Factory

To design and build something like a factory requires many co-ordinated steps.  It is first a “top-down” effort starting with objectives, and resources of all types.  A plan must be made that figures out how to utilize the available resources to put together the pieces that will make the plant work.  The details of how the plant will perform each process step that will be needed, and how all of the steps can be coordinated to make sure they will work together.  Then you have to go the bottom, and design the parts, test them, assemble multiple parts, make sure they work together, fixing problems as they arise, and work back upwards until the whole plant is assembled and tested.

As part of the design process, the process of moving the materials required in the overall process must be designed and built and installed.

When the plant is all together, the process must be started.  In order to do it sucessfully, one must preload materials, place all machines in a particular state, or metaphorically speaking, set all switches in the right position and prime all the pumps, before hitting the “start” button that applies power to everything.

, the means of doing this has to be designed and in place. that have to move in a precise, coordinated fashion that  build But this is but a small fraction of the tasks that must be performed.

Concepts to be added:  Life is a process that uses intelligent machines to enable a living entity.  The need to recognize, base on the fact that life is a process, the functionalty that has to exist., and the detail involved.  It is far greater than presently acknoledged by thosese writing about life.  The “process” elemdnets involve all of the detail.= functions that have to be performed to allow life to exist.  This is far more involved thanthe general categories such as “reproductionn”.  Reproduction invoves dozens, maybee hundreds or thousands of actual functional steps t.

ver since Darwin’s book Origin of Species was published in 1859, there has been a steady advance toward the idea that our existence can be explained by science – there is no need to invoke a God or other super-natural entity.  Darwin’s theory seemingly provided an explanation of how all life forms evolved from the first cell, and, by extension, assumes a natural cause explanation of the origin of life.

Since Darwin wrote his book, much has been learned about life.  It is much more complicated than expected.  We now know that organisms have what appears to be a designed mechanism for evolution, one which can account for adaptation of plant and animal forms, but not the evolution of new forms.  And there is no progress in the development of a theory for beginning life occurring from natural causes.

Studying the inter workings of the cell is science, and the knowledge gained makes the  argument for Neo-Darwinism weaker by the day.  The reality is that if Darwin knew what we know today about life and the record of life, and if he was honest, he would not have written his book based upon the doubts he expressed, and the methods of science that he expounded.  Even so, the mainstream field of biology clings to the belief in Darwin’s theory and to the idea that life began by natural causes.

So today there is a huge chasm in the field of biology – Darwinist vs. those who embrace the evidence of what is being learned.

This engineer has become interested in this field partly because of the natural need to know how and why we exist, and partly because of what seems to be a denial, or maybe it is purely lack of knowledge, of the field of chemistry to see the difference between chemical reactions vs. the physical building of macro-molecules.

A probable explanation of this chasm and how it has evolved is that biologists early on did not realize that actual molecular machinery was involved in the cell.  Once they did, they assumed that these machines could be described as an advanced catalyst, hence the term enzyme with the definition of it being an enzyme.  They were not, and, it seems, for the most part, not aware of the fact that they are dealing with a whole different paradigm that involves machinery sensors, actuators and process control systems in addition to the chemistry which they are trained in.

It is easy, as an engineer, to look at this situation and recognize what seem to be pitfalls, but limited the knowledge in biology and chemistry leaves many questions unanswered and leads to the possibility that conclusions drawn may be wrong.

Two Paradigms
These are two separate paradigms.  Chemical reactions are due to natural causes driven by the laws of physics and chemistry.  The physical building of macro-molecules is the work of intelligent machines working in a process control system, intelligently using the laws of phycis to accomplish things that natural causes cannot.  Life uses both of them to exist.  The world of biology still seems to think that enzymes are just catalysts that speed up a natural chemical reaction.

Life is a Process
From this engineer’s perspective, the fact that life is an intelligently controlled process is the easiest way to appreciate and understand the difference between living and non-living matter; that life is matter with embedded intelligence.

The field of electronics deals with devices in the nm range, which is the same size range of proteins.  But there are several differences between ultra-small electronic entities compared to life molecules.  Electronic chips are layered two dimensional static devices, compared to life molecules that, in the living condition, moving in all three dimensions.  The other big difference is that even though the electronic structures at these dimensions are hard to see, the designs normally supply test points that allow the engineer to discern what is happening even at these small dimensions by electrical measurements.  The point is that we do not have the means to track exactly what is happening inside the cell because “our fingers are too large” and we cannot see or probe inside the cell walls to “reverse engineer” the life process that is in motion.

Past, Present, Future
However, the bio-medical field is doing amazing things involving manipulating of the genome.  This engineer is clueless how these feats are accomplished.  The assumption is that researchers are learning how to use the cellular machinery to determine functionality indirectly.  This is a scary because it is obvious that the overall understanding of the process control system in the cell is very limited.  In addition, the lack of knowledge of process control in general leads to the prospect of not appreciating the probable interrelationships between the numerous control loops that must exist in the cell.  This could lead to unintended consequences, some which could be very subtle and/or dangerous.

It has been intuitively obvious to man since the earliest recorded history that life was something much different from inanimate nature.  Darwinism has given those who do not want to believe that an intelligent entity was responsible for our existence a way, as Dawkins put it “to be intellectually fulfilled.”  To others, life itself, is proof that there must have been some intelligent intervention with nature in order to create life.

The reality is that we do not understand the totality of physics; like dark matter and energy, gravity and entanglement.  Perhaps if we did, we would know which side of this chasm is correct.  The science we do understand leaves Darwinism in a black hole.

Frustrations of This Engineer
Lack of appreciation of the impacts of the 2nd law of thermodynamics:Reason that natural causes cannot build all of the molecules of life
Reason why there is no pathway for complexity to increase over time to “evolve” first life
The reason that life has to be a process
Terminology used in Biology & lack of precision of definitions
Understanding the full implications of life being a process
Appreciation of the difference between information and intelligence
Appreciation of the difference between design and actual building something
Appreciation of the difference between static things and machines that do work.
Purpose of This (ID) Site
This site will be a forum to discuss the frustrations listed above.  It is the hope that there are others, particularly thoughtful engineers who share some of these frustrations and would like to have the ability to have discourse on these and similar topics will find this site.

It seems obvious that the fields of biology and engineering are merging, and it is exciting to be able to participate in this merger.  If this engineer was a young man, he would become a bio-engineer.

This engineer, being very interested in understanding what is known about life; what it is and how it works, has spent countless hours reading and thinking about the topic. The engineer’s perspective is quite different from the Darwinist point of view and the differences have many implications: thermodynamic, theoretical, philosophic, political, and theological.

It is the belief of this engineer that the approximately 97% of the DNA that is not used to express proteins is essentially the life process “code”; that chucks of this DNA are converted to RNA that works with proteins to provide the functionality needed for the life process.  This assumption is made based on what seems to be the obvious reality that life is a process, and knowing what is require to make a process work, coupled with the knowledge that the protein/RNA combination is already known to provide some of the functionality of the life process, e.g., the ribosome.

The key to understand life, it seems to this engineer, is to understand the details of how this process works.  As mentioned, this is hard because our fingers and eyes are too big.  Engineers like myself have ideas about what to be looking for including some thoughts regarding where and how.  But we (speaking for myself) have only a little knowledge of what currently is known, and almost zero knowledge about the tools available to gain additional knowledge.

So the purpose of this site is to serve as a forum for this engineer and others to share ideas, learning resources and, in general, be a place to kindle thinking on the topic.

To submit a post, please use the Contact form in the footer.

This is a quote from my sophomore physics class textbook: “By means of the statistical definition of entropy, Eq. 25-13, we can give meaning to the entropy of a system in a nonequilibrium state. A nonequilibrium state has a definite entropy because it has a definite degree of disorder. Therefore, the second law can be put on a statistical basis, for the direction in which natural processes take place (toward higher entropy) is determined by the laws of probability (toward a more probable state). From this point of view a violation of the second law, strictly speaking, is not an impossibility. If we waited long enough, for example, we might find water in a pond suddenly freeze over on a hot summer day. Such an occurrence is possible, but the probability of it happening, when computed, turns out to be incredibly small; for this to happen once would take on the average a time of the order of 10^10 times the age of the universe. Hence, the second law of thermodynamics shows us the most probable course of events, not the only possible ones. But its area of application is so broad and the chance of nature’s contradicting it is so small that it occupies the distinction of being one of the most useful and general laws in all science.”

That was over 50 years ago and I remember thinking at the time that this was false – it didn’t make common sense. But more significant, equation 25-14 discussed the statistical variation of the velocity (think momentum) of the molecules.  The molecules of water in a lake are exchanging momentum by the collisions with each other, and by the first law of thermodynamics (conservation of energy) this momentum (temperature of the water) had to be consurved, therefore the average temperature of the lake as a whole would be constant.  In other words, this statistical improbablity is true looking at one molecule over time, but is not true for the average of all the molecules as a function of time.  So the probability is zero, not some crazy low number.

But there is also another problem.  Assume that the all of the lake’s water molecules did have the probability distribution described.  The changes in temperature would be happening so fast that one would be unaware of them.  In other words, the freezing events would be so fleeting that one would be unaware of them.

It has been my belief that there is a corellary between this example and the study of the probability of a given protein being produced by natural causes.  It is my belief that the probablitity that natural cases can produce all of the functional proteins needed for life is also zero.  The explanation for this belief is  part of the purpose of the ID section of this website.

The process of thinking about this topic has lead to considering other issues, such as what life is from a physics/engineering point of view, specific information, specific work, machines and intelligence. From this comes definitions and theories and proofs that natural causes could not have been responsible for begining life.

The main difference between the approach to thinking about these topics that I, as an engineer think about them, compared to non-engineers, is to focus on nature’s ability to actually build and start life and to think of life as a process as opposed to being a “material state.”

The result of this engineer’s deliberations on this topic lead to the conclusions that follow.  More detail in contained in referenced posts, which provide the reader the opportunity to respond to specific concepts.  The reality is that I am not a biologist and very possibly draw some incorrect conclusions about things that I’ve (thought to have) learned.  I’m hopeful to get corrective feedback.

 Frustrations of This Engineer

1. Lack of appreciation of the impacts of the 2nd law of thermodynamics:
   1. Reason that natural causes cannot build all of the molecules of life
   2. Reason why there is no pathway for complexity to increase over time to “evolve” first life
   3. The reason that life has to be a process
2. Terminology used in Biology & lack of precision of definitions
3. Understanding the full implications of life being a process
4. Appreciation of the difference between information and intelligence
5. Appreciation of the difference between design and actual building something
6. Appreciation of the difference between static things and machines that do work.

A. C. McIntosh, in a scholarly paper¹regarding information in life, concludes by saying: “..that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate. The idea of information, a static product of intelligence, could be “constraining” thermodynamics”  makes an ambiguous connection, at least from an engineering point of view. But this line of thinking an inquiry is inherent in the field of biology today asking the question “where does the information come from?”

Information is a static, non-material construct of intelligence which can, and is embedded in matter by the use of language, codes, media, protocols, etc., Life, to this engineer, is a process that is continually doing things and burning energy just to maintain its living status.  McIntosh points out in his paper, “The functional machinery of biological systems such as DNA, RNA and proteins requires that precise, non-spontaneous raised free energies be formed in the molecular bonds which are maintained in a far from equilibrium state.”

The idea of life being a process that “constrains thermodynamics” to maintain “a far from equilibrium state” using machines that make intelligent choices answers the  ambiguity of information vs. intelligence expressed by McIntosh.  ********

A probable explanation of this chasm and how it has evolved is that biologists early on did not realize that actual molecular machinery was involved in the cell.  Once they did, they assumed that these machines could be described as an advanced catalyst, hence the term enzyme with the definition of it being an enzyme.  They were not, and, it seems, for the most part, not aware of the fact that they are dealing with a whole different paradigm that involves machinery sensors, actuators and process control systems in addition to the chemistry which they are trained in.

it is easy, as an engineer, to look at this situation and recognize what seem to be pitfalls, but limited the knowledge in biology and chemistry leaves many questions unanswered and leads to the possibility that conclusions drawn may be wrong.

Thinking Out Loud

The idea behind this post is to an ongoing list of questions that I (and others that hopefully join the blog) maintain that we’d like to have authoritative answers to.  It is hard to find answers to many questions for a number of reasons.  For me, this mostly is to fill gaps of knowledge about biology, and what is understood and not.  Another reason is to gather information for “truth-testing.”  Partly my interest in this field is to find truth where many practitioners have beliefs that are expounded as truth.  This is particularly a problem for an outsider like me.

It is my general belief that there is much misunderstanding due to mixing micro and macro effects.  A prime example of this is the “lake freezing over in summer” problem.  An observation at the micro level does not extend to the macro world.  At the micro world level, one cannot see or observe “wasted energy” – all you can see are molecules interacting with each other, photons emitting off of electrons when they change orbitals, etc..  At the micro level you do not see the loss of energy due to frictional heat, or something breaking, all you see are molecules moving faster.  The second law is a macro world, not a micro world phenomenon.  Theoretically, the second law makes it impossible for life to start from natural causes because it does not allow what I would call “specific order” or “specific (negative) entropy” increases.  I understand this from a theoretical point of view, but not so well at the “what is happening from an interaction of matter and energy” point of view.  My suspicion is that the problem stems from the micro/macro phenomenon.

I believe I understand the reason that machines make it possible to do things that natural causes cannot:  machines can apply the right force, at the right place, time time, direction, profile, etc., etc., where natural causes are limited to work the drives matter/energy to higher entropy (disorder, equilibrium), so it cannot produce the order needed for life.  But life is at a micro level.  And what is secret sauce that makes it possible for us to design machines that can do what nature cannot?

One thing that instinctively drives my thinking – that life is a process of processes at many different levels, time, and purposes.  I can’t get it out of my head that understanding how the cell accomplishes the life process control functions in the cell is the key to understanding life itself.  Most of the questions I have about “what is needed to be learned” revolves understanding how DNA/RNA and proteins plus whatever else hasn’t been discovered yet, achieves the life as we know it.

General Topics About Beginning Life

• Is a seed alive when it is dormant?  What I’ve read indicates it is alive, but at a low respiration rate.  True.  Is this true in all cases?
• Are there any instances where a cell goes from a “live state” to  a “dead state” and then back to an “alive state”? [looking for initial conditions to start life]
• Can all molecules in life be synthesized in the lab?  If so, what is involved?
• I think that from both a theoretical and logic point of view, that it is impossible for all of life’s molecules to be produced by natural causes, that is, without intelligent intervention.   Are these reasons true?:
  • • The second law of thermodynamics reduces specificity, not increase it, and
    • Because of the way chemical bonds are created by changes in mixtures and free energy limits possible bond combinations.  This limitation results because of nature’s limitation of controlling the matter and energy on a bond by bond basis – the materials and free energy will be applied to all bonds of a molecule at the same time.  This, in part, is just probably a physical description of why the second law exists – natural causes disperse matter and energy except for state changes which do not apply to life molecules.

  DNA Manipulation

  • • 1. What are to tools and capabilities to figure out what purpose of a particular segment of DNA is?  This probably could/should be broken down into dozens of more specific questions – it probably involves a general education about what is known about DNA, how the molecular machines find start and end points of segments, etc., etc..  How can one learn about this?
      2. How has what is known about the functionality of DNA →RNA/protein combinations been obtained?

  Stopping and Restarting Life

  The fact that proteins have half lives would seem to be a reason that life cannot be stopped and then re-started.  If life stopped, and a protein (or any other molecule) that is necessary for the production of proteins becomes dysfunctional because it has naturally dropped to a more stable equilibrium point, the life process could not be restarted.

  This begs another question regarding how to stop life with the idea of being able to restart it.  I suspect that there is no “ON-OFF” life switch, so the only way to stop it is to distroy or disable a function.  Unless there was some way to reinstate this function, it would be impossible to restart life.