Life Has to be a Process

This Post is under construction

What is life?  Life, as we know it, is an activity, matter held in a state of tenuous equilibrium by intelligent process control.  This understanding has to be broken down into two parts, the first is what “matter held in a state of tenuous equilibrium” means and the second is what is “intelligent process control?”

Equilibrium is an Order

Equilibrium is a state where the elements of a system interact with each other in a manner that predictable results (an order) will occur.  Such an order can be static or dynamic and with varying degrees of stability.  And they can be an equilibrium maintained by natural causes or by an intelligent servo control loop, or a combination of the two.

An example of a stable equilibrium is a glass of water sitting on a table.  Normally, the glass and the water are still.  If the table is lightly bumped, it will cause a ripple in the water which will gradually die down and reach the still state.  The bump did not impart enough energy to cause the system to seek a new equilibrium and the natural force of gravity caused the system to return to its original stable equilibrium and the entropy of the system was unchanged.

If the table is bumped hard enough such that the glass tilts beyond its tipping point, it will fall to a new equilibrium where the glass is on its side, or on the floor, and the water flows to the low point available to it.  The matter involved is at a higher entropy because it would require work to get the glass and water it back to its original position.

Now let us talk about dynamic equilibrium and stability, or, order.  Atoms, molecules, planets, solar systems, galaxies, traffic, the American Governmental system as designed by the Constitution, the free market economic system, factories, processing plants and life are all examples of dynamic equilibrium with varying degrees of stability.  The first five (atoms to galaxies) are all natural orders created by the laws of physics.  Without getting into the details of the prevailing theory of the history from the Big Bang to our present universe, we can say that presently there are the examples of atoms to galaxies conditions of relative stability, interrupted by events  that disrupt the equilibrium of the system.  This results in new orders whereby the energy/matter systems fall towards a new equilibrium according to the Second Law of Thermodynamics.  This applies at all scales of size, from microscopic to the extent of the universe.  In all cases entropy stays the same or increases with the flow of time, matter and energy.

Order That Natural Causes Can’t Provide Require Intelligent Control

The last six examples of order, traffic to life, are different from the first five examples insofar as the order achieved is the result of an additional element: intelligence.  Most biologists today might argue that life belongs in the category of natural order, so we will set life aside while laying the foundation of the line of reasoning being presented.

Intelligence is inherent in the examples of order from traffic to processing plants in the sense that actions (work) is performed to achieve a desired end (equilibrium with sufficient stability to achieve the needed order).  Such work requires the use of machines that have their own energy source to apply the right matter and energy in the prescribed form needed, at the time needed. We will call this Specified Work.  Such machines must be have means to measure process parameter requirements to meet the desired result (sensors), means to process the information (logic processor) and means to perform any adjustments required (actuators), and the power source to operate the sensors, logic processor and actuators.  These devices are the necessary components of the intelligent servo control loop mentioned above.  The adjective “intelligence” is not needed as logical intelligence, at a minimum, is inherent in a servo loop.  In other words, a servo loop by its very nature, has embedded intelligence, based on the definition of the term used herein..

Work performed by natural causes may at times be able to mimic Specified Work performed by machines, but rarely.  The reason is that natural causes distribute material and energy and cannot apply the right energy source or material, at exactly the correct location of the correct magnitude, direction and time on demand, without disturbing the matter around the target location.

Why Natural Causes Cannot Build a House

Think of the process of building a house.  Assume that all the materials, wood, nails etc. are on the ground at the building location.  What natural forces can lift the wood pieces in place and simultaneously nail the pieces together?  From a free energy point of view, it would take something on the order of a tornado.  But the energy of the tornado is being applied to all the wood and nails at once, and will rip things apart much more than to put them together.  This is how the Second Law of Thermodynamics applies to functional systems that require a high degree of specificity of material result.  Natural Causes reduces specificity[i], not increase it because Natural Laws tends to disperse matter and energy.

Nor Build the Molecules of Life

This same analogy applies to the “building” of molecules of life.  To make a molecule that has a wide range of bond strengths by normal chemical reactions necessitates raising the temperature high enough to supply enough free (Gibbs) energy to activate the strong-bond reactions.  But there is no provision in nature to heat up one bond at a time, so this free energy is applied to all of the bond sites in the molecule.  While at the high temperatures, weaker bonds will not “stick” because the free energy will break them immediately.  .  As the temperature is lowered, weaker bonds may be formed, but only at the remaining available sites.  The impact of this fact is that not all possible molecules can occur.  This process eliminates many of the possible combinations and permutations of possible bonds because bond sites that may need to have a lower energy bond will already be occupied.  We know this applies to most of the proteins in the cell, because they have short half lives which means they are not at stable equilibrium point.

This admittedly is a simplified explanation because there are a number of different types of bonds, that have other factors other than temperature involved, and folding of the proteins and the impact that catalysts (not enzymes) might have is not discussed.  However, the general concept is valid and by itself, is a reason why natural causes cannot make many of the molecules needed for life.  This article provides a more complete explanation that includes other reasons why natural causes could not have produced the needed life molecules.  The limited possibilities that thermodynamics imposes is one that an physicist/engineer understands.

Complexity, Information and Entropy

The reason that specified order creates a lower entropy is the fact that it required work to get the matter to the specified state.  Natural causes that impact this new order will always have the tendency either to not change or to reduce specificity thereby increasing entropy.

The Second Law has the effect of distributing matter and energy, which, by itself is a reason that natural causes cannot make all of the molecules necessary for life, or build a house.  This is why the tornado destroying a house run backwards is an accurate depiction of the capabilities of natural causes: to destroy specificity (increase entropy), not create specificity (decrease entropy).

Why is a Logically Intelligent Process Required to Sustain Life?

This gets us back to the discussion of life.  Biologists of all stripes agree that most protein molecules have a limited life.  This due to the fact that most proteins are not at a stable equilibrium point, and sooner or later will fall to a more stable state (higher entropy point), impairing functionality thus causing the life process to fail.

To maintain life, it is necessary to repair or replace the protein.  This requires a process control system that can detect when the protein becomes non-functional, determine whether a repair will work or whether replacement is required and to execute all of the work steps needed to do this.  This is the definition of a process control system.  Natural chemical reactions cannot perform any of these actions.

And it means that the functionality of a process control system has to be embedded in the cell.

What Capabilities are Needed to Implement a Logically Intelligent Process

This requires that inside each cell there has to be the equivalent of sensors, logical processing (computer like) means, and actuators.  The equivalent of languages, algorithms, and protocols are required because all of these elements must adhere work together.  There are hundreds of different proteins in the typical cell that have to be built and maintained.  This functionality alone involves many tasks which somehow have to be accomplished.  Think of a factory.  To build But this is but a small fraction of the tasks that must be performed.

How Does Life Implement the Needed Capabilities?

Explain how it appears that the combination of Protein Machines, DNA and the use of RNA to serve various functions, it seems technically realistic to assume that sensors, actuators and computer logic functionality could be realized.  It appears that much of what we would think of as the “hardware” would be protein machines that are built when needed, then recycled with the function is completed.  Go through a list of equivalent components used by man to make process control systems to implement analogous life type functions.  Explain the many holes in detail that jump off the page that seem to be “assumed”, but have to exist somehow, somewhere in the process control “code”.  Explain why “breaking the DNA Process Control Code” is so important – that this is the key to understanding life – the Life Process.  Subsections might discuss things to look for, e.g., reverse transcription.  Could there be some ingenious algorithm that uses reverse transcription to create a mating protein shape?  If this, or something equivalent is true, think of the implications!  Not only in the practice of medicine, but for the ID argument.

Starting of Life Requires an Intelligent Action

Explain how processes have to be started (and stopped, if required to restart) by first setting up initial conditions, and for life, there must be hundreds or thousands of them.  Then some intelligent action needs to be performed to start the process.  Point out the first time start of the life process has to be  totally different from the reproduction process in life – that the start of life had to include the reproduction process control code….  Point out how from an information point of view, we do not know what the initial conditions would have to be to start life.  A process is an environment where the “state of things”, think state variables, are constantly changing.  To start life, what are the “state variables”?  What action starts the process?  It seems to me that studying seeds would be a good way investigate this question.  Many examples can be given to illustrate this point that we can all relate to, and to “poke fun” at materialists, such as starting a watch, setting a mousetrap.  But we can also relate to booting up and booting down computers, using intelligence in traffic and how we know what “initial conditions” we use instinctively to make traffic work, etc., etc..  It will be easy to provide examples that everyone will have an intuitive appreciation of the problem.

The Life Process Was Designed

Point out how it had to be a “Top Down” – “Bottom Up” process – Behe is right.  Go through the design process, starting with goal, review of capabilities and resources, developing concepts, identifying potential problems, doing preliminary investigation and testing to insure that potential problems are avoided, designing languages, algorithms, protocols, designing components, testing and verifying , sub assemblies, assemblies, testing, etc., etc..  Illustrate with examples the inter-relationships/dependencies that exist, that no single modification to the process code or material embodiment will hardly ever add or change functionality.  Almost always, many, coordinated changes are required to make any change in functionality, and these changes/additions will occur at various locations in the code.  And point out that even one bit of error in the coding will usually cause failure, and that much error checking, redundancy etc., are required to make the process work.  And point out that it is much simpler for human designs, because we can stop and fix problems if something goes wrong.  All this has to be “built-in” in the case of life.

Life Had to Have Been, and Has to be Assembled

One thing that puzzles me is how little is made of the assembly processes that had to occur for first life, for repairs and for reproduction for all life.  Each of them is different, and they are processes in themselves.  The logistics of assembly of the materials, delivering them to the right place at the right time, what the co-ordinate system is and how it is implemented, how the materials and fluids are “corralled” during building process, etc., etc. are all questions that have not been adequately answered, IMO. This would be mostly asking a number of questions.  Human’s “hands” are too big, and our “sight” does not have the resolution to build things at the molecular level.  How was it done?

Evidence of a Master Plan

There is a lot of discussion about many aspects of a master plan that starts with the “fine tuning” of physical constants.  We also learned about using early life to change the early atmosphere in order to support life organisms later.  Judging from the fact that life requires a atoms from a number of different elements, that there had to be multiple single celled animals whose purpose was to “mine” the materials needed for later life.  Could “geomicrobiology” be evidence of this?  Were extinctions part of a bigger grand plan?  There are several thoughts along these lines that involve more design, more long-term processes that had been executed, and some, perhaps are in work now.

Top Down or Spontaneous Order

We do not know if the cell is totally a spontaneous order or if there is also some top down order mechanism.  Will be learned when the DNA code is completely understood.

Thermodynamic Implications

There is no correlation between intelligence and entropy.  The two are two separate, unconnected paradigms.  All we can say is that life, like any other logically intelligent process consumes energy just to maintain itself. The work done in the cell does not violate the 2^nd Law, it is just that the energy

[i] Specificity, in the sense used here, means specified by design to achieve desired function.[ii] Lodish, Berk, Zipursky, AMatsudatra, Baltimore, Darnell, Molecular Cell Biology, W. H. Freeman and Company.  Fourth Edition, 2000.  Pages 474-481.[iii] Ibid, Pages 63, 64, 66, 67.[iv] McIntosh, A. C., Information and Thermodynamics in Living Systems, www.worldscientific.com