Biocosmology Investigation for Readers of Cellular Life and Forces of Nature

Introduction

A series of scientific articles aims at practical notions about how biological life intersects with forces of physical universe in experiment and logic.

Starter

Reading requires college-level of education. Familiarity with biology and physics, music, and information theory is advisable.

Goals

Determining new elements in physics and information theory, finding new views on biological life for practical purposes.

Development

Numerous experiments conducted by students or scientists in university research centers.

Articles

A Multi-Disciplinary Survey of Biocomputing:

1. Molecular and Cellular Level ^pdf 1.2Mb

The first part of this two-part survey examines the molecular and cel-
lular aspects of information processing in biological organisms (biocomputing) with
an intent to reveal its differences from information processing in digital computers.
The discussion is conducted in the framework of the microscopic-macroscopic model
pioneered by Conrad. It is essentially a nested hierarchical networks of information
processing. The original mesoscopic link between the microscopic and the macro-
scopic dynamics is elevated to a new level: mesoscopic dynamics. The control laws
that govern the input-output relationships at various levels of biocomputing are
examined. The visualization of microscopic intracellular dynamics, as a collection
of diffusion and reaction processes, conveys a sense of "randomness" in biocomput-
ing. Conversely, a view of biological determinism that is an extension of (absolute)
physical determinism has persisted, and is dramatized by the well-known conflict
of free will and determinism that dates back to St. Augustine's time or earlier. This
survey presents a view that is somewhat removed from these two extreme pictures.
Short-range non-covalent bond interactions are the key factors that rescue bio-
computing from complete randomness. Molecular recognition relies on random
searching to increase the probability of encounters at large distances but switches
to heuristic searching at mesoscopic distances of close encounters. However, ran-
domness still makes a conspicuous presence, as exemplified by ion channel fluctu-
ations. The presence of this endogenous noise in such a crucial process of nerve
impulse generation suggests that biocomputing practices a weaker form of deter-
minism. However, the endogenous noise does not propagate and does not become
steadily amplified in the subsequent steps because the control law re-converges to
a well-defined law at higher levels of biocomputing. Thus, information processing
proceeds through various hierarchical levels, the control laws swing alternatingly
between nearly random to nearly deterministic but never reach either extremes. Fur-
thermore, the network structure in biocomputing is not rigidly fixed, but is partly
"hard-wired" and partly loosely connected and re-configurable. The computing re-
source can be dynamically adjusted in accordance with the needs of the system. It
appears that the inherent randomness included in biocomputing processes and the
dynamic nature of the network structures are essential for the intelligent behavior
of a living organism. However, the biological organization imposes a top-down con-
straint to curtail the occurrence of possible rampant randomness. The implication
of this weaker form of determinism to creativity and free will is discussed in Part 2.

2. Systems and Evolutionary Levels, and

Technological Applications ^pdf 2.5Mb

The second part of this survey examines biocomputing in intact multi-
cellular organisms. The parallelism between creative problem solving and evolution is emphasized: both processes invoke heuristic searching and feature modularity
prominently. Simonton's chance-configuration theory of creative problem solving is
recast in terms of pattern recognition and analyzed in terms of parallel and se-
quential processing. An attempt is made to demystify the creative process that is
commonly thought to be the monopoly of geniuses. It is shown that the procedures
utilized in high creativity and in everyday ingenuity are fundamentally the same,
but geniuses push the creative process to the extreme. A re-interpretation of Freud's
concept of the unconscious in terms of selective attention is invoked to dispel the
mystery surrounding the introspective account of Henri Poincaré on mathematical
creation.
Among the many attributes of consciousness, the elusive free will problem is
singled out for analysis in terms of biological control laws. While free will is a
philosophical problem, the conflict of free will and determinism can be treated as
a scientific problem. Specific electrophysiological evidence is presented to indicate
that Nature (evolution) specifically recruited "partial randomness" as a crucial
component for biocomputing. It is argued that ion channel fluctuations are mani-
festation of endogenous noise and are governed by critically "designed" probabilis-
tic control laws deviations from a normal control law may result in diseases,
known as channelopathies. The validity of microscopic reversibility which underlies
Laplace's original argument of physical determinism is also called into question.
It is shown that microscopic reversibility is not fully compatible with macroscopic
irreversibility whereas microscopic irreversibility and chaos theory can account for
macroscopic irreversibility. The common belief that the uncertainty principle of
quantum mechanics does not enter life processes is disputed. However, absolute
physical determinism, as enunciated by Laplace, can neither be proved nor dis-
proved, and is therefore an epistemological choice. This survey includes a section
on philosophy and sociology of science and a section on technological applications
of biocomputing. The emerging field of molecular electronics is evaluated in terms
of biocomputing principles.

Magnetic Field Effects on Biomolecules, Cells, and Living Organisms ^pdf 3.1Mb

This article surveys three major areas of biomagnetic research.....

The Early Receptor Potential and its Analog in Bacteriorhodopsin Membranes ^pdf 1.4Mb

Almost four decades ago, Brown and Murakami1,2 discovered a tiny electrical signal in the retina of
Cymolgus monkey, when they stimulated the retina with an intense millisecond flash light. The photo-
signal appeared almost instantaneously upon light stimulation; the latency was undetectable and was
estimated to be less than 1 µs (Figure 128.1). This signal was thought to be a new type of bioelectric
phenomenon (for earlier reviews, see the literature39). It was named the early receptor potential (ERP) so as to distinguish it from the then-known receptor potential in the retina -- the a-wave of the
electroretinogram (ERG).10 The latter has a latency of about 1.7 ms, and was then renamed the late
receptor potential (LRP). Unlike LRP, ERP is small in amplitude and requires a significantly more intense
flash light to elicit. While LRP can be abolished by anoxia or by other treatments that disrupt the supply
of metabolic energy, ERP persists under these rough treatments. ERP consists of two separate signal components: R1 and R2. The fast component, R1, has a cornea-positive polarity, whereas the slow component, R2, has the opposite polarity. R2 can be reversibly inhibited by low temperature, but R1 persists even at -35°C [Figure 128.1(C) through Figure 128.1(E)].11,12 ERP from cone photoreceptors is similar: it consists of a brief depolarizing phase (R1) followed by a hyper-polarizing R2 phase.1315 ERP-like signals were also found in plant leaves and other pigmented animal tissues.16 ERP and ERP-like photosignals were generically referred to as fast photovoltages or displacement photocurrents.
Before the discovery of ERP, all known bioelectric signals were generated by ionic diffusion. For
example, LRP is associated with the light-induced Na+ influx at the outer segment of the retinal photo-
receptor.17 The latency of ERP is too short to be accounted for by ionic diffusion. Investigators concluded.....

Molecular Electronic Switches in Photobiology ^pdf 0.9Mb

Light is used by bioorganisms for two major purposes: sensory perception and energy conversion. The functional requirements of molecular devices are drastically different for these two purposes. The former demands sensitivity and a wide dynamic range of photon energy detection, and the latter demands efficiency of photon energy conversion. Superficially, there seems to be a dichotomy of nature's choice of molecular materials for these two diverse functions: visual membranes utilize retinal as the chromophore, whereas photosynthetic membranes utilize magnesium porphyrin as the chromophore. Fundamentally, there are features in common to these two types of photobiological membranes. In Chapter 128, light-induced charge separation and the photoelectric effect are examined in detail. In this chapter, we will consider the molecular switching processes in these two diverse systems from a broad perspective.
The vertebrate rod is a highly sensitive photoreceptor. Hecht and coworkers demonstrated that a
single visible photon absorbed by a single molecule of rhodopsin is capable of eliciting an electrical
response of the vertebrate rod photoreceptor. The energy required for the generation of a synaptic
potential -- the generator potential -- is not provided by the absorbed photon alone. Rather, photon
energy merely serves as the trigger for releasing previously stored energy in the form of transmembrane
Na+ gradient. The latter event constitutes the generator potential of a visual photoreceptor, which was identified with the a wave of the electroretinogram (ERG).2 What transpires in the process of absorptionexcitation coupling is an energy amplification of 100,000-fold. In this sense, rhodopsin is a light-sensitive molecular switch. In order for this switch to be reliable and useful, several requirements must be met in addition to an amplification mechanism. The rise time of the trigger signal must be fast.....

Towards Physical Dynamic Tolerance: An Approach to Resolve the Conflict Between Free Will and Physical Determinism ^pdf 0.3Mb

This paper attempts to resolve the conflict between free will and determinism. The problem is approached by demonstrating that: (a) some well-established experimental observations indicate that irreversibility persists at the molecular level, (b) microscopic reversibility is not fully compatible with macroscopic irreversibility, (c) an overall consistency can be maintained if microscopic reversibility is regarded only as an excellent approximation, whereas microscopic irreversibility together with chaos can account for macroscopic reversibility, and (d) endogenous noise serves a vital function of nerve excitation. Thus, the mean of position and momentum specified by a non-deterministic law of motion gives the law its superficially deterministic behavior and predictability, whereas its dispersion grants dynamic tolerance and irreversibility. Therefore, causality is preserved while a limited degree of freedom allows for the exercise of free will. However, it is argued that free will can never be proven or disproven by a conventional behavioral experiment.

The Enigma of Creative Problem Solving: A Biocomputing Perspective ^pdf 13.7Mb

One of the most important attributes that distinguish the human brain from a sequential digital computer is creative cognition.....

Deciphering the Enigma of Human Creativity: Can a Digital Computer Think? ^doc 0.2Mb

It is possible to understand how scientific geniuses made discoveries, if we treat the paths leading to a discovery as a process of pattern recognition and we further recognize that there are two different modes of reasoning that can be used to generate solutions but are used by highly creative and less creative individuals with different proportions: visual thinking and verbal thinking. The power of visual thinking lies in its inherent parallel processing and random access. These feature can explain why geniuses often had no clue as to how the solution had been arrived at. Intuition, which is intimately related to parallel processing and visual thinking, is so difficult to articulate since articulation is a sequential process, and a suitable parallel-to-serial conversion must be sought for in advance. However, the pitfalls of visual thinking include liability to additional errors and a lack of objectivity. However, potential solutions discovered by visual thinking must be strictly verified by logical reasoning, which is sequential and inherently verbal in nature. When the latter is done properly, it is highly objective and less error-prone, and can eliminate most errors incurred at the stage of solution generation. There is no straight answer to the question whether a digital computer can think, because there is a gray scale of thinking and understanding. Taking Herbert Simon’s programs as examples, we found that some of these programs did indeed surpass the intellectual performance of a special class of human being: the so-called high achievers who are strong in taking standardized tests but weak in formulating ideas to solve problems that have not been taught previously or covered in the textbook. But human geniuses seemed so far to be able to stay one step ahead of these programs, because Simon’s programs were constructed by pooling together thinking strategies of many past creators, so as to generate heuristics. As for the creative performance of future computers, it is better to suspend our judgment. Science and technology history taught us a lesson: never say never, except perhaps just this once.

MOZART EFFECT:

1. Mozart’s Parallel Processing of Tone Patterns ^pdf 0.02Mb

Shown below is a scanned copy of Mozart's letter from P.E. Vernon's
compilation. It was part a letter Mozart wrote to one of his admirer -- a Baron
von P -- who sent Mozart a gift of fine wines.....

2. MOZART EFFECT: An Assessment Based on Cognitive Science and Biocomputing ^pdf 0.03Mb

Don Campbell, a music teacher and famed music therapist, wrote a best seller "The
Mozart Effect: Tapping the Power of Music to Heal the Body, Strengthen the Mind and Unlock the Creative Spirit."

3. A Comment on the Dictation Scene of the Movie “Amadeus” ^pdf 0.2Mb

The dictation scene in the Movie "Amadeus" illustrates parallel processing
in music. Wolfgang Amadeus Mozart had it all in his head (gleich alles
zusammen) but he could only dictate one line, or one part, at a time to Antonio
Salieri in a sequential fashion. The piece also illustrates the characteristic
Mozartian feature of running two or more melodies at the same time.

4. Detailed Commentary: The Overture of the Magic Flute ^pdf 0.03Mb

The overture of the Magic Flute (Die Zauberflöte) is also in the sonata form. The
introduction is a slow adagio and starts with the presentations of triple chords (Der
dreimalige Akkord).

5. A Detailed Commentary of the First Movement of Prague Symphony ^pdf 0.05Mb

First, a brief explanation of notations. The accompanied music notes are "cut-off" (cut
and paste) from an orchestral score published by Ricordi, the famed Italian music publisher.

Interfacial Photochemistry of Retinal Proteins ^pdf 2.1Mb

Retinal proteins are membrane-bound protein pigments that contain vitamin A aldehyde
(retinal) as the chromophore. They include the visual pigment rhodopsin and four
additional ones in the plasma membrane of Halobacterium salinarium (formerly
Halobacterium halobium ). These proteins maintain a ®xed and asymmetric orientation in
the membranes, and respond to a light stimulus by generating vectorial charge movement,
which can be detected as an electric potential across the membrane or an electric current
through the membrane. These phenomena are collectively called the photoelectric eects,
which defy a rigorous quantitative treatment by means of either conventional (solution
phase) photochemistry or conventional electrophysiology. As an alternative to the
mainstream approach, we utilize the analytic tools of electrochemical surface science and
electrophysiology to analyze two molecular models of light-induced charge separation and
recombination. Being tutorial in nature, this article demands no prior knowledge about the
subject. A parsimonious equivalent circuit model is developed. Data obtained from
reconstituted bacteriorhodopsin membranes are used to validate the theoretical model and
the analytical approach. Data generated and used by critics to refute our approach is
shown to actually support it. The present analysis is suciently general to be applicable to
other pigment-containing membranes, such as the visual photoreceptor membrane and the
chlorophyll-based photosynthetic membranes. It provides a coherent description of a wide
range of light-induced phenomena associated with various pigment-containing membranes.
In contrast, the mainstream approach has been plagued with self-contradictions and
paradoxes. Last, but not least, the alternative bioelectrochemical approach also exhibits a
predictive power that has hitherto been generally lacking. Comparison of the photoelectric
eects is made with regard to bacteriorhodopsin, rhodopsin, and the chlorophyll-based
photosynthetic apparatus in the spirit of reverse engineering (biomimetic science). The
technological applications of bacteriorhodopsin as an advanced material.....

The Risk of Robotization ^pdf 0.07Mb

The advent of digital computers has ushered in a
of human affairs: education and health care. In particular, we
revolution that has begun to transform both our society and
shall analyze the problems from the point of view of how the
human life. Most experts are concerned with a division of the
human brain works (cognitive science) and how a computer or
society into two classes -- "have" and "have-not" --regarding
robot works (artificial intelligence). In order to set the stage, we
the access to the information technology (so-called "Great
shall first briefly discuss how humans perform creative work.
Divide"). Yet, as a veteran teacher, I have observed a strange
Specifically, we shall focus on the chance-configuration theory
trend: while the new generation of computers have become
of creative problem solving, proposed by Simonton [1]. We
more human-like, a significant fraction of our students of high
have recently demonstrated that, by recasting Simonton's
marks have become more robot-like. Based on new insights
theory in terms of pattern recognition in the context of parallel
gained into human creativity, harmful impacts of robotization
processing and sequential processing, it is possible to explain
will be analyzed and possible solutions will be suggested in two
elusive terms such as insight, intuition and inspiration in
major areas: education and health care.

Picture-Based vs. Rule-Based Learning ^html 0.3Mb

Like most educators, I have taken for granted the conventional view of two modes of learning.....

Contact Information

E-mail address

fhong at med.wayne.edu

FAX: Country code 1, (313) 577-5494

Thank you for your interest.

Felix T. Hong

Department of Physiology

Wayne State University

540 E. Canfield Avenue

Detroit, Michigan 48201

USA

Last revised: 8.5.2004.

Number of visitors to this page: