Questions That Need to be Asked and Answered

by Mike Van Schoiack | Mar 8, 2017 | Uncategorized

Questions That Need to be Asked and Answered

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.

Our Fingers Are Too Big

by Mike Van Schoiack | Mar 6, 2017 | ID Topic

Our Fingers Are Too Big

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 around 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 at the 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.

The assumption is that much of the structure of the molecules in the cell are discerned by scanning electron microscopes, which, I think only work with dead biological material. This would be very limiting, it would seem. However there appears to be other devices that claim to have “high-speed imaging, in vivo” capability, a multiphoton laser scanning microscope and more recently a new sub-optical phonon (sound) imaging technique. An inherent problem is that the objects of interest are as small or smaller than the wavelengths of observation radiation and the energy involved can cause damage. It is hard to tell how much detail understanding of the process going on inside the cell can be discerned from the tools available today.

However, the bio-medical field is doing amazing things involving manipulating 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 achieve their own purposes. This is a scary prospect as 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.

It would seem to this engineer that the best possibility to learn about the process control system in the cell is by indirect means using the techniques of DNA manipulation, correlating changes made to cell operation. Understanding life, it seems, depends heavily upon gaining an in-depth knowledge of the control system.

Fake Biology

by Mike Van Schoiack | Mar 5, 2017 | ID Topic

Fake Biology

“Fake” Molecular Cell Biology

This is a book recommended by my PhD. biologist friend to learn about the cell’s mechanisms. I’ve learned a lot. One overall impression is the sheer volume of things going on. But I could not believe my eyes when I read the following which is part of the introduction to Chapter 2:

“About 7 percent of the weight of living matter is composed of inorganic ions and small molecules such as nucleotides (the building blocks of DNA and RNA), amino acids (the building blocks of proteins), and sugars. All these small molecules can be chemically synthesized in the laboratory. The principal cellular macro-molecules – DNA, RNA and protein – comprise the remainder of living matter. Like the small molecules found in cells, these very large molecules follow the general rules of chemistry and can be chemically synthesized.” Then further down the paragraph, it says this:

“The realization that complex processes such as evolution, development of an organism from a fertilized egg, motion, perception, and thought follow the rules of chemistry and physics – and that no vital or supernatural force is involved – has profound philosophical and even political implications.”

The book defines an enzyme as: “a biological macro-molecule that acts as a catalyst” and a catalyst as: “A substance that increases the rate of a chemical reaction without undergoing a permanent change in its structure. Enzymes are protein catalysts.”

These definitions assume that the work of the molecular machinery is chemistry, the result of natural causes. There is no recognition of the fact that machine work is fundamentally different from natural work. The chemical synthesized molecules are the result of careful process control, not the result of unguided natural causes. In addition, the specificity required for at least some the functional proteins is beyond the reach of lab synthesis as far as I can tell from the literature.

In addition, it seems that some variation of the word evolution, or some reference to evolution is on every page. There is no doubt in my mind that part of the “knowledge” this book is conveying is materialist doctrine without supporting evidence.

For these reasons, I feel this book deserves the “Fake” label in the title.

Life

by Mike Van Schoiack | Mar 4, 2017 | Definition

Life

Merrian-Webster Definition

The quality that distinguishes a vital and functional being from a dead body
a principle of force that is considered to underlie the distinctive quality of animate beings
an organismic state characterized by capacity for metabolism, growth, reaction to stimuli, and reproduction.

Webster provides additional definitions that are not descriptive of what life actually is.

This Engineer’s Definition

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

The definitions in textbooks tend to be a long list of characteristics. For example, Biology¹ devotes a page to the definition in a section entitled “Life defies simple definition.” It then describes “seven characteristics:” Cellular organization, Ordered complexity, Sensitivity (response to stimuli), Growth, development and reproduction, Energy utilization, Homeostasis, and Evolutionary adaptation. Biochemistry² devotes three pages in a section entitled “What is Life?” The characteristics it describes are Complex and dynamic, Organized and self-sustaining, Cellular, Information-based, and Adapts and evolves.

The posited definition that life is an intelligent process whose purpose is to sustain and propagate itself is concise and accurate. Life is an intelligent process at all levels. Life’s creation was an intelligent process. Early life cells were intelligent processes used to tera-form the earth’s atmosphere, oceans, and soil. The creation of multicelled organisms that created a food-chain was a process. The creation of abstract intelligent mankind was a process. The creation-to death of each type of life form and each individual of the life form is a process.

Realizing that life is an intelligent process defines functionalities that must exist in it. Past wisdom was that life was all chemistry. The tide is turning toward the realization that machinery is involved. We have learned a lot about life especially considering the fact that it is molecular machinery at the boundary of the micro and macro world. But the obstacles to instrument and measure at this size and speed scale make it impossible to reverse engineer life to any measure close to what we can with human creations. It appears that we learning a lot at the high, systems-level, but much less regarding how the molecular machinery works in detail.

However, knowing that life is a process implemented by molecular machinery, coupled with our ability to understand the functionalities required to make such machinery work, we can answer some questions such as whether or not the life machinery can be created, initial conditions for the life process set, and started by natural causes. We do not need to all the details how life achieves these functionalities – just whether natural causes are capable of creating them. This knowledge defines the elements of functionality that must exist in the cell. It also tells us that certain initial conditions had to exist to start life. Before we know what these conditions are, we need to better understand the process itself, including languages, algorithms, and protocols that exist to control and coordinate the process.

Intelligence

by Mike Van Schoiack | Mar 4, 2017 | Definition

Intelligence

Merriam-Webster Definition

The ability to learn or understand or to deal with new or trying situations: reason; also: the skilled use of reason. The ability to apply knowledge to manipulate one’s environment or to think abstractly as measured by objective criteria.
The ability to perform computer functions.

This Engineer’s Definition

The ability to make logical choices. (Logical Intelligence)
The ability to think, reason, design. and to have self-consciousness. (Abstract Intelligence)

The two definitions listed here correspond (in reverse order) to the Webster definitions. Logical intelligence is what is found in computer code. Humans can design intelligent machines like computers and systems that use computers. But humans do not have the capability to design abstract intelligent machines. Many have argued that given time, we will learn to do this. This engineer has his doubts. It is something we are gifted with, like migrating birds being gifted with the ability to find migration destinations, but neither we or migrating birds understand how we do it.

Intelligence is an entity unlike entities we understand from the physical sciences – we cannot write an equation using physics parameters that equate to intelligence. We do not understand the relationship, if there is any, between a mind and physics. Natural causes cannot make logical decisions, let alone perform abstraction. Natural causes perform work that is defined solely by the laws of physics, not a mind. Life, even though it follows the laws of physics, could not result from natural causes because of its embedded intelligence. Only abstract entities that can perform intelligent work can produce machines. Intelligence of any form has meaning only to an entity that has abstract intelligence.

Additional Clarification

For purposes of clarity and precision, there is a need to define different levels of capability and means of implementation of the term intelligence. This is like the realm of space with levels of position, velocity and acceleration. For the realm of intelligence, the levels would be information, logical intelligence, abstract intelligence and supreme intelligence.

Information

Specified Information is not intelligence per se, but it is a starting point for intelligent activity, like a point (position) is a starting point for considerations for distance, velocity and acceleration in the realm of space.

All matter can be defined by state variables that are information, Matter (static) that has been manipulated by intelligent work, but is not a machine, is called a tool, and includes all human static creations such as entities we normally call tools such as a screwdriver, hammer or saw, but also with things like jewelry, art (paintings, pottery), glass, and building supplies (wood, nails). All these are creations by an abstract intelligent entity (humans). A bird’s nest is made by a logically intelligent living entity (a bird). All specified information comes from an intelligent entity.

Logical Intelligence

Logical Intelligence is the ability to perform logical functions, that is, to make choices (output) to achieve the desired end that dictates a logical algorithm that processes supplied information (inputs).

Matter that has embedded logical intelligence is called a machine or a component of a machine. Examples include mousetrap, engine, drill, watch, and computer. Embedded logically intelligent devices require an abstract intelligent machine to actualize them, and the only example on earth is humans. Life also has embedded logical intelligence – it runs the life process going on in every living cell. Life, especially life with abstract intelligence is beyond the ability of humans, in my opinion. This is the product of a supremely intelligent machine, with not only the ability to design, but build the cells. This involves “hand building” the first molecular machines, which requires fingers orders of magnitude smaller than ours.

Neural Network Intelligence

As far as I know, virtually all animals have brains consisting of networks of neurons, axons and dentrites.³ Some years ago, a reseacher from the University of British Columbia who was studying neural networks by observing the operation of some sea worm brain that consisted of 30+ neurons. It was fascinating. The description explained pre-knowledge, learning, forgetting, and why memeory isn’t always instantenous. The description also explained how the brain controls actions, and why these actions can change with experience.

Engineers can mimic a neural network using analog circuits. However, the quantity of such elements and interconnections required this approach impractical. However, digital computers can mimic neural networks with much less hardware but at the expense of lots of computing and are called artifical neural networks, (ANN).⁴ This use of ANNs is on the rise because solutions to many problems do not lend themselves to linear logic, e.g., face recognition or control of traffic lights.

The machines in the cell use appear (to me) to be either logic or analog

Abstract Intelligence

Abstract Intelligence is the ability to think, reason, design and to have self-consciousness.

The only example on earth is human beings, which can be considered an abstractly intelligent machine.

Creation of humans requires intelligence much greater than ours and fingers much smaller.