplines, they are searching for novel fundamental ideas, theories, and practices that integrates a full range of scientific inquiries that will help us understand the complexities of reality. Much of the order and self-building of living cells are being understood by non-equilibrium thermodynamics and negentropy (also referred by terms such as negative entropy or anti-entropy) and phase transitions in early pre-biotic systems rich with a wide varieties of biomolecules.

This is a small book of only 168 pages that reads quickly. It is well described and easy to follow. However, the author proposes that we need new physics to explain the oddities of a living cell: This may be far-fetched!