Quantum Biology?

Quantum Biology?

I came across a YouTube video about quantum biology and was compelled to watch it.  I thought biology was all about chemistry until I saw the video Steve Meyer showed at his Signature in the Cell book release party that clearly showed a functioning process using machinery.  Being a designer of processes and machines, I was aware of the enormous complexity required to achieve the functionality that exists in life.  So could quantum field theory explain how natural causes can do intelligent work; the missing “vital dust” needed to create beginning life?  I’d better check it out.

The early thinking about quantum physics regarding life was that quantum effects are normally lost in the “macro noise” at “life” temperatures and configuration, so none probably existed. However, there have been a few mysteries that might be explained by quantum phenomena.  One example is that quantum effects may have something to do with electron transfer in photosynthesis which is much more efficient than thought possible1.  Another is called “visual phototransduction”, the converting light to an action potential.2 And another is quantum tunneling in enzymes.3 There is no hint regarding how quantum field physics can create intelligence or to perform intelligent work.

This is not surprising.  If there was a way to make life less complicated, it would be less complicated.   It appears quantum effects may be used in life like we use quantum effects in electronics – time and research will tell.  But no conclusions described in this web site are diminished, namely: natural causes cannot achieve all possible outcomes, life is a process that requires machinery, and machines require logical processing capability.

It seems that life might be a good place to learn more about quantum theory where discoveries of its implementation are found.  I seriously doubt that man would have invented neural networks without its discovery in life.

© 2018 Mike Van Schoiack

The “Wishful Thinking” Principle

The “Wishful Thinking” Principle

Post Under Construction

This post will expand upon the “lake freezing over” example about the fact that even if the lake could freeze over, it would be a transient event and not even noticed.  The point is that the idea that if “magical” events were theoretically possible, they still wouldn’t come into existence for something like life because many such events would be needed, and the time will destroy any miracle because of the 2nd law which will occur at rates many, many orders of magnitude faster.  It would be like “one step forward, a trillion steps backward.  Bottom line conclusion: even if the logical constraints did not exist, life could never start by natural causes. 

Life, A Process

ON THE LIMITS OF NATURAL CAUSES

Life, A Process

There is no universally accepted or official definition of life, but it has been thought[i],[ii] and written[iii] about since the beginnings of civilization.  From the outside, the reason seems to be that there is no universal agreement what life is, how it started or how it works.

In college I learned that all life evolved from a single cell, and later learned that first life occurred by natural causes.  This view continued until attending Steve Meyer’s Signature in the Cell book launch party.[iv] He gave a presentation that included this video which he narrated.  I was shocked because this shattered my understanding that life was chemistry, never imagining that machines, were involved, particularly molecular machines. That seemed impossible.  Machines are something I understand as I spent my life designing them.  But there was a concern as well.  The movie seemed to be oversimplified.  Piece parts that were being placed just “floated” into position which does not happen naturally.  How did the RNA know where to go?   How did the membrane gate know to “open the door” for the RNA?  How was the membrane sealed as it went through?  Many questions such as these lingered because my experience was that every detail of such an intelligent process must have a mechanism that controls the outcome of each step to insure success.  It seemed that the process had to involve much more than was shown in the movie.

 

My experience and intuition both told me that there is no possibility that such an intelligent process could start by natural causes. Not only would the first cell need the information to make it work, it would have to be constructed and the process started. How could this occur?

This was the beginning of my interest in the ID debate.

Life is an Intelligent Process

From an engineering perspective, life, [v] at all levels, is an intelligent process, a series of actions designed to maintain, perpetuate and grow itself.  Biologists often refer to life as a process, not realizing they are dealing with an intelligent process, not a natural one. All life, taken together is an intelligent process because life depends upon other life by means of environmental transformation, a “food-chain” and systematic recycling of raw materials.  At the cell level, the life processes find and gather raw materials, extract energy to run and maintain the cell’s life processes including cell division.  The same is true at the organism level except maintaining and growing the population is accomplished by reproduction and functionality is obtained by specialized cells. Each organism has hundreds of intelligent processes that control the temperature, digestion, respiration, etc.

Comparison of Life and Manmade Machines

All life forms are machines because they do intelligent work.  However, even the simplest life is much more; it is an intellignet process that is self-sufficient and adaptable to the point of reproducing so that it can continue to exist even after the demise of the original life form.  This is an indication of the high level of embedded intelligence especially when compared to manmade machines.

The other major difference is scale.  Life’s machines are highly complex, specified molecules whereas man’s machines are macro structures.  Life’s smallest living unit, the cell, is so small that we cannot see it without a microscope.  Life also has macro level forms, organisms, that are composed of trillions of specialized cells. Groups of specialized cells are used to build macro machines, organs, and other macro structures such as fingernails, hair and teeth enamel using specialized molecules.

Compared to lifeless machines, living machines are orders of magnitude more complex and sophisticated.  However, both obey the laws of physics and therefore both must have the logical functionality required of machines.  This concurs with observation despite our limited ability to see and instrument at the microscopic size and speed levels.  This lends credence to the belief that we are not missing some yet-to-be-discovered property that makes life different regarding ability to perform logical actions due to our incomplete knowledge of physics.

I would like to be able to put together a process action diagram like Figure 1 and Figure 2 for some action that takes place in life, such as the building of a protein shown in the video.  There are seven high level steps to this intelligent process as shown in Figure 3 and there are several machines involved as displayed in the video above, but there are far, far more details involved that are not shown.  A molecular cell biology textbook explains[vi]: “A ribosome is composed of several different ribosomal RNA (rRNA) molecules and more than 50 proteins, organized into large subunit and small subunit.”

The complexity is obvious.  A process action diagram like Figure 2 for building a protein molecule would likely take several hundred pages.  Such a diagram would have to explain how the functionality of every functional protein is accomplished. It is obvious that much has been learned at a high level despite the difficulties of understanding what is going on in real time at the molecular level. However, this understanding is miniscule compared to the understanding engineers have of the very much simpler machines we design and build. It is obvious there is much yet to be learned about life.

[i] Palyi, G.; Zucchi, C.; Caglioti,L. Proceedings of the Workshop on Life: A Satellite Meeting before the Millennial World Meeting of University Professors, Modena, Italy, 3–8 September 2000.

[ii] Abel, D. Is Life Unique?, Life, ISSN 2075-1729, 19 December 2011

[iii] Rizzotti, M. Defining Life: The Central Problem in Theoretical Biology; University of Padova Press: Padova, Italy, 1996.

[iv] Here is a link to Steve Meyer’s talk; the video starts at the 15 minute mark. Here is link to Video 1.

[v] Author’s Definition, Life:

a: a state of matter/energy continuously running a vital process in a cell or organism that sustains and perpetuates itself as distinguished from dead matter/energy.

See additional definitions and comments here.

[vi] Lodish et al, Molecular Cell Biology, Fourth Edition, 1

In college I learned that all life evolved from a single cell, and later learned that first life occurred by natural causes.  This view continued until attending Steve Meyer’s Signature in the Cell book launch party.[iv] He gave a presentation that included this video which he narrated.  I was shocked because this shattered my understanding that life was chemistry, never imagining that machines, were involved, particularly molecular machines. That seemed impossible.  Machines are something I understand as I spent my life designing them.  But there was a concern as well.  The movie seemed to be oversimplified.  Piece parts that were being placed just “floated” into position which does not happen naturally.  How did the RNA know where to go?   How did the membrane gate know to “open the door” for the RNA?  How was the membrane sealed as it went through?  Many questions such as these lingered because my experience was that every detail of such an intelligent process must have a mechanism that controls the outcome of each step to insure success.  It seemed that the process had to involve much more than was shown in the movie.

 

My experience and intuition both told me that there is no possibility that such an intelligent process could start by natural causes. Not only would the first cell need the information to make it work, it would have to be constructed and the process started. How could this occur?

This was the beginning of my interest in the ID debate.

Life is an Intelligent Process

From an engineering perspective, life, [v] at all levels, is an intelligent process, a series of actions designed to maintain, perpetuate and grow itself.  Biologists often refer to life as a process, not realizing they are dealing with an intelligent process, not a natural one. All life, taken together is an intelligent process because life depends upon other life by means of environmental transformation, a “food-chain” and systematic recycling of raw materials.  At the cell level, the life processes find and gather raw materials, extract energy to run and maintain the cell’s life processes including cell division.  The same is true at the organism level except maintaining and growing the population is accomplished by reproduction and functionality is obtained by specialized cells. Each organism has hundreds of intelligent processes that control the temperature, digestion, respiration, etc.

Comparison of Life and Manmade Machines

All life forms are machines because they do intelligent work.  However, even the simplest life is much more; it is an intellignet process that is self-sufficient and adaptable to the point of reproducing so that it can continue to exist even after the demise of the original life form.  This is an indication of the high level of embedded intelligence especially when compared to manmade machines.

The other major difference is scale.  Life’s machines are highly complex, specified molecules whereas man’s machines are macro structures.  Life’s smallest living unit, the cell, is so small that we cannot see it without a microscope.  Life also has macro level forms, organisms, that are composed of trillions of specialized cells. Groups of specialized cells are used to build macro machines, organs, and other macro structures such as fingernails, hair and teeth enamel using specialized molecules.

Compared to lifeless machines, living machines are orders of magnitude more complex and sophisticated.  However, both obey the laws of physics and therefore both must have the logical functionality required of machines.  This concurs with observation despite our limited ability to see and instrument at the microscopic size and speed levels.  This lends credence to the belief that we are not missing some yet-to-be-discovered property that makes life different regarding ability to perform logical actions due to our incomplete knowledge of physics.

I would like to be able to put together a process action diagram like Figure 1 and Figure 2 for some action that takes place in life, such as the building of a protein shown in the video.  There are seven high level steps to this intelligent process as shown in Figure 3 and there are several machines involved as displayed in the video above, but there are far, far more details involved that are not shown.  A molecular cell biology textbook explains[vi]: “A ribosome is composed of several different ribosomal RNA (rRNA) molecules and more than 50 proteins, organized into large subunit and small subunit.”

The complexity is obvious.  A process action diagram like Figure 2 for building a protein molecule would likely take several hundred pages.  Such a diagram would have to explain how the functionality of every functional protein is accomplished. It is obvious that much has been learned at a high level despite the difficulties of understanding what is going on in real time at the molecular level. However, this understanding is miniscule compared to the understanding engineers have of the very much simpler machines we design and build. It is obvious there is much yet to be learned about life.

[i] Palyi, G.; Zucchi, C.; Caglioti,L. Proceedings of the Workshop on Life: A Satellite Meeting before the Millennial World Meeting of University Professors, Modena, Italy, 3–8 September 2000.

[ii] Abel, D. Is Life Unique?, Life, ISSN 2075-1729, 19 December 2011

[iii] Rizzotti, M. Defining Life: The Central Problem in Theoretical Biology; University of Padova Press: Padova, Italy, 1996.

[iv] Here is a link to Steve Meyer’s talk; the video starts at the 15 minute mark. Here is link to Video 1.

[v] Author’s Definition, Life:

a: a state of matter/energy continuously running a vital process in a cell or organism that sustains and perpetuates itself as distinguished from dead matter/energy.

See additional definitions and comments here.

[vi] Lodish et al, Molecular Cell Biology, Fourth Edition, 125

© 2018 Mike Van Schoiack

Life, A Process Enabled By Machines

ON THE LIMITS OF NATURAL CAUSES

Life, A Process Enabled By Machines

There is no universally accepted or official definition of life, but it has been thought[i],[ii] and written[iii] about since the beginnings of civilization.  From the outside, the reason seems to be that there is no universal agreement what life is, how it started or how it works.

In college I learned that all life evolved from a single cell, and later learned that first life occurred by natural causes.  This view continued until attending Steve Meyer’s Signature in the Cell book launch party.[iv] He gave a presentation that included this video which he narrated.  I was shocked because this shattered my understanding that life was chemistry, never imagining that machines, were involved, particularly molecular machines. That seemed impossible.  Machines are something I understand as I spent my life designing them.  But there was a concern as well.  The movie seemed to be oversimplified.  Piece parts that were being placed just “floated” into position which does not happen naturally.  How did the RNA know where to go?   How did the membrane gate know to “open the door” for the RNA?  How was the membrane sealed as it went through?  Many questions such as these lingered because my experience was that every detail of such an intelligent process must have a mechanism that controls the outcome of each step to insure success.  It seemed that the process had to involve much more than was shown in the movie.

 

My experience and intuition both told me that there is no possibility that such an intelligent process could start by natural causes. Not only would the first cell need the information to make it work, it would have to be constructed and the process started. How could this occur?

This was the beginning of my interest in the ID debate.

Life is an Intelligent Process

From an engineering perspective, life, [v] at all levels, is an intelligent process, a series of actions designed to maintain, perpetuate and grow itself.  Biologists often refer to life as a process, not realizing they are dealing with an intelligent process, not a natural one. All life, taken together is an intelligent process because life depends upon other life by means of environmental transformation, a “food-chain” and systematic recycling of raw materials.  At the cell level, the life processes find and gather raw materials, extract energy to run and maintain the cell’s life processes including cell division.  The same is true at the organism level except maintaining and growing the population is accomplished by reproduction and functionality is obtained by specialized cells. Each organism has hundreds of intelligent processes that control the temperature, digestion, respiration, etc.

Comparison of Life and Manmade Machines

All life forms are machines because they do intelligent work.  However, even the simplest life is much more; it is an intellignet process that is self-sufficient and adaptable to the point of reproducing so that it can continue to exist even after the demise of the original life form.  This is an indication of the high level of embedded intelligence especially when compared to manmade machines.

The other major difference is scale.  Life’s machines are highly complex, specified molecules whereas man’s machines are macro structures.  Life’s smallest living unit, the cell, is so small that we cannot see it without a microscope.  Life also has macro level forms, organisms, that are composed of trillions of specialized cells. Groups of specialized cells are used to build macro machines, organs, and other macro structures such as fingernails, hair and teeth enamel using specialized molecules.

Compared to lifeless machines, living machines are orders of magnitude more complex and sophisticated.  However, both obey the laws of physics and therefore both must have the logical functionality required of machines.  This concurs with observation despite our limited ability to see and instrument at the microscopic size and speed levels.  This lends credence to the belief that we are not missing some yet-to-be-discovered property that makes life different regarding ability to perform logical actions due to our incomplete knowledge of physics.

I would like to be able to put together a process action diagram like Figure 1 and Figure 2 for some action that takes place in life, such as the building of a protein shown in the video.  There are seven high level steps to this intelligent process as shown in Figure 3 and there are several machines involved as displayed in the video above, but there are far, far more details involved that are not shown.  A molecular cell biology textbook explains[vi]: “A ribosome is composed of several different ribosomal RNA (rRNA) molecules and more than 50 proteins, organized into large subunit and small subunit.”

The complexity is obvious.  A process action diagram like Figure 2 for building a protein molecule would likely take several hundred pages.  Such a diagram would have to explain how the functionality of every functional protein is accomplished. It is obvious that much has been learned at a high level despite the difficulties of understanding what is going on in real time at the molecular level. However, this understanding is miniscule compared to the understanding engineers have of the very much simpler machines we design and build. It is obvious there is much yet to be learned about life.

[i] Palyi, G.; Zucchi, C.; Caglioti,L. Proceedings of the Workshop on Life: A Satellite Meeting before the Millennial World Meeting of University Professors, Modena, Italy, 3–8 September 2000.

[ii] Abel, D. Is Life Unique?, Life, ISSN 2075-1729, 19 December 2011

[iii] Rizzotti, M. Defining Life: The Central Problem in Theoretical Biology; University of Padova Press: Padova, Italy, 1996.

[iv] Here is a link to Steve Meyer’s talk; the video starts at the 15 minute mark. Here is link to Video 1.

[v] Author’s Definition, Life:

a: a state of matter/energy continuously running a vital process in a cell or organism that sustains and perpetuates itself as distinguished from dead matter/energy.

See additional definitions and comments here.

[vi] Lodish et al, Molecular Cell Biology, Fourth Edition, 125

© 2018 Mike Van Schoiack

An Engineering Perspective

ON THE LIMITS OF NATURAL CAUSES

An Engineering Perspective

Engineers[i] think of themselves as “applied scientists,”[ii] as opposed to those who embed intelligence into matter/energy, and, as a result, are a link between the realms of science and philosophy. Therefore, this theorem is logically true:

Theorem:  Engineering merges the realms of science and philosophy. 

An alternative definition of an engineer could be: those who perform intelligent work to create entities that natural causes either cannot or cannot in the quantity, time or speed desired.

The experience of doing this work leaves an engineer with some valuable lessons.

All designs must have a mechanism,[iii] defined broadly to mean the methodology that determines the outcome of any action.  Engineers design mechanisms as they are the means of creating functionalities.  To work, mechanisms must follow the laws of physics and at the same time, overcome the limitations of materials, sources of useable energy, and other logical limitations. 

An engineer quickly realizes not all outcomes that do not violate the laws of physics are possible, for many reasons.  In addition to design, an engineer builds prototypes and tests them.  Each is an unpublished experiment and an education regarding the difficulty of making complex systems work.   There are thousands of mistakes that can be made, and any one of them can result in failure making engineers keenly aware of limitations that restrict outcomes.

Complex systems have many components and subsystems that share information and cooperate with each other.  This produces the need for standards, specifications, protocols, and languages to achieve the coherence necessary for all the pieces to work together.  One impact is that the information needed for any given functionality will be intertwined with others and therefore is dispersed.  This fact also means that the idea of evolution by singular changes in a system is, in most cases, impossible due to information being required in multiple locations.

Natural causes and time are enemies of engineers.  Metals corrode.  Plastics age and change properties.  Sealed areas are breached.  Fluids become contaminated. And the list goes on.  The second law of thermodynamics tends to degrade engineered entities by reducing the specifitivity of the embedded information.

There is no such thing as perfection.  Everything is a trade-off.  Virtually all designs must balance performance, cost, reliability, appearance, longevity, size and weight, capabilities not possible by natural causes. 

Perhaps the most valuable lesson is the realization of the difficulty of finding and inventing designs that work and finding the fine balance that is usually needed to achieve the desired result.  Many physicists marvel at the “fine tuning” required to create a universe that could support our life. Engineers routinely deal with this problem. We are surrounded by marvels of complex design and mistakenly take them for granted.[iv]

Tools – All Static Things Embedded With Information

The discussion to this point has been about engineered machines. But there is a whole different category of intelligent work creations which are not machines.  For the purposes of this paper all such entities will be called tools.  Therefore, the definition for the term tool will be: an object created by intelligent work that does not perform intelligent work.  This is a very broad definition because it includes everything created by life except for machines.  This includes things we think of as tools (hammer, saw, wrench) but also art (paintings, literature, music, sculpture), medicines, buildings and other structures, telescopes, batteries, makeup, birds nest, bee hive, etc. 

Tools are made by intelligent machines, that is, living things plus machines designed and built by engineers.  Tools have embedded information, but not embedded intelligence like machines.  A logical distinction is that there is a statistical probability that natural causes could create some tools.  In this sense, the ID argument “where does the information come from” is treating life as a tool instead of a machine; both massive understatement because life is so much more than either!

Natural Causes can create objects that can be used as tools.  An example is a rock that has a shape that makes it convenient to use as a hammer.  Or a human can shape a rock to do the same thing.  Other tools, such as an adjustable (Crescent) wrench, must be engineered, i.e., designed and fabricated using intelligent work.

[i] Author’s Definition, Engineer:

Noun 1. a person who designs and builds machines and objects for a specified purpose.

Verb  1. Design and build a machine or object for a specified purpose.

Note: This definition is included to distinguish the design aspect with actualization as it seems they are often conflated and to exclude maintenance which is typically the role of a technician.

See other definitions here.

[ii] Princeton University calls their engineering department “School of Engineering and Applied Science”, see:  https://engineering.princeton.edu/

[iii] Author’s Definition, Mechanism:

  1. a methodology including components, elements, parts and the associated energy and information flows enabling a machine, process or system that has demonstrated the ability to achieve its intended result.

Note: This definition is tweaked to include only proven methodologies.  See additional definitions here.

[iv] The reality of the gross disconnect of the complexity of complex systems is expanded in this post:  https://cs21c.com/marvels-taken-for-granted/.

© 2018 Mike Van Schoiack