Fine-Tuning - Moleculat Biology

“The Application of Fine-Tuning to Molecular Biology” by Charles E. Warren, P.E., PhD
Steinar Thorvaldsen and Ola Hössjer in their article “Using statistical methods to model the fine-tuning of molecular machines and systems” stated: “The real world is complicated, and scientific models must handle it by simplifying matters, . . . .” In the article they discussed and applied in detail various rather complex statistical mathematical models for understanding the phenomena of the fine-tuning of the universe as well as the fine-tuning of molecular machines and systems. Their discussions were excellent and very helpful, particularly as related to the concept of intelligent design (ID); however, I believe that there is a much greater simplifying model taken from systems engineering that can be used with even greater conceptual clarity to model fine-tuning of molecular machines and systems. Franklin Harold, in his book In Search of Cell History: The Evolution of Life’s Building Blocks. (Chicago: University of Chicago Press, 2014.), made the following statements: “It follows that when biochemists grind cells into a pulp, something irretrievable is indeed lost: the organization that makes the cellular system work.” (p. 13) “More important, I believe, is the fact that cell heredity transmits the living system’s pattern of global organization. Should that structure be lost, it cannot be reconstituted; that is the irretrievable essence that is destroyed when we grind living cells into a homogenate . . .” (p. 93) Harold believes that “the living system’s pattern of global organization” is the essence of living systems and is essential for both function and propagation of life. This interpretation by Harold affirms the long known concept that “it takes a cell to make a cell.” Denis Noble, in his book Dance to the Tune of Life: Biological Relativity. Cambridge University Press. © Cambridge University Press (2017). Kindle Edition made the following statements: “It is not the atoms themselves which make organisms special, it is how they are arranged and controlled that defines a living organism.” (p. 38) “At the moment of death it is the processes of life that will cease.” (p. 255) Noble also states in The Music of Life. OUP Oxford. Kindle Edition: “Any well-regulated biological system must involve feedback controls. Clearly, then, the expression of a gene (in the rather misleading jargon) will involve levels of activity that are determined by the system as a whole.” (p. 46) Therefore both Noble and Harold attest to the fact that the structural arrangement of the matter that constitutes the material portion of life and the non-material prescriptive information at the heart of the genome regulatory system processes are both necessary to sustain life as we know it. These facts are why scientists have known for decades that “it takes a cell to make a cell” and therefore that the cell is “irreducibly complex.” Noble also stresses the necessity of feedback for any “well-regulated biological system” to function properly. Feedback is the essential configuration (arrangement) that makes control possible. The closed loop feedback control system model is used extensively in the field of systems engineering. This model depicts very accurately the essential relationship between the necessary organization (arrangement) of a system’s components and it regulatory control system. The diagram below is the simplest model representing a closed loop feedback control system and will be used to illustrate the basic first principles of closed loop feedback systems. BIOLOGICAL: TELEOLOGICAL CLOSED LOOP SYSTEM In order to grasp the fundamental concept of the way in which closed loop feedback control systems function a simple thought experiment will do the job. Imagine driving your car in the midst of heavy city traffic and suddenly being struck blind. With this loss of all visual feedback it will be impossible for you to exercise meaningful control of your car in order to avoid crashing into some other car or object. Feedback is therefore an absolutely necessary component of any functional control system. The loss of feedback results in loss of control. The fundamental concept is extremely simple, but when plumbing the details of the many applications of the concept, such as to biological systems, we immediately encounter many “barriers of complexity.” Although the details may remain murky the fundamental principles applied hold. There are several self-evident principles or prerequisites applicable to formulating or constructing a fully functional closed loop control system. These prerequisites are listed below. Note that these prerequisites can be categorized as either specified complexity or irreducible complexity. Specified Complexity: Any automatic-control mechanisms/systems must have all of the following elements as a minimum: Feedback is essential to all automatic-control mechanisms/systems. A pre-defined parameter to be controlled, such as temperature, pulse rate, etc. A pre-defined standard/value (set point) for the parameter to be controlled. A pre-defined acceptable limit or tolerance from the standard set point. The ability to sense and measure the real-time parameter value. The ability to transcribe and translate the units of measure of the set-point and the units of measure of the parameter to control in order to make possible detecting the difference between the two. For example our sensory mechanisms: from air pressure-to-electrical nerve signals (ear assemblies) or from photons-to-electrical nerve signals (eye assemblies). Our manufacturing assemblies/systems: from DNA code-to-amino acid code (RNA assemblies), etc. The ability to measure the difference (error) between the standard set point and the actual real-time parameter value. The ability to automatically modify the parameter to be controlled such that the error is minimized. These essential components must be integrated and organized in a functionally specific arrangement (see diagram above). Irreducible Complexity: All the above elements of the system must be present and functional simultaneously at the point in time of initial execution of the system function. How does all this relate to modeling the fine-tuning of molecular machines and systems? Biological homeostatic systems function as closed loop negative feedback systems. And homeostatic systems are ubiquitous throughout all organisms. Their major function is to continuously fine-tune (maintain) the specified parameter — such as blood pressure, heart rate, etc., for which the system is in place to control — at a specified value. Biological developmental systems also function as closed loop negative feedback systems. For example, the cell cycle is an extremely complex closed loop feedback system composed of at least four nested closed loops (cell cycle check-points) within the main closed loop. This system monitors and controls the processes with which cells reproduce. This cell-cycle process (mitosis) is at the heart of the biological developmental system as a whole, whether for single cell or multicellular organisms, with few exceptions. Sculpturing of body parts during organism developmental processes is another example of utilizing fine-tuning to model molecular machines and systems. Eric H. Davidson in his book (The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. London: Academic Press. 2006.) made the following statement: “The developmental ‘subroutines’ summarized in (ii) [progenitor field regulators] and (iii) [subregional regulatory functions] may often be deployed recursively, on finer and finer scales up to the most detailed level of species-specific, morphogenetic sculpting of the body part.” (p. 114) An organism’s body parts are finely sculptured (tuned) by a process that iteratively shapes and hones the body part to its ultimate species-specific final form. Thus the fundamental concept of closed loop feedback control systems accurately models the concept of fine tuning from a systems engineering perspective. The parameter being controlled by the closed loop feedback system is continuously fine tuned to reduce and maintain the system error to zero, or nearest to zero, within the capacity of the system. The most critical concept to recognize in what is presented above is the fact that prior to the origination and execution of any biological process that employs feedback control the prerequisite items listed in 1 and 2 above for that process must have been accomplished. This fact is both logically and chronologically necessary. As such, it would be impossible for an a posteriori process of chance mutations, natural selection, and environmental effects to “cobble together” systems whose complexities baffle human understanding. Particularly troubling is comprehending the way in which an a posteriori process such as chance mutations, natural selection, and environmental effects could instantiate non-material prescriptive information into material matter in order to form a completed and functional biological system.
June 19, 2020

“The Application of Fine-Tuning to Molecular Biology”

by Charles E. Warren, P.E., PhD

Steinar Thorvaldsen and Ola Hössjer in their article “Using statistical methods to model the fine-tuning of molecular machines and systems” stated:

“The real world is complicated, and scientific models must handle it by simplifying matters, . . . .”

In the article they discussed and applied in detail various rather complex statistical mathematical models for understanding the phenomena of the fine-tuning of the universe as well as the fine-tuning of molecular machines and systems. Their discussions were excellent and very helpful, particularly as related to the concept of intelligent design (ID); however, I believe that there is a much greater simplifying model taken from systems engineering that can be used with even greater conceptual clarity to model fine-tuning of molecular machines and systems.

Franklin Harold, in his book In Search of Cell History: The Evolution of Life’s Building Blocks. (Chicago: University of Chicago Press, 2014.), made the following statements:

“It follows that when biochemists grind cells into a pulp, something irretrievable is indeed lost: the organization that makes the cellular system work.” (p. 13)

“More important, I believe, is the fact that cell heredity transmits the living system’s pattern of global organization. Should that structure be lost, it cannot be reconstituted; that is the irretrievable essence that is destroyed when we grind living cells into a homogenate . . .” (p. 93)

Harold believes that “the living system’s pattern of global organization” is the essence of living systems and is essential for both function and propagation of life. This interpretation by Harold affirms the long known concept that “it takes a cell to make a cell.”

Denis Noble, in his book Dance to the Tune of Life: Biological Relativity. Cambridge University Press. © Cambridge University Press (2017). Kindle Edition made the following statements:

“It is not the atoms themselves which make organisms special, it is how they are arranged and controlled that defines a living organism.” (p. 38)

“At the moment of death it is the processes of life that will cease.” (p. 255)

Noble also states in The Music of Life. OUP Oxford. Kindle Edition:

“Any well-regulated biological system must involve feedback controls. Clearly, then, the expression of a gene (in the rather misleading jargon) will involve levels of activity that are determined by the system as a whole.” (p. 46)

Therefore both Noble and Harold attest to the fact that the structural arrangement of the matter that constitutes the material portion of life and the non-material prescriptive information at the heart of the genome regulatory system processes are both necessary to sustain life as we know it. These facts are why scientists have known for decades that “it takes a cell to make a cell” and therefore that the cell is “irreducibly complex.” Noble also stresses the necessity of feedback for any “well-regulated biological system” to function properly. Feedback is the essential configuration (arrangement) that makes control possible.

The closed loop feedback control system model is used extensively in the field of systems engineering. This model depicts very accurately the essential relationship between the necessary organization (arrangement) of a system’s components and it regulatory control system. The diagram below is the simplest model representing a closed loop feedback control system and will be used to illustrate the basic first principles of closed loop feedback systems.

BIOLOGICAL: TELEOLOGICAL CLOSED LOOP SYSTEM

In order to grasp the fundamental concept of the way in which closed loop feedback control systems function a simple thought experiment will do the job. Imagine driving your car in the midst of heavy city traffic and suddenly being struck blind. With this loss of all visual feedback it will be impossible for you to exercise meaningful control of your car in order to avoid crashing into some other car or object. Feedback is therefore an absolutely necessary component of any functional control system. The loss of feedback results in loss of control. The fundamental concept is extremely simple, but when plumbing the details of the many applications of the concept, such as to biological systems, we immediately encounter many “barriers of complexity.” Although the details may remain murky the fundamental principles applied hold.

There are several self-evident principles or prerequisites applicable to formulating or constructing a fully functional closed loop control system. These prerequisites are listed below. Note that these prerequisites can be categorized as either specified complexity or irreducible complexity.

Specified Complexity: Any automatic-control mechanisms/systems must have all of the following elements as a minimum:

Feedback is essential to all automatic-control mechanisms/systems.
A pre-defined parameter to be controlled, such as temperature, pulse rate, etc.
A pre-defined standard/value (set point) for the parameter to be controlled.
A pre-defined acceptable limit or tolerance from the standard set point.
The ability to sense and measure the real-time parameter value.
The ability to transcribe and translate the units of measure of the set-point and the units of measure of the parameter to control in order to make possible detecting the difference between the two. For example our sensory mechanisms: from air pressure-to-electrical nerve signals (ear assemblies) or from photons-to-electrical nerve signals (eye assemblies). Our manufacturing assemblies/systems: from DNA code-to-amino acid code (RNA assemblies), etc.
The ability to measure the difference (error) between the standard set point and the actual real-time parameter value.
The ability to automatically modify the parameter to be controlled such that the error is minimized.
These essential components must be integrated and organized in a functionally specific arrangement (see diagram above).

Irreducible Complexity: All the above elements of the system must be present and functional simultaneously at the point in time of initial execution of the system function.

How does all this relate to modeling the fine-tuning of molecular machines and systems? Biological homeostatic systems function as closed loop negative feedback systems. And homeostatic systems are ubiquitous throughout all organisms. Their major function is to continuously fine-tune (maintain) the specified parameter — such as blood pressure, heart rate, etc., for which the system is in place to control — at a specified value.

Biological developmental systems also function as closed loop negative feedback systems. For example, the cell cycle is an extremely complex closed loop feedback system composed of at least four nested closed loops (cell cycle check-points) within the main closed loop. This system monitors and controls the processes with which cells reproduce. This cell-cycle process (mitosis) is at the heart of the biological developmental system as a whole, whether for single cell or multicellular organisms, with few exceptions.

Sculpturing of body parts during organism developmental processes is another example of utilizing fine-tuning to model molecular machines and systems. Eric H. Davidson in his book (The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. London: Academic Press. 2006.) made the following statement:

“The developmental ‘subroutines’ summarized in (ii) [progenitor field regulators] and (iii) [subregional regulatory functions] may often be deployed recursively, on finer and finer scales up to the most detailed level of species-specific, morphogenetic sculpting of the body part.” (p. 114)

An organism’s body parts are finely sculptured (tuned) by a process that iteratively shapes and hones the body part to its ultimate species-specific final form. Thus the fundamental concept of closed loop feedback control systems accurately models the concept of fine tuning from a systems engineering perspective. The parameter being controlled by the closed loop feedback system is continuously fine tuned to reduce and maintain the system error to zero, or nearest to zero, within the capacity of the system.

The most critical concept to recognize in what is presented above is the fact that prior to the origination and execution of any biological process that employs feedback control the prerequisite items listed in 1 and 2 above for that process must have been accomplished. This fact is both logically and chronologically necessary. As such, it would be impossible for an a posteriori process of chance mutations, natural selection, and environmental effects to “cobble together” systems whose complexities baffle human understanding. Particularly troubling is comprehending the way in which an a posteriori process such as chance mutations, natural selection, and environmental effects could instantiate non-material prescriptive information into material matter in order to form a completed and functional biological system.

June 19, 2020