ID vs. Materialism Debate – An Opinion

It is Memorial Day.  The headline story in the Seattle Times paper this morning is entitled “Science curriculum debate moves to School Board vote.”  The piece uses an 8th-grade teacher explaining mutation as an example of the Amplify Science program which the vote is about.  I think we can all surmise which side of the ID debate this program is on.

“ID is not science and therefore cannot be taught in schools” is a response virtually all our friends give, including the theists,  when this subject is being discussed.

The arguments “irreducible complexity,” “where does the information come from,” coherence, causal circularity (a new argument?) do not confront the “not science” argument directly.

But the realization that machines depend upon logical functionality as a minimum, (it could be a higher level, e.g., neural network, abstract or supreme levels), that logic is a form (the lowest) of intelligence, and that life depends upon machines in each cell, we have the argument that life itself is not all science; it is science plus intelligence! 

And the argument does not end there.  We can show, several ways, that natural causes cannot create machines:

  • Machines must have logical functionality – natural causes do not have any mechanism to deal with logical causes – the means to do so requires manipulation of matter/energy to and the ability to deal with and act upon the information.
  • All machines require matter that is held in a state of unstable or off equilibrium while the machine is running, which is a violation of the 2nd law for non-intelligently altered matter/energy.
  • Machines with the help of added energy (logical functionality consumes energy) can both increase free energy and reduce entropy at the same time which also is a violation of the 2nd law for non-intelligently altered matter/energy.
  • Machines require configurations of matter/energy that natural causes cannot create because they require intelligent work – something only machines can do (causal circularity).  Note: this point requires explanation, which, of course, we (EWG) will be more than happy to provide.

Since machines depend upon embedded intelligence, we can add to the argument “where did the information come from” the argument “where did the information come from?”

Since we can show why all machines require logical functionality, there is a method to falsify the claim that natural causes can perform the work of a machine, that is: demonstrate natural causes performing logical functionality.

I believe the machine argument is the best in the ID quiver.  It is different and more powerful.  It directly ties intelligence to life.  It provides new, better arguments about why natural causes cannot create life. It is falsifiable. This is an engineering orientated argument that is right down our alley.

I also think there is an impressive way to illustrate and teach some of the principles involved with the machine-life connection. An egg is a two-way metaphor for life; Christian/Easter, and the chicken-egg conundrum. The idea is to design a machine inside the egg that, when running keeps the egg balanced on an end (unstable equilibrium), tilts (away from equilibrium) when the egg is “sick” and falls over on its side when “dead” (equilibrium). Imagine ID talks starting with the speaker setting the “ID egg” on the podium and in classrooms when the teacher is teaching biology. I’m working on it.

© 2019 Mike Van Schoiack

Enzyme Energy Analysis Needed

Enzyme Energy Analysis Needed

Note to Self and Joe D.

This post was written as a “note-to-self” lamenting whether or not the enzyme Aconitase is a machine in the sense described in the referenced paper I recently wrote. The claim made in the paper is that some enzymes are machines and function differently than normal chemical reactions, including those involving catalysts – that enzyme action is a different paradigm. The paper discusses what machines are, from an engineering point of view, and watching the video showing the Aconitase enzyme in action shows some, but not all what I expected based on the characteristics of what I define as a “machine”.  

Do Molecular Machines Always Require Added Energy?

In the paper “On the Limits of Natural Causes” the claim is made that all machines require logical functionality enabled by energy.  But is energy always lost, that is, not recovered? The reason this question arises is video 2 in the paper which is an animation of the Aconitase enzyme converting a citrate molecule to an isocitrate molecule.  These two molecules have the same atoms and types of bonds, so it would seem that the bond energy and entropy of the molecules is the same. There is no hint that any expended ATP molecules for the enzyme to facilitate the conversion which suggests that the claim is not always true in the lossless molecular world. The claim is based on the concept that machines perform specified work which requires logical functionality which requires energy expenditure. An energy analysis of this enzyme’s operation should answer this question. However, knowing that the entropy and enthalpy are the same both before and after the conversion is possibly proof that no energy was lost during the process.1

A colleague suggested that the starting and ending entropy are different that accounts for the energy lost due to logical functionality. But I am not convinced.2 The Aconitase enzyme is required to create isocitrate molecules when needed, and building the enzyme does take materials and energy. So the question (do some enzymes not consume energy to power their logical functionality?) posed here does not impact the arguments made in the paper, that is, that intelligence requires expenditure of energy that otherwise (in the natural world, no intelligence involved} would not be necessary. The paper would require some adjustment to the intelligent work definition that makes an exception for some molecular enzymes whose intelligence is embedded in the specified mechanical configuration of the enzyme. And the explanation that sometines the logical energy is recoverable without loss would need to be added. However, the fact remains that the specified configuration of the enzyme molecule is a requirement to achieve a timely conversion of the citrate molecule to an isocitrate molecule.

Figure 1. Citrate, w/electrostatic bond detail

Figure 1 is the chemical equation for the citrate molecule with the electrostatic bonds shown in the video added, shown as dash and dotted lines. My original thought was that if the magnitude of these bond energies could be calculated for each state of the process,  one could determine if energy was conserved or not.  But on second thought, it would seem that one is making and breaking the same bonds, therefore the net sum would be zero.3

Assuming the transformation of the citrate to isocitrate molecule is achieved without any free energy change to the system, the next question is: what causes the each of the next process steps to take place? The logical answer (to me) is that each step establishes new initial conditions that provide a singular, specified state change with the available free energy. If this is true, then the enzyme design is very, very sophisticated!  The last state change would have to “eject” the newly formed isocitrate molecule. 

The figures below are my interpretation of the covalent bonds made and broken at each step of the conversion process as shown in the video.  The emzine amino acid involved in these interactions is identified, and the water molecule that is formed in the process is also shown.  The electrostatic forces involved in each of these stages is not shown in the video nor shown in these figures.

Great Deceiverism 101

Great Deceiverism 101

Jeff Hester Columns in Astronomy October 2017 and April 2018 issues

This is a response, based on the ideas presented on this site to this column and this column.

Jeff Hester, in his October 2017 and April 2018 columns is right about the “random march of entropy produces structure” as it does create atoms, molecules, suns, galaxies, weather, erosion, plate tectonics, etc. These are all examples of natural dynamic equilibriums and natural process. But machines and life are a different paradigm because they require embedded intelligence and are examples of intelligent equilibriums and processes. Based on the laws of physics we think we know, plus observation and logic, embedded intelligence can only exist by intelligent manipulation of matter/energy.  

Life is an intelligent process. Each molecular machine in each cell is running a process that makes logical decisions and controls the use of energy. Natural causes are incapable of logical functionality and intelligent control of energy, and incapable of designing, building, setting initial conditions and starting any machine, let alone something as complex as life. Natural processes have no mechanism to create such entities even though these entities do not violate any laws of physics.  Logical, not scientific constraints make it impossible for natural causes to create intelligent entities.

Dr. Hester, obviously you are not aware of the beyond belief complexity of life. I seriously doubt that mankind will ever be able to reverse engineer life to the level of understanding we engineers have of our machine creations. If natural causes can create life, they can easily create a simple machine, something simple like a mousetrap. Finding such a machine, or even an example of logic functionality caused by natural causes would falsify the concepts presented here. Read more about these ideas at https://cs21c.com/paper-on-the-limits-of-natural-causes/.

Mike Van Schoiack, Bellevue, WA

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