Intelligent Design, the best explanation of Origins
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Intelligent Design, the best explanation of Origins

This is my personal virtual library, where i collect information, which leads in my view to Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


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Intelligent Design, the best explanation of Origins » Does God exist ? origin of God - metaphysical reality » Syllogistic - Arguments of Gods existence based on positive evidence

Syllogistic - Arguments of Gods existence based on positive evidence

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Otangelo


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Syllogistic - Arguments of Gods existence based on positive evidence

https://reasonandscience.catsboard.com/t2895-syllogistic-arguments-of-gods-existence-based-on-positive-evidence

Cosmological arguments
Origin of life arguments
Instructional complex Information
The Cell
Cells are factories
Arguments based on biocomplexity and biodiversity
Arguments based on morality
Argument from logic
Argument from consciousness
Syllogisms about irreducible complexity

Intelligent design theory is like a sword with two edges

Intelligent design wins using eliminative induction based on the fact that its competitors are false. Materialism explains basically nothing consistently in regards to origins but is based on unwarranted consensus and scientific materialism, a philosophical framework, that should never have been applied to historical sciences. Evidence should be permitted to lead wherever it is. Also, eventually, to an intelligent agency as the best explanation of origins.

And intelligent design wins based on abductive reasoning, using inference to the best explanation, relying on positive evidence, on the fact that basically all-natural phenomena demonstrate the imprints and signature of intelligent input and setup. We see an unfolding plan, a universe governed by laws, that follows mathematical principles, finely adjusted on all levels, from the Big Bang, to the earth, to permit life, which is governed by instructional complex information stored in genes and epigenetically, encoding, transmitting and decoding information, used to build, control and maintain molecular machines ( proteins ) that are build based on integrated functional complex parts ( primary to quaternary polypeptide strands and active centers ), which are literally nanorobots with internal communication systems, fully automated manufacturing production lines, transport carriers, turbines, transistors, computers, and factory parks, employed to give rise to a wide range, millions of species, of unimaginably complex multicellular organisms.

Chance to find a message written on a cloud in the sky: "Jesus loves you" randomly,  is as DNA creating its own software, and upon it, writing a complex algorithm to make a protein by accident. DNA base sequencing cannot be explained by chance nor physical necessity any more than the information in a newspaper headline can be explained by reference to the chemical properties of ink. Nor can the conventions of the genetic code that determine the assignments between nucleotide triplets and amino acids during translation be explained in this manner. The genetic code functions like a grammatical convention in a human language.
https://www.youtube.com/watch?v=FT-RsCo1Flg

https://reasonandscience.catsboard.com/t2895-syllogistic-arguments-of-gods-existence-based-on-positive-evidence#7048

A mental plan or scheme for accomplishing a goal
An underlying scheme that governs functioning, developing, or unfolding pattern and motif <the general design of the epic>
A plan or protocol for carrying out or accomplishing something
The arrangement of elements or details in a product or work of art
To create, fashion, execute, or construct according to plan: devise, contrive
To conceive and plan out in the mind <he designed the perfect machine>
To have as a purpose: intend <she design ed to excel in her studies>
To devise for a specific function or end <a book designed primarily as a college textbook>
To make a drawing, pattern, or sketch of
To draw the plans for <design a building>

Creation is evidence of a Creator. But not everybody ( is willing ) to see it.
Romans 1.19 - 23 What may be known about God is plain to them because God has made it plain to them. For since the creation of the world God’s invisible qualities—his eternal power and divine nature—have been clearly seen, being understood from what has been made, so that people are without excuse.

The (past) action or signature of an intelligent designer can be detected when we see :

- an object in nature very similar to human-made things
- something made based on mathematical principles
- systems and networks functioning based on logic gates
- something purposefully made for specific goals
- specified complexity, the instructional blueprint or a codified message  
- irreducible complex and interdependent systems or artifacts composed of several interlocked, well-matched parts contributing to a higher end of a complex system that would be useful only in the completion of that much larger system.
- order or orderly patterns
- hierarchically arranged systems of parts
- intelligence can create artifacts which use might be employed in different systems ( a wheel is used in cars and airplanes )
- Fine-tuning

The origin of the physical universe, life and biodiversity are scientific, philosophical, and theological questions. 
Either, at the bottom of all reality, there is a conscious necessary mind which created all contingent beings, or not. 
What is observed in the natural world, is either best explained by the (past) action of an eternal creator or not? 
The theory of Intelligent design supports the notion that a designer best explains the evidence unraveled in the natural world, 
while Cosmic, chemical and biological evolution attempt to explain the natural world without a creative agency beyond the time-space continuum, giving support to the idea that
there is no evidence of a creator, which then would be unnecessary.

Religion/theology attempts to explain and address other questions, like the identity of the creator, and his motivations.



Last edited by Otangelo on Fri Jan 22, 2021 6:09 am; edited 81 times in total

https://reasonandscience.catsboard.com

2Syllogistic - Arguments of Gods existence based on positive evidence Empty Cosmological arguments Fri Nov 27, 2020 8:36 am

Otangelo


Admin
Cosmological arguments

It is absurd and unthinkable for an atheist to believe that God can make everything out of nothing ( see Creation, Views of ), but is then forced to adhere to the thinkable that nothing should turn itself into anything, or that eternal regress in time is somehow possible.

First cause arguments:

How is a worldview without a necessary cause rational?
1. Contingent (dependent) beings exist.
2. Contingent beings require a necessary, self-existent being in order to exist.
3. Therefore, an eternal, non-created, self-existent being must exist ( modus ponens: The rule of logic stating that if a conditional statement (“if p then q ”) is accepted, and the antecedent ( p ) holds, then the consequent ( q ) may be inferred. ) Dependent beings cannot exist independently. Since the universe had a beginning, it is dependent on an external necessary cause. Aquinas showed us that the attributes of a true God are logically deduced.

Gods existence can be logically proven: 
1. A series of events exists.   One event is added to another to get us to today.  But we know that whenever we pause, we can't have an infinite number of events.  This means that there is not an infinite number of events that go backward from this point in time. Adding individual events together can never get to an infinite period of time.  
2. The series of events exists as caused and not as uncaused(necessary)
3. There must exist an uncaused necessary being that is the cause of all contingent being
4. Since that cause created space, time, and matter, it must be above and beyond physical reality. That cause must be timeless, uncaused, eternal, spaceless, and personal. We call it God.
https://www.youtube.com/watch?v=FPCzEP0oD7I&t=8s

1. The physical universe exists. 
2. Existence cannot come from non-existence. 
3. Since we exist, then being has always been in one form or another.
4. The universe had a beginning. It cannot be the product of an infinite serie of regress, nor be caused by nothing. 
5. Therefore, a non-physical being must have existed beyond the universe, causing the universe into existence.
6. That being is God.

1. Either the universe is eternal, or it began from nothing by nothing, or it was created by a creator.  
2. The universe is not past eternal.
3. The present moment cannot be reached by adding individual events together from eternity.
4. The second law of thermodynamics refutes the hypothesis of an eternal universe.
5. The universe cannot start from nothing.
6. Viirtual particles do not come from nothing. They depend on a quantum vacuum, a state with the lowest possible energy.
7. Where did THAT energy come from ?  
8. The universe had a beginning, therefore a cause
9. That cause must be timeless, spaceless, and personal. We call it God.

1. The universe cannot be past eternal.
2. Neither could it be self-caused.
3. Therefore, it must have been caused by something else.
4. Since that cause created space, time, and matter, it must be above and beyond physical reality.
5. That cause must be timeless, spaceless, and personal.
6. We call it God.

1. If nothing ever existed, then there would still be nothing.
2. Since we exist, something has always existed.
3. Since the universe had a beginning, it was caused into existence by something else.
4. That cause must be either personal or non-personal.
5. A non-personal cause would be of physical substance, and so subject to change and time. That cause would also need to have a beginning, and be caused by something else, leading to infinite regress which is impossible.
6. The best explanation as cause of the universe is a personal creator, independent, immaterial existing in an eternal timeless dimension, triggering the Big bang and creating the universe

1. Being cannot come into existence from absolutely nothing.  If there ever would have been a state of absolutely nothing, then that state would not change, but remain so.  Since there is existence, being has always been.  
3. Since the physical universe had a beginning, and infinite regress of physical causes is not possible. the cause must be non-physical and eternal.  
3. That “being” must have existed without beginning, eternally, and be spiritual in nature. This being, we call God.
 
1. Something cannot come into existence from absolutely nothing.
2. The universe had a beginning, therefore, it had a cause. So the existence of the universe depends on the existence of that cause.
3. The present moment cannot be reached by adding individual events together from eternity.
4. The second law of thermodynamics refutes the hypothesis of an eternal universe.
5. Therefore an eternal & necessary first cause is the best explanation of our existence.
6. An agent endowed with free will can have a determination in a timeless dimension to operate causally at a (first) moment of time and thereby to produce a temporally first effect.


1. Contingent or non-necessary beings depend on an external cause that made them come into existence - the physical universe – is also contingent.
2. Since that external cause has to be outside the whole aggregate of contingent things, it cannot itself be contingent. So it is necessary.
3. Hey presto, we’ve demonstrated that there is a necessarily existent, uncreated, non-contingent being which causes all other things! And this, of course, is God.

1. Since the physical universe came into existence at a finite time ago, the cause must be non-physical.
2. Another term for the “non-physical” would be “spirit.”
3. Therefore, that “something” must have existed eternally, and be and spiritual in nature. This being, we call God.

The Thomistic Cosmological Argument
1. There are dependent beings.
2. If something is a dependent being, then its continued existence must be sustained by something else.
3. If a dependent being is sustained by something else, then either the chain of sustained beings regresses infinitely or terminates in an independent being that is not itself sustained.
4. The chain of sustained beings cannot regress infinitely.
5. Therefore, the chain of sustained beings must terminate in an independent being that is not itself sustained.

1. The universe is either eternal, or it had a beginning. Most probably it had a beginning, based on philosophical and scientific considerations. 
2. Everything which has a beginning has a cause.
3. Therefore, the Universe had a cause.

1. Contingent (dependent) beings exist.
2. Contingent beings require a necessary, self-existent being in order to exist.
3. Therefore, an eternal, non-created, self-existent being must exist ( modus ponens: The rule of logic stating that if a conditional statement (“if p then q ”) is accepted, and the antecedent ( p ) holds, then the consequent ( q ) may be inferred. ) Dependent beings cannot exist independently.
https://www.youtube.com/watch?v=FPCzEP0oD7I&t=8s

Properties of the first cause:
Dependent beings cannot exist independently. Since the universe had a beginning, it is dependent on an external necessary cause.  Aquinas showed us that the attributes of a true God are logically deduced. Properties of the first cause:

1. Supernatural in nature, (As it exists outside and beyond of the natural physical universe),
2. Uncaused, beginningless, and eternal (self-existent, as it exists without a cause, outside of time and space, besides the fact that infinite regress of causes is impossible. ),
3. Omnipresent & all-knowing (It created space and is not limited by it),
4. Changeless ( Change depends on physical being )
5. Timeless ( Without physical events, there can be no time, and time began with the Big Bang )
6. Immaterial (Because He transcends space and created matter),
7. Spaceless ( Since it created space)
8. Personal (The impersonal can’t create personality, and only a personal, free agent can cause a change from a changeless state )
9. Enormously Powerful ( Since it brought the entire universe, space-time and matter into existence )
10. Necessary (As everything else depends on it),
11. Absolutely independent and self-existent ( It does not depend on a higher causal agency to exist otherwise there would be infinite regress which is impossible )
12. Infinite and singular (As you cannot have two infinities),
13. Diverse yet has unity (As all multiplicity implies a prior singularity),
14. Intelligent (Supremely, to create everything, in special language, complexity, factories and machines),
15. Purposeful (As it deliberately created everything with goals in mind),

An agent endowed with free will can have a determination in a timeless dimension to operate causally at a (first) moment of time and thereby to produce a temporally first effect

1. God is supernatural in nature Acts 17:24-25
2. God is uncaused, beginningless, and eternal 1 Timothy 1:17
3. God is omnipresent & all-knowing Psalm 139:7-12; Jeremiah 23:24
4. God is unchanging Malachi 3:6
5. God is immaterial (spirit) John 4:24
6. God is personal John 4:24, 1 Thessalonians 5:18, Isaiah 25:1, Isaiah 63:7, Psalm 78:1, 1 Chronicles 16:8, Micah 4:12, Job 29:4, 2 Corinthians 13:14
7. God is enormously Powerful Genesis 17:1
8. God is timeless Revelation 1:8
9. God is necessary Genesis 1:1
10. God is omniscient ( All-knowing ) Psalm 147:4-5
11. God is absolutely independent and self-existent Isaiah 46:9
12. God is One, yet He exists in three persons Matthew 3:16-17
13. God is extraordinarily intelligent Jeremiah 32:17
14. God is all-understanding Psalm 147:5
15. God is purposeful

https://www.youtube.com/watch?v=FPCzEP0oD7I&t=8s


Laws of physics:

1. The Laws of physics are like the computer software, driving the physical universe, which corresponds to the hardware. All the known fundamental laws of physics are expressed in terms of differentiable functions defined over the set of real or complex numbers. The properties of the physical universe depend in an obvious way on the laws of physics, but the basic laws themselves depend not one iota on what happens in the physical universe.There is thus a fundamental asymmetry: the states of the world are affected by the laws, but the laws are completely unaffected by the states. Einstein was a physicist and he believed that math is invented, not discovered. His sharpest statement on this is his declaration that “the series of integers is obviously an invention of the human mind, a self-created tool which simplifies the ordering of certain sensory experiences.” All concepts, even those closest to experience, are from the point of view of logic freely chosen posits. . .
2. The laws of physics are immutable: absolute, perfect mathematical relationships, infinitely precise in form. The laws were imprinted on the universe at the moment of creation, i.e. at the big bang, and have since remained fixed in both space and time. 
3. The ultimate source of the laws transcend the universe itself, i.e. to lie beyond the physical world. The only rational inference is that the physical laws emanate from the mind of God. 
 https://arxiv.org/pdf/math/0302333.pdf


1. The laws of physics are immutable: absolute, eternal, perfect mathematical relationships, infinitely precise in form.
2. The laws were imprinted on the universe at the moment of creation, i.e. at the big bang, and have since remained fixed in both space and time.
3. The ultimate source of the laws transcend the universe itself, i.e. to lie beyond the physical world.
1. The universe obeys laws and rules of mathematics and physics, a specific set of equations, upon which it operates with stability, Constance and regularity.
2. The implementation of laws of mathematics and physics depends on the action of an intelligent rational agency.
3. Therefore, the physical universe which operates in an interdependent manner with the laws of physics was with high certainty implemented by an intelligent creator. 

1. The universe obeys laws and rules of mathematics and physics, a specific set of equations, upon which it can exist and operate. That includes Newtonian Gravity of point particles, General Relativity and Quantum Field Theory. Everything in the universe is part of a mathematical structure. All matter is made up of particles, which have properties such as charge and spin, but these properties are purely mathematical.
2. The implementation of laws of mathematics and physics depends on the action of an intelligent rational agency.
3. Therefore, most probably, an intelligent creator of the universe exists.

1. Physical laws are descriptive of what has never been observed. But there is no particular reason or physical necessity for why they are the way they are, and making a life-permitting universe possible. In fact, these sets could take any value, and be different.
2. The explanation of why the universe obeys in specific these life-permitting laws and set of equations can be due to either the existence of an infinite set of laws in an infinite number of universes, each obeying a different set of physical laws, which are not life-permitting, or the set-up by a powerful intelligent creator.
3. Multiverses are undetectable and unobservable, and there is no evidence of their existence. Furthermore, it would take  10^123 attempts to fine-tune the cosmological constant, to have a universe, either life permitting, or non-life permitting. There are about 10^80 atoms in the known universe. And either our universe or a set of multiverses had to have a beginning, so a cause cannot be avoided.  So the multiverse proposal is not only entirely unscientific but disregarding Occam's razor, where the least speculation is usually better.

1. The physical universe is governed by physical laws. Both are interdependent and irreducible. There would not be one without the other.
2. Laws and require a lawgiver. And interdependent systems a creator
3. Therefore, nature, the laws of nature, and their interdependence require a creator.

The argument of the supervision of order
1. We find in nature many laws like the law of gravitation, the laws of motion, the laws of thermodynamics.
2. Just as in any state, the government or the king makes different laws and supervises their subjects that the laws are carried out, so the laws of nature had to be generated and supervised by some intelligent being.
3. So, for everything that happens according to those laws there has to be a supervisor or controller.
4. Man can create small laws and control limited things in his domain, but nature’s grand laws had to be created by a big brain, an extraordinarily powerful person who can supervise that those laws are carried out.
5. Such an extraordinary, omnipotent person can be only God.
6. Hence, God exists.


1. The laws of physics are immutable: absolute, eternal, perfect mathematical relationships, infinitely precise in form.
2. The laws were imprinted on the universe at the moment of creation, i.e. at the big bang, and have since remained fixed in both space and time.
3. The ultimate source of the laws transcend the universe itself, i.e. to lie beyond the physical world.
4. Laws and mathematical formulas objectively, exist, and originate in the mind of conscious intelligent beings.
5. Therefore, the physical laws that govern the universe came from God.

1. Laws and mathematical formulas objectively, exist and originate in the mind of conscious intelligent beings.
2. The physical laws that govern the physical universe therefore had to emerge from a mind.
3. That was Gods mind.


1.  The laws of physics and cosmological parameters are finely tuned to the extreme to permit life.  
2.  The fine-tuning of the universe is either due to chance, physical necessity, or intelligent design.
3.  This fine-tuning is too improbable to be due to chance, and there was no physical necessity or constraint to permit only the parameters that actually exist.
4.  Therefore, the fine-tuning is most likely due to intelligent design.

The argument of the supervision of order
1. We find in nature many laws like the law of gravitation, the laws of motion, the laws of thermodynamics.
2. Just as in any state, the government or the king makes different laws and supervises their subjects that the laws are carried out, so the laws of nature had to be generated and supervised by some intelligent being.
3. So, for everything that happens according to those laws there has to be a supervisor or controller.
4. Man can create small laws and control limited things in his domain, but nature’s grand laws had to be created by a big brain, an extraordinarily powerful person who can supervise that those laws are carried out.
5. Such an extraordinary, omnipotent person can be only God.
6. Hence, God exists.

Fine-tuning arguments

1. Either we are the product of a fortituous extremely unlikely accident, or the product of an intelligent agent with foresight, which knew beforehand how to finetune the laws of nature, the constants of physics, and the initial conditions of the universe.
2. Finetuning is extremely unlikely due to the selection amongst an infinite pool of options.
3. Therefore, it is most probably due to a unimaginably brilliant and infinitely intelligent, powerful creator which did set up the universe in the most precise exact fashion to permit life on earth.

1. The initial conditions of the universe, subatomic particles, the Big Bang, the fundamental forces of the universe, the Solar System, the earth and the moon, are finely tuned to permit life. Over 150 fine-tuning parameters are known.
2. Finetuning is either due to chance, necessity or design.
3. Finetuning is extremely unlikely due to chance or necessity. Therefore, it is most probably due to a powerful creator which did set up the universe in the most precise exact fashion to permit life on earth.

How is a worldview without a necessary cause rational?

1. Contingent (dependent) beings exist.
2. Contingent beings require a necessary, self-existent being in order to exist.
3. Therefore, an eternal, non-created, self-existent being must exist ( modus ponens: The rule of logic stating that if a conditional statement (“if p then q ”) is accepted, and the antecedent ( p ) holds, then the consequent ( q ) may be inferred. 



Last edited by Otangelo on Thu Jan 07, 2021 12:13 pm; edited 13 times in total

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3Syllogistic - Arguments of Gods existence based on positive evidence Empty Origin of life arguments Fri Nov 27, 2020 8:36 am

Otangelo


Admin
Origin of life arguments

1. Either life is due to natural processes, or intelligent design.
2. Life is not due to natural processes,
3. Therefore it is due to intelligent design.

The lack of prebiotic natural selection: A big problem for unguided origin of life narratives
1. Life requires the use of a limited set of complex biomolecules, a universal convention and unity which is composed of the four basic building blocks of life ( RNA and DNA's, amino acids, phospholipids, and carbohydrates). They are of a very specific complex functional composition and made by cells in extremely sophisticated orchestrated metabolic pathways, which were not extant on the early earth. If abiogenesis were true, these biomolecules had to be prebiotically available and naturally occurring (in non enzyme-catalyzed ways by natural means ) and then somehow join in an organized way and form the first living cells. They had to be available in big quantities, and concentrated at one specific building site. 
2. Making things for a specific purpose, for a distant goal, requires goaldirectedness. And that's a big problem for naturalistic explanations of the origin of life. There was a potentially unlimited variety of molecules on the prebiotic earth. Competition and selection among them would never have occurred at all, to promote a separation of those molecules that are used in life, from those that are useless. Selection is a scope and powerless mechanism  to explain all the living order, and even the ability to maintain order in the short term, and to explain the emergence, overall organization, and long-term persistence of life from non-living precursors. It is an error of false conceptual reduction to suppose that competition and selection  will thereby be the source of explanation for all relevant forms of the living order.
3. We know that a) unguided random purposeless events are unlikely to the extreme to make specific purposeful elementary components to build large integrated macromolecular systems, and b) intelligence has goal-directedness. Bricks do not form from clay by themselves, and then line up to make walls. Someone made them. Phospholipids do not form from glycerol, a phosphate group, and two fatty acid chains by themselves, and line up to make cell membranes. Someone made them. That is God.


No experimental evidence has led to the re-creation of life
1. Origin of life research during over half a century has demonstrated that the prebiotic origin of the four classes of the basic building blocks of life by random, unguided processes, and consequently, living self-replicating cells, is not possible. 
2. Eliminative inductions argue for the truth of a proposition by demonstrating that competitors to that proposition are false. Either the origin of the basic building blocks of life and self-replicating cells are the result of the creative act by an intelligent designer, or the result of unguided random chemical reactions on the early earth.
3. Science, rather than coming closer to demonstrate how life could have started, has not advanced and is further away to generating living cells starting with small molecules.  Therefore, most likely, cells were created by an intelligent designer.

1. On the one side, we have the putative prebiotic soup with the random chaotic floating around of the basic building blocks of life, and on the other side, the first living self-replicating cell ( LUCA ), a supposed fully operational minimal self-replicating cell, using the highly specific and sophisticated molecular milieu with a large team of enzymes which catalyze the reactions to produce the four basic building blocks of life in a cooperative manner, and furthermore, able to maintain intracellular homeostasis, reproduce, obtaining energy and converting it into a usable form, getting rid of toxic waste, protecting itself from dangers of the environment, doing the cellular repair, and communicate.
2. The science paper: Structural analyses of a hypothetical minimal metabolism proposes a minimal number of 50 enzymatic steps catalyzed by the associated encoded proteins. They don't, however, include the steps to synthesize the 20 amino acids required in life. Including those, the minimal metabolome would consist of 221 enzymes & proteins. A large number of molecular machines, co-factors, scaffold proteins, and chaperones are not included, required to build this highly sophisticated chemical factory.
3. There simply no feasible viable prebiotic route to go from a random prebiotic soup to this minimal proteome to kick-start metabolism by unguided means. This is not a conclusion by ignorance & incredulity, but it is reasonable to be skeptic, that this irreducibly complex biological system, entire factory complexes composed of myriads of interconnected highly optimized production lines, full of computers and robots could emerge naturally defying known and reasonable principles of the limited range of random unguided events and physical necessity. Comparing the two competing hypotheses, chance vs intelligent design, the second is simply by far the more case-adequate & reasonable explanation.

The Classical Teleological Argument
1. The essential parts of a living cell cohere only because they have a function such as membrane proteins ( factory portals ), DNA hardware ), the genetic code and instructional complex information stored in DNA (software),  RNA polymerase information retrieval/encoding )  messenger RNA transmission ) Ribosome ( translation/decoding ) proteins complex machines )  dynein, kinesin taxis ) tubulins molecular highways )  mitochondria ( power generating plants ) ATP synthase ( power turbines ) the metabolic network ( electric circuits  and so on, which are found forming an integrated interdependent system because they make it possible together for the cell to self-replicate, adapt, and remain alive.
2. Whenever there are things that cohere only because of a purpose or function (for example, all the complicated parts of a watch that allow it to keep time), we know that they had a designer who designed them with the function in mind; they are too improbable to have arisen by random physical processes. (A hurricane blowing through a junk yard could not assemble a 747.)
3. These chemicals, building blocks, and macromolecules must have a designer who designed them with their function in mind: just as a watch implies a watchmaker, a machine implies a machine designer. Living cells were not created by human designers. Therefore, living cells must have had a non-human intelligent designer

1. The essential parts of a living cell cohere to a functional whole. They are found to form an integrated complex system because they make it possible together for the cell to self-replicate, adapt, and remain aliveThere is an organizational structure between the domain of specified complex information that cleverly directs the making of all functional parts and controls molecular mechanical dynamics and self-replication.
2. Whenever there are things that cohere only because of a purpose or function (for example, all the complicated parts of a watch that allow it to keep time), we know that they had a designer who designed them with the function in mind; they are too improbable to have arisen by random physical processes. (A hurricane blowing through a hardware store could not assemble a watch.)
3. The functional organization which makes chemicals, building blocks, and macromolecules must have a designer who designed the system with the function in mind: just as a watch implies a watchmaker, a machine implies a machine designer, and a factory, a factory maker. Living cell factories full of machines made through the instructional genetic information was not created by human designers. Therefore, living cells must have had a non-human intelligent designer

1. The synthesis of proteins and nucleic acids from small molecule precursors, and the formation of amide bonds without the assistance of enzymes represents one of the most difficult challenges to the model of pre-vital ( chemical) evolution, and for theories of the origin of life.
2. The best one can hope for from such a scenario is a racemic polymer of proteinous and non-proteinous amino acids with no relevance to living systems.
3. Polymerization is a reaction in which water is a product. Thus it will only be favored in the absence of water. The presence of precursors in an ocean of water favors depolymerization of any molecules that might be formed.
4. Even if there were billions of simultaneous trials as the billions of building block molecules interacted in the oceans, or on the thousands of kilometers of shorelines that could provide catalytic surfaces or templates, even if, as is claimed, there was no oxygen in the prebiotic earth, then there would be no protection from UV light, which would destroy and disintegrate prebiotic organic compounds. Secondly, even if there would be a sequence, producing a functional folding protein, by itself, if not inserted in a functional way in the cell, it would absolutely no function. It would just lay around, and then soon disintegrate. Furthermore, in modern cells proteins are tagged and transported on molecular highways to their precise destination, where they are utilized. Obviously, all this was not extant on the early earth.
5. To form a chain, it is necessary to react bifunctional monomers, that is, molecules with two functional groups so they combine with two others. If a unifunctional monomer (with only one functional group) reacts with the end of the chain, the chain can grow no further at this end. If only a small fraction of unifunctional molecules were present, long polymers could not form. But all ‘prebiotic simulation’ experiments produce at least three times more unifunctional molecules than bifunctional molecules.



Last edited by Otangelo on Tue Jan 26, 2021 9:30 am; edited 4 times in total

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Otangelo


Admin
The origin of instructional complex Information & codes 

The argument of the information transmission system in the cell
1. In cells, information is stored in the genome through the genetic code. The genetic code is a set of rules, stored in sequences of (DNA) nucleotide triplets called codons ( words). It directs the making of amino acid polypeptide sequences, which are the basic components of proteins ( the molecular machines, the working horses of the cell ). The genetic information is transmitted by over 25 extremely complex interconnected and interdependent molecular machines. This communication system encodes, sends, and decodes genetic texts, which requires as well error check and repair mechanisms along the way to maintain low genetic mutation rate, and minimizing replication, transcription, and translation errors, and permit organisms to pass accurately genetic information to their offspring, and survive. This system had to be set-up prior to when life began because it depends on it.
2. A code is a system of rules where a symbol, letters, words, or even sounds, gestures, or images, are assigned to something else. Transmitting information, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan. The genetic code can be described as a universal cipher, which assigns 61 codons (4x4x4=64-3 stop and start=64) to 20 amino acids.
3. Assigning the meaning of characters through a code system, where symbols of one language are assigned to symbols of another language that mean the same, requires a common agreement of meaning in order to establish communication, through encoding, sending, and decoding. Semantics, Synthax, and pragmatics are always set up by intelligence. The assignment of codons (triplet nucleotides) to amino acids is, therefore, best explained by the pre-established agreement of meaning by a mind. The origin of such complex communication systems is best explained by an intelligent designer.  
https://www.youtube.com/watch?v=X_tYrnv_o6A

Preprogrammed decision making of the gene regulatory network 
1. Cells continuously process a multitude of input signals to make decisions about their appropriate responses that lead to changes in gene expression, enzymatic activity, rewiring of their signaling networks, migration, growth, or division, as well as programmed cell death as the output information. In a computing device, the input information is mathematically processed into a digital signal. This signal is a code representation of the physical cues and assumes a sequence of discrete values. For instance, in the case of a binary code, the basic unit of information is denoted as a series of “0” and “1” digits. The binary digits indicate the two states of the logic circuit. A threshold is implemented to define the input and output range that can be categorized under each logic set. If the value is either lower or higher than the threshold, the state of the circuit is defined as either “0” or “1”, respectively. Digital circuits make extensive use of logic elements that are interconnected to create logic gates, capable of executing Boolean logic functions including NOT, OR, AND, and all their possible combinations
2. Molecular and biomolecular logic gates and their networks process chemical input signals similar to human-made computers. The similarities in the processing of information by biological systems and human-designed devices are broadly recognized by many researchers.
3. Decision making is either a) something performed directly by intelligence, or b) programmed by intelligence to be performed by machines, like computers. It has never been observed, that unguided, evolutionary mechanisms could produce a decision making machine with the purpose to generate specific outcomes further ahead. Foresight is a quality exclusively performed by intelligence.  If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself. A metaphor (“A biological cell is like a production system”) demonstrates that similar behaviors are driven by similar causal mechanisms.
4. Therefore, the decision-making process observed in the cell is most probably the result of divine superintelligent design.

Chance to find a message written on a cloud in the sky: "Jesus loves you" randomly,  is as DNA creating its own software, and upon it, writing a complex algorithm to make a protein by accident.

The chance to find a message written on a cloud in the sky: "Jesus loves you" randomly,  is the same as DNA nucleotides creating their own software code, and upon it, writing an instructional complex algorithm to make a protein by a random accident.

Intelligence can and does describe reality, and objects in the real world. That's descriptive information. But intelligence also structures, organizes, forms, transforms, creates emergent properties, controls, and orders reality. It does so, using prescriptive instructional, complex information. That is a quality of power - exclusive to intelligence.

1. The pattern in DNA is a code.
2. All codes we know the origin of com from a intelligent mind
3. Therefore we have 100% inference that DNA comes from an intelligent mind and 0% inference that it is not.

1. DNA stores coded information. 
2. All codes come from intelligence. 
3. Therefore, DNA comes from a mind.

1. Symbols are defined as: something which represents something else.
2. Symbols carry thoughts (or messages) from a personal, intelligent, mind. No exceptions.
3. Scientific inquiry has discovered that DNA carries encoded symbolic instructions.

1: RNA Building Blocks Are Hard to Synthesize and Easy to Destroy
2: Ribozymes Are Poor Substitutes for Proteins
3: An RNA-based Translation and Coding System Is Implausible
4: The RNA World Doesn’t Explain the Origin of Genetic Information

1. A transistor can be considered an artificial Neuron. Every living cell within us is a hybrid analog–digital supercomputer. The brain is like 100 billion computers working together.
2. Biological cells are programmed to be experts at taking inputs, running them through a complicated series of logic gates through circuit-like operations and producing the desired programmed output.
3. The origin of programs, logic gates, and complex circuits to obtain a purposeful specific outcome is always tracked back to intelligent implementation.

The origin of the genetic information

1.The information stored in DNA is a template. It is equal to a recipe or program. Nucleic acids contain information in a semantic (meaningful) sense. Instructing consists in an advance specification of the kind and order of steps yielding a certain outcome if the steps are carried out. The amino acid arrangement and sequence to make functional proteins is the product of the information stored in DNA. 
2. Recipes and programs do not just bring about a particular outcome; they are designed to do so. They are usually formulated with a purpose. The computer program output is the result of executing a pre-specified series of operations.  A purely physical description does not capture the instructional nature of the process. Instructional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process. This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry... it is never going to happen!  Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind.
3. Therefore, the instructional information stored in DNA comes most likely from an intelligent designer. 

The Law of information
1. Anything material such as physical/chemical processes cannot create something non-material
2. Information is a non-material fundamental entity and not a property of matter
3. Information requires an material medium for storage and transmission
4. Information cannot arise fRom Statistical processes
5. There can be no information without a code ie. No knowledge can be shared without a code
6. All codes result from an intentional choice and agreement between sender and recipient
7. The determination of meaning for and from a set of symbols is a mental process that requires intelligence
8. There can be no new information without an intelligent purposeful sender
9. Any given chain of information can be traced back to an intelligent source
10. Information comprises the non-material foundation for all
a. Technological systems
b. Works of art
c. Biological systems
Therefore:
A. since the DNA code of all life is clearly within the definition domain of information, we can conclude there must be a sender.
B. Since the density and complexity of the DNA encoded information is billions of times greater than man's present technology , we conclude that the sender must be extremely intelligent
C. Since the sender must have
- encoded (stored) the information into the DNA molecules
- Constructed the molecular biomachines required for the encoding, decoding, and synthesizing process and
- Designed all the features for the original life forms
it can be concluded that:
- the sender must be purposeful and supremely powerful and must have a non-material component
- Since information is a non-material fundamental entity and cannot originate from material quantities, and since information also originates from man then mans nature must have a non-material component or SPIRIT.
- then the assumption that the Universe is comprised solely of mass and energy is false
- Since biological information originates only from an intelligent sender and all theories of chemical and biological evolution require that information must originate solely from mass and energy alone (without a sender) then al, theories or concepts of biological evolution is false.
- Just 2mm of a DNA strand contains as much information as 100 million 40GB hard drives, think about that a little, do you really think that is the result of pure Undirected random natural processes?

Prescriptive vs Descriptive Information
1. Intelligence can and does describe reality, and objects in the real world. That's descriptive information.
2. But intelligence also structures, organizes, controls, and orders reality. That's using prescriptive information.
3. That is a quality of power - exclusive to intelligence.

Prescriptive information is non-physical, and comes always from a mind
1. Genetic and epigenetic information is characterized containing prescriptive codified information, which result in functional outcomes due to the right particular specified complex sequence, the proper order of triplet codons and ultimately the translated sequencing of amino acid building blocks into protein strings, and highly specific regulatory micro RNAs and other epigenetic factors.
2. Algorithms, prescribing functional instructions, digital programming, using symbols and coding systems are abstract and non-physical and originate always from thought—from conscious or intelligent activity.
3. Therefore, genetic and epigenetic information comes from an intelligent mind. Since there was no human mind present to create life, it must have been a supernatural agency.

Information is not physical
1. Life is a software/information-driven process.
2. Information is not physical it is conceptual.
3. The only known source of semiotic information is intelligence.
4. Life is therefore the direct product of a deliberate creative intellectual processes.

Languages, Software, and Information come always from intelligent minds
1. DNA stores instructional complex information to assemble proteins using the software "language" of the genetic code, a set of rules, where the meaning of 64 trinucleotide codons (words) are assigned to 20 amino acids.  
2. That DNA could create its own software language, and upon it, writing a complex algorithm, prescriptive information, and a translation system to make a protein by accident, is as well, nil. 
3. That is similar to find a message written on a cloud in the sky: "Jesus loves you" randomly. It is extremely unlikely, basically zero. We only know of intelligence producing codified language, and upon it, writing messages, and producing prescriptive information.
4. Therefore, most likely, the genetic code, and upon it, the storage of prescribed, functional, instructional complex information is of intelligent origin. That intelligence is God. 

Genetic and epigenetic information comes always from a mind
1. Genetic and epigenetic information is characterized containing prescriptive codified information, which result in functional outcomes due to the right particular specified complex sequence of triplet codons and ultimately the translated sequencing of amino acid building blocks into protein strings.  The sequencing of nucleotides in DNA also prescribes highly specific regulatory micro RNAs and other epigenetic factors.
2. Algorithms, prescribing functional instructions, digital programming, using symbols and coding systems are abstract and non-physical, and originate always from thought—from conscious or intelligent activity. 
3. Therefore, genetic and epigenetic information comes from an intelligent mind. Since there was no human mind present to create life, it must have been a supernatural agency. 

Conceptual Information has always mental origin
1.Life depends on vast quantity of semiotic information. 
2.Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process. This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry... it is never going to happen!  Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind.
3. Life is no accident, and provides powerful positive evidence that we have been designed. A scientist working at the cutting edge of our understanding of the programming information in biology, he described what he saw as an “alien technology written by an engineer a million times smarter than us”

The argument of fast communciation networks
1. The more sophisticated and fast a Information transmission
systems is, the more intelligence is required to project and
implement it .
2. Light-fidelity, or Li-Fi, is a 5th generation cutting edge technology,
the fastest information transmission system so far invented by man.
3. Life uses not only light, but quantum entanglement to transmit
information, which occurs basically instantly.
4. It is logical, therefore, to infer a super-intelligent agency created
lifes awesome high-speed internet on a molecular level.

The irreducible interdependence of information generation and transmission systems
1. Codified information transmission system depends on: 
a) A language where a symbol, letters, words, waves or frequency variations, sounds, pulses, or a combination of those are assigned to something else. Assigning meaning of characters through a code system requires a common agreement of meaning. Statistics, Semantics, Synthax, and Pragmatics are used according to combinatorial, context-dependent, and content-coherent rules. 
b) An information storage system, 
c) Information encoded through that code,
d) An information transmission system, that is encoding, transmitting, and decoding.
e) Eventually translation ( the assignment of the meaning of one language to another )
f)  Eventually conversion ( digital-analog conversion, modulators, amplifiers)
g) Eventually transduction converting the nonelectrical signals into electrical signals
2. In living cells, information is encoded through at least 30 genetic, and almost 30 epigenetic codes that form various sets of rules and languages. They are transmitted through a variety of means, that is the cell cilia as the center of communication, microRNA's influencing cell function, the nervous system, the system synaptic transmission, neuromuscular transmission, transmission b/w nerves & body cells, axons as wires, the transmission of electrical impulses by nerves between brain & receptor/target cells, vesicles, exosomes, platelets, hormones, biophotons, biomagnetism, cytokines and chemokines, elaborate communication channels related to the defense of microbe attacks, nuclei as modulators-amplifiers. These information transmission systems are essential for keeping all biological functions, that is organismal growth and development, metabolism, regulating nutrition demands, controlling reproduction, homeostasis, constructing biological architecture, complexity, form, controlling organismal adaptation, change,  regeneration/repair, and promoting survival. 
3. The origin of such complex communication systems is best explained by an intelligent designer. Since no humans were involved in creating these complex computing systems, a suprahuman super-intelligent agency must have been the creator of the communication systems used in life. 

The software and hardware of the cell are irreducibly complex
1. The cell contains a complex information storage medium through DNA.
2. The cell has a complex information processing system ( through  RNA polymerase, transcription factors, a spliceosome, a  ribosome,  chaperone enzymes, specialized transport proteins, and ATP
3. The cell contains a genetic code that is at or very close to a global optimum for error minimization across plausible parameter space
4. The cell stores complex, specified, coded information ( the software )
5. The cell has a complex translation system through a universal cipher, which assigns 61 codons (4x4x4=64-3 stop and start=64) to 20 amino acids and permits the translation of the genetic code into functional proteins
6. This constitutes a logical structure of information processing: DNA>>RNA>>>Protein, based on software and hardware. Both aspects must be explained.
7. There is no reason for information processing machinery to exist without the software, and vice versa.
8. Systems of interconnected software and hardware are irreducibly complex.
9. A irreducible complex system can not arise in a stepwise, evolutionary manner.
10. Only minds are capable to conceptualise and implement  instructional information control systems transformed into molecular dynamics
11. Therefore, an intelligent designer exists.

1. The cell coordinates its functions by virtue of a ‘genetic program’ encoded in the DNA that directs and controls the expression of a specific set of RNAs and proteins, which assemble deterministically into stable ‘molecular machines’ that reliably and efficiently execute predetermined operations according to the mechanisms of cell division, endocytosis, signal transduction, etc.
2. This is analogous to engineers, which produce blueprints, which prescribe and instruct the making and assembly of machines for specific purposes. 
3. Herschel 1830 1987, p. 148: “If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.” A metaphor (“A biological cell is like a production system”) demonstrates that similar behaviors are driven by similar causal mechanisms.
4. Since there was no human mind present when life started, we can conclude that a nonhuman higher intelligent agency must have created life. 


The origin of the genetic code

1.DNA is not merely a molecule with a pattern; it is a information storage mechanism, using the genetic code.
2.All codes we know the origin of are created by a conscious mind.  
3.Therefore DNA was designed by a mind, and language and information are proof of the action of a Superintelligence.
http://evo2.org/read-prove-god-exists/

Codes have always a mental origin
1. In cells, the genetic code assigns 61 codons and 3 start/stop codons to 20 amino acids, using the Ribosome as a translation mechanism.
2. All codes require arbitrary values being assigned and determined to represent something else.
3. All codes require a translation mechanism, adapter, key, or process of some kind to exist prior to translation
4. Foreknowledge is required both, a) to get a functional outcome through the information system, and b) to set up the entire system.
5. Therefore, translation directing the making of proteins used in life was most probably designed.

Codes come always from intelligence
1. In cells,  the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
2. A code is a system of rules where a symbol, letters, words, etc. are assigned to something else. Transmitting information, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan. That requires a common agreement of meaning. 
3. Therefore, the triplet codons (triplet nucleotides) to amino acids must be pre-established by a mind. The origin of the genetic code is best explained by an intelligent designer.  

The Genetic Code was most likely implemented by intelligence.
1. In communications and information processing, code is a system of rules to convert information—such as assigning the meaning of a letter, word, into another form, ( as another word, letter, etc. ) 
2. In translation, 64 genetic codons are assigned to 20 amino acids. It refers to the assignment of the codons to the amino acids, thus being the cornerstone template underling the translation process.
3. Assignment means designating, dictating, ascribing, corresponding, correlating, specifying, representing, determining, mapping, permutating.    
4. The universal triple-nucleotide genetic code can be the result either of a) a random selection through evolution, or b) the result of intelligent implementation.
5. We know by experience, that performing value assignment and codification is always a process of intelligence with an intended result. Non-intelligence, aka matter, molecules, nucleotides, etc. have never demonstrated to be able to generate codes, and have neither intent nor distant goals with a foresight to produce specific outcomes.  
6. Therefore, the genetic code is the result of an intelligent setup.

The argument of the origin of codes
1. In cells, information is encoded through the genetic code which is a set of rules, stored in DNA sequences of nucleotide triplets called codons. The information distributed along a strand of DNA is biologically relevant. In computerspeak, genetic data are semantic data. Consider the way in which the four bases A, G, C, and T are arranged in DNA. As explained, these sequences are like letters in an alphabet, and the letters may spell out, in code, the instructions for making proteins. A different sequence of letters would almost certainly be biologically useless. Only a very tiny fraction of all possible sequences spell out a biologically meaningful message. Codons are used to translate genetic information into amino acid polypeptide sequences, which make proteins ( the molecular machines, the working horses of the cell ). And so, the information which is sent through the system, as well as the communication channels that permit encoding, sending, and decoding, which in life is done by over 25 extremely complex molecular machine systems, which do as well error check and repair to maintain genetic stability, and minimizing replication, transcription and translation errors, and permit organisms to pass accurately genetic information to their offspring, and survive. This system had to be set-up prior to life began because life depends on it.
2. A code is a system of rules where a symbol, letters, words, or even sounds, gestures, or images, are assigned to something else. Translating information through a key, code, or cipher, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan.
3. Intelligent design is the most case-adequate explanation for the origin of the sequence-specific digital information (the genetic text) necessary to produce a minimal proteome to kick-start life. The assembly information stored in genes, and the assignment of codons (triplet nucleotides) to amino acids must be pre-established by a mind. Assignment which means designating, ascribing, corresponding, or correlating meaning of characters through a code system, where symbols of one language are assigned to symbols of another language that mean the same, requires a common agreement of meaning in order to establish communication, trough encoding, sending, and decoding. Semantics, Syntax, and pragmatics are always set up by intelligence. The origin of such complex communication systems is best explained by an intelligent designer.

1. The origin of the genetic cipher 
1.Triplet codons must be assigned to amino acids to establish a genetic cipher.  Nucleic-acid bases and amino acids don’t recognize each other directly but have to deal via chemical intermediaries ( tRNA's and  Aminoacyl tRNA synthetase ), there is no obvious reason why particular triplets should go with particular amino acids.
2. Other translation assignments are conceivable, but whatever cipher is established, the right amino acids must be assigned to permit polypeptide chains, which fold to active functional proteins. Functional amino acid chains in sequence space are rare.  There are two possibilities to explain the correct assignment of the codons to the right amino acids. Chance, and design. Natural selection is not an option, since DNA replication is not set up at the stage prior to a self-replicating cell, but this assignment had to be established before.
3. If it were a lucky accident that happened by chance, luck would have hit the jackpot through trial and error amongst 1.5 × 10^84 possible genetic code tables. That is the number of atoms in the whole universe. That puts any real possibility of a chance of providing the feat out of question. Its, using  Borel's law, in the realm of impossibility. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that's universal. Put simply, the chemical lottery lacks the time necessary to find the universal genetic code. 
4. We have not even considered that there are also over 500 possible amino acids, which would have to be sorted out, to get only 20, and select all L amino and R sugar bases......
5. We know that minds do invent languages, codes, translation systems, ciphers, and complex, specified information all the time. 
6. Put it in other words: The task compares to invent two languages, two alphabets, and a translation system, and the information content of a book ( for example hamlet)  being created and written in English, and translated to Chinese, through the invention and application of an extremely sophisticated hardware system. 
7. The genetic code and its translation system are best explained through the action of an intelligent designer. 

The genetic piano
1. The work of the gene regulatory network “corresponds to a pianist playing a piece of music. Like keys on a piano, DNA is the blueprint to make the proteins that cells require. Epigenetic information provides dynamic, flexible instructions as to how, where, and when the information stored in DNA will be expressed.
2.  There must be an origin of the information required to produce function. Who’s the pianist and who’s the conductor?  The environment cannot be the director. Heredity cannot be the musician; it has no foresight to orchestrate the collection of processes organized into a meaningful, functional outcome.
3. Science is supposed to seek efficient and adequate causes, not just-so stories, or appeals to chance based on circular reasoning.  The alternative and the only explanation is therefore intelligent design with a known cause sufficient to produce functional instructional information: an intelligent agent.


The Wobble hypothesis points to an intelligent setup!
1. In translation, the wobble hypothesis is a set of four relationships. The first two bases in the codon create the coding specificity, for they form strong Watson-Crick base pairs and bond strongly to the anticodon of the tRNA.
2. When reading 5' to 3' the first nucleotide in the anticodon (which is on the tRNA and pairs with the last nucleotide of the codon on the mRNA) determines how many nucleotides the tRNA actually distinguishes.
If the first nucleotide in the anticodon is a C or an A, pairing is specific and acknowledges original Watson-Crick pairing, that is: only one specific codon can be paired to that tRNA. If the first nucleotide is U or G, the pairing is less specific and in fact, two bases can be interchangeably recognized by the tRNA. Inosine displays the true qualities of wobble, in that if that is the first nucleotide in the anticodon then any of three bases in the original codon can be matched with the tRNA.
3. Due to the specificity inherent in the first two nucleotides of the codon, if one amino acid is coded for by multiple anticodons and those anticodons differ in either the second or third position (first or second position in the codon) then a different tRNA is required for that anticodon.
4. The minimum requirement to satisfy all possible codons (61 excluding three stop codons) is 32 tRNAs. Which is 31 tRNAs for the amino acids and one initiation codon. Aside from the obvious necessity of wobble, that our bodies have a limited amount of tRNAs and wobble allows for broad specificity, wobble base pairs have been shown to facilitate many biological functions. This has another AMAZING implication which points to intelligent set up:  The science paper: The genetic code is one in a million, confesses: If we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.
5. This, all, by all means, screams out literally of intelligent DESIGN !!

1. First, it would seem that the early codons need have used only two bases (which could code for up to 16 amino acids); but a subsequent change to three bases (to accommodate 20) would seriously disrupt the code. Recognizing this difficulty, most researchers assume that the code used 3-base codons from the outset; which was remarkably fortuitous or implies some measure of foresight on the part of evolution (which, of course, is not allowed).
2. Much more serious are the implications for proteins based on a severely limited set of amino acids. In particular, if the code was limited to only a few amino acids, then it must be presumed that early activating enzymes comprised only that limited set of amino acids, and yet had the necessary level of specificity for reliable implementation of the code. There is no evidence of this; and subsequent reorganization of the enzymes as they made use of newly available amino acids would require highly improbable changes in their configuration. Similar limitations would apply to the protein components of the ribosomes which have an equally essential role in translation.
3. Further, tRNAs tend to have atypical bases which are synthesized in the usual way but subsequently modified. These modifications are carried out by enzymes, so these enzymes too would need to have started life based on a limited number of amino acids; or it has to be assumed that these modifications are later refinements - even though they appear to be necessary for reliable implementation of the code.
4. Finally, what is going to motivate the addition of new amino acids to the genetic code? They would have little if any utility until incorporated into proteins - but that will not happen until they are included in the genetic code. So the new amino acids must be synthesized and somehow incorporated into useful proteins (by enzymes that lack them), and all of the necessary machinery for including them in the code (dedicated tRNAs and activating enzymes) put in place – and all done opportunistically! Totally incredible!

https://evolutionunderthemicroscope.com/ool02.html


1. D
2. D -> A & B & C
3. A & B & C -> requires Intelligence
4. Therefore Intelligence

A: Information, Biosemiotics ( instructional complex mRNA codon sequences transcribed from DNA )
B: Translation mechanism ( adapter, key, or process of some kind to exist prior to translation = ribosome )
C: Genetic Code
D: Functional proteins

1. Life depends on proteins ( molecular machines ) (D). Their function depends on the correct arrangement of a specified complex sequence of amino acids.
2. That depends on the translation of genetic information (A) through the ribosome (B) and the genetic code (C), which assigns 61 codons and 3 start/stop codons to 20 amino acids
3. Instructional complex Information ( Biosemiotics: Semantics, Synthax, and pragmatics (A)) is only generated by intelligent beings with foresight. Only intelligence with foresight can conceptualize and instantiate complex machines with specific purposes, like translation using adapter keys (ribosome, tRNA, aminoacyl tRNA synthetases (B)) All codes require arbitrary values being assigned and determined by agency to represent something else ( genetic code (C)).
4. Therefore, Proteins being the product of semiotics/algorithmic information including translation through the genetic code, and the manufacturing system ( information directing manufacturing ) are most probably the product of a divine intelligent designer.


The problem of translation through the Ribosome is threefold:

1. The origin of Information stored in the genome.

1. Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process.
2. This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry... it is never going to happen!  Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind.
3. Since life depends on the vast quantity of semiotic information, life is no accident and provides powerful positive evidence that we have been designed. A scientist working at the cutting edge of our understanding of the programming information in biology, he described what he saw as an “alien technology written by an engineer a million times smarter than us”

2. The origin of the adapter, key, or process of some kind to exist prior to translation = ribosome

1. Ribosomes have the purpose to translate genetic information into proteins. According to Craig Venter, the ribosome is “an incredibly beautiful complex entity” which requires a minimum of 53 proteins. It is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products…  They are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They can halt the translation process on the fly, and coordinate extremely complex movements. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.
2. For the assembly of this protein-making factory, consisting of multiple parts, the following is required: genetic information to produce the ribosome assembly proteins, chaperones, all ribosome subunits, and assembly cofactors. a full set of tRNA's, a full set of aminoacyl tRNA synthetases, the signal recognition particle, elongation factors, mRNA, etc. The individual parts must be available,  precisely fit together, and assembly must be coordinated. A ribosome cannot perform its function unless all subparts are fully set up and interlocked. 
3. The making of a translation machine makes only sense if there is a source code, and information to be translated. Eugene Koonin: Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage is extremely difficult even within a speculative scheme let alone experimentally. Speaking of ribosomes, they are so well-structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working.  Design some machinery that behaves like this and I personally will build a temple to your name! Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. The origin of the ribosome is better explained through a brilliant intelligent and powerful designer, rather than mindless natural processes by chance, or/and evolution since we observe all the time minds capabilities producing machines and factories.

3. The origin of the genetic code

1. A code is a system of rules where a symbol, letters, words, etc. are assigned to something else. Transmitting information, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan.  In cells,  the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
2. Assigning meaning of characters through a code system, where symbols of one language are assigned to symbols of another language that mean the same, requires a common agreement of meaning. The assignment of triplet codons (triplet nucleotides) to amino acids must be pre-established by a mind.
3. Therefore, the origin of the genetic code is best explained by an intelligent designer. 



Last edited by Otangelo on Tue Feb 16, 2021 4:56 am; edited 47 times in total

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5Syllogistic - Arguments of Gods existence based on positive evidence Empty The Cell Fri Nov 27, 2020 8:38 am

Otangelo


Admin
The Cell

1. Making a cake needs a recipe (information) and the right ingredients (matter) and a stove (energy).
2. Living cells require a recipe (Instructional assembly information stored in DNA); the right building blocks (nucleotides, RNA and DNA, 20 amino acids, phospholipids and carbohydrates) and energy in the form of ATP.
3. Making the recipe, selecting and preparing the ingredients (in the right quantity), and generating energy always requires an intelligent source. Therefore, life requires an intelligent designer.

1. The cell has a sophisticated information-processing system. It is not only analogous to a man-made computer but operates literally as a computer.  
2. Computer programs require programmers, conscious agents with knowledge and foresight who can code the needed instructions, in the right sequence, to generate a functioning and information-rich program.
3. Since cells contain an information storage system (DNA), a code language ( the genetic code), and instructions encoded through the genetic code stored in DNA, and an information transmission system, that is 1. encoding ( transcription into messenger RNA (mRNA) through RNA polymerase enzyme catalysts ( transcription), 2.  sending ( mRNA), and 3. translation ( mRNA to amino acids through the Ribosome), all this requires a programmer. The programmer is with high probability an intelligent designer ( God ).

The Cells GPS system
Imagine a self-driving car. Even today, the programming of self-driving cars that are secure enough on the street are not market ready. The amount of information processing required to direct a car from A to B on a highway is monumental. And to develop a software which is able to direct cars autonomously is a truly an extraordinary feat, which has required up to know thousands of highly skilled software engineers to develop these software programs. But the program alone is not enough. The car itself must be interface compatible to interpret the information input from and direction from the program and transmit it to the wheels etc. Up to now, the human brain does what humans try to delegate to autonomous cars. 

1. The cell has sophisticated cargo loading, transport, and delivery systems. It is not only analogous to a man-made transport system but operates literally as such.
2. Cargo loading, transport, and delivery require specialists that operate and execute the delivery based on advanced planning, logistic software systems, GPS  Positioning Systems and information management, monitoring, and control systems.
3. Once proteins are synthesized, they are tagged through the signal transduction particle ( which is life-essential), carried on molecular cargo carriers ( dynein, and kinesin motor proteins ) on molecular highways ( tubulins), and delivered at the destination where the protein cargo will be employed for operation. 
4. The programming of all those steps requires with high probability of an intelligent programmer ( God).  
https://www.youtube.com/watch?v=wJyUtbn0O5Y

1. DNA stores information based on a code system, and codified, complex, instructional information, with the same function as a blueprint.  
2. All codes and blueprints come from intelligence.
3. Therefore, the genetic code and the instructions to build cells and complex biological organisms, stored in DNA, were most likely created by an intelligent agency.

1. Protein domains appear analogous to words in natural languages in which the rules of word association are dictated by linguistic rules or grammar.
2. The set up of words, languages, rules of association and linguistic rules, and grammar come always from intelligence
3. Therefore the set up of rules existing for protein domains is best explained by an intelligent designer

1. Cells use sophisticated information selection ( the Gene regulatory network ) encoding and transcription ( DNA & RNA polymerase machines ) transmission (mRNA), and decoding ( Ribosome ) systems.
2. Setup of information transmission systems, aka.  Selection, encoding, transmission, and decoding are always a deliberate act of intelligence
3. The existence of the genetic information transmission system is best explained by the implementation of an intelligent designer.    

1. Blueprints, instructional information, and master plans, and the make of complex machines and factories upon these are both always tracked back to an intelligent source which made both for purposeful, specific goals.
2. The Blueprint and instructional information stored in DNA, which directs the making of biological cells and organisms - the origin of both is, therefore, best explained by intelligent design.

1. Without information, the inflow of energy would not lead to self-organization. Information in this sense is more than information in the Shannon and Weaver (1949 ) sense; it is functional and can be thought of as information in both an “ instructional ” and “ control ” sense, as it requires information that creates complex structures — for example, enzymatic proteins — and metabolic pathways that productively channel the flow of energy both within an organism and between the latter and its environment.
2. Blueprints, instructional information, and master plans, which permit the autonomous self-organization and control of complex machines and factories upon these are both always tracked back to an intelligent source which made both for purposeful, specific goals.
3. The Blueprint and instructional information stored in DNA, together with epigenetic codified instructional information, which directs the make and controls biological cells and organisms - the origin of both is, therefore, best explained by intelligent design.

1. If information is immaterial, and non-random information requires an intelligent agent, then intelligent agents are required for a controlled process instruction. 
2. If coding and programming information is immaterial, and the medium it contains it is not relevant to its existence, then no undirected process can create it
3. If codes require intelligence to assign arbitrary values, and decoding requires equally arbitrarily assigned values, and the genetic code is encoded, transferred, and decoded, and gene expression requires translation of arbitrary values, then a mind was required for the genetic code to exist. 

1. Information processing systems require both, the hardware, and software, all at once since such things, by their very nature, work in direct synergy and thus cannot evolve bit by bit.
2. The genetic code and the genetic information together include features like semantic logic and the meaningful ordering of characters—things not dictated by any laws of physics, chemistry, or random fortuitous accidents.
3. The information processing system in living cells is therefore best explained by the (past) implementation of an intelligent designer.  

1. The Morse code was created by an intelligent mind, that of Samuel F.B. Morse. The barcode was invented by the brilliant Norman Joseph Woodland and the ASCII code by the visionary Robert Bemer. 
2. Codes always have code-makers.
3. Therefore, the genetic code had most probably a code-maker: God. 

The irreducible complexity of the cell
1. On the one side, we have the putative prebiotic soup with the random chaotic floating around of the basic building blocks of life, and on the other side,  the first living self-replicating cell ( LUCA ), a supposed fully operational minimal self-replicating cell, using the highly specific and sophisticated molecular milieu with a large team of enzymes which catalyze the reactions to produce the four basic building blocks of life in a cooperative manner, and furthermore, able to maintain intracellular homeostasis, reproduce, obtaining energy and converting it into a usable form, getting rid of toxic waste, protecting itself from dangers of the environment, doing the cellular repair, and communicate.  
2. The science paper: Structural analyses of a hypothetical minimal metabolism proposes a minimal number of 50 enzymatic steps catalyzed by the associated encoded proteins. They don't, however, include the steps to synthesize the 20 amino acids required in life. Including those, the minimal metabolome would consist of 221 enzymes & proteins. A large number of molecular machines, co-factors, scaffold proteins, and chaperones are not included, required to build this highly sophisticated chemical factory.
3. There is simply no feasible viable prebiotic route to go from a random prebiotic soup to this minimal proteome to kick-start metabolism by unguided means. This is not a conclusion by ignorance & incredulity, but it is reasonable to be skeptic, that this irreducibly complex biological system, entire factory complexes composed of myriads of interconnected highly optimized production lines, full of computers and robots could emerge naturally defying known and reasonable principles of the limited range of random unguided events and physical necessity. Comparing the two competing hypotheses, chance vs intelligent design, the second is simply by far the more case-adequate & reasonable explanation.

1. The essential parts of a living cell cohere only because they have a function such as membrane proteins ( factory portals ), DNA hardware ), the genetic code and instructional complex information stored in DNA (software),  RNA polymerase information retrieval/encoding )  messenger RNA transmission ) Ribosome ( translation/decoding ) proteins complex machines )  dynein, kinesin taxis ) tubulins molecular highways )  mitochondria ( power generating plants ) ATP synthase ( power turbines ) the metabolic network ( electric circuits  and so on, which are found forming an integrated interdependent system because they make it possible together for the cell to self-replicate, adapt, and remain alive.
2. Whenever there are things that cohere only because of a purpose or function (for example, all the complicated parts of a watch that allow it to keep time), we know that they had a designer who designed them with the function in mind; they are too improbable to have arisen by random physical processes. (A hurricane blowing through a junk yard could not assemble a 747.) It is extraordinarily unlikely, statistically, and chemically, that blind fortune would be up to the task.
3. Actions like engineering, architecting, orchestrating, organizing, programming, translating, setting up communication channels, electric networks, logistic networks, organizing modular systems, recycling systems, making power plants in nanoscale dimensions, product planning and control, establishing product quality and variant flexibility, setting up waste disposal and management systems, creating languages and instructional information, coordinating, setting up strategies, regulating, controlling, recruiting, interpreting and responding, setting up switch mechanisms based on logic gates, setting up transport highways and GPS systems, and controlled factory implosion, are ALWAYS and EXCLUSIVELY assigned to the action of intelligent agents. No exceptions. We see all those things being performed in living cells. 
4. We can conclude, therefore, that biological systems, which cleverly perform all the demanding, multifaceted job activities described above, are most likely due to the set up of an intelligent designer(s).  Only a master player with foresight guided by superb chemical wisdom, putting all those systems together in a proper way is an explanation that makes sense.These chemicals, building blocks, and macromolecules must have a designer who designed them with their function in mind: just as a watch implies a watchmaker, a machine implies a machine designer. Living cells were not created by human designers. Therefore, living cells must have had most likely a non-human intelligent designer



Last edited by Otangelo on Mon Feb 01, 2021 5:15 am; edited 4 times in total

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6Syllogistic - Arguments of Gods existence based on positive evidence Empty Cells are factories Fri Nov 27, 2020 8:38 am

Otangelo


Admin
Cells are factories

1. Cells are literally chemical nano-factories, that operate based on molecular machines, protein robots, kinesin protein carriers, autonomous self-regulated production lines, generate energy through turbines, have neuron transistors, and computers

2. Such things are always set up by intelligent designers
3. Therefore, most probably, Cell factories  are the product of an intelligent designer.

1. Cells host molecular machines, each with a specific purpose.
2. A machine made for specific purposes originates as a mental concept in the mind.
3. Therefore, they had to be conceptualized by an intelligent designer.

Blueprints, machines, and factories come only from Intelligence
1. Living Cells store very complex genetic and epigenetic information through the genetic code, and over fourty epigenetic languages. This information is transmitted through transcription, translation,  and signaling networks. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks.These information systems instruct the making and operation of cells and multicellular organisms, millions of interconnected molecular machines, production lines and factories analogous to factories made by man.  Cells operate robot-like,  autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advance and sophistication.
2. The origin of blueprints containing the information to fabricate complex machines and interlinked factories which produce goods for specific purposes are both always the result of intelligent setup.
3. Therefore, the origin of biological information and self-replicating cell factories is best explained by the action of an intelligent designer, who created a life for his own purposes.

The Cell factory argument
1. Cells are cybernetic, ingeniously crafted cities full of factories, the most sophisticated self-replicating factory of the universe -  containing an information translation system through the genetic code,  programming languages like our alphabet or computer code, more versatile than C, Visual Basic, or PHP, and more robust and error-free than any other code system out of 1 million alternatives -  using a communication protocol which wastes far less space than human-made ones - using furthermore a collection of rules and regularities of information coding for instructional complex texts -  defined by alphabet, grammar, a collection of punctuation marks and regulatory sites, and semantics,   and then uses that code system to create a blueprint for a self-replicating factory, which requires about 1500 books, each with 300 pages, 300.000,00 characters per book, each containing the precise complex instructions and information to create this factory,  and stored in the smallest storage device possible and known, a trillion times denser than a CD, used to prescribe, drive, direct, operate and control interlinked compartmentalized self-replicating cell factory parks that perpetuate and thrive life. Large high-tech multimolecular robotlike machines ( proteins ) and factory assembly lines of striking complexity ( fatty acid synthase, non-ribosomal peptide synthase ) are interconnected into functional large metabolic networks.  All this, of course, requires energy. Responsible for energy generation are high-efficiency power turbines ( ATP synthase )- superb power generating plants ( mitochondria ) and electric circuits ( highly intricate metabolic networks ). 
2.Complex factories, made based on the precise instruction of prescribed instructional complex blueprints, containing production lines, interdependent complex machines that produce complex machine parts and subunits that are, after made, assembled in the right way; manufacturing machines that work independently of outside input of information, but that were pre-programmed to do their job autonomously like robots, with quality control departments, error check and fix mechanisms to keep the smallest error rate, walls that make a separation of the inside to the outside of the factory for protection, and with gates that permits cargo in and out, recognition mechanisms that let only the right cargo in, and lead it to the right specific sites and production lines, highways and cargo carriers that have tags which recognize where to drop the cargo where it's needed, clean up waste and have waste bins and sophisticated recycle mechanisms, storage departments, producing its energy and shuttles it to where it's needed, and last not least, does reproduce itself, requires undoubtedly  intelligent minds to set all up.
3. All information storage devices, code languages, blueprints, information transmission systems, translation ciphers, with the purpose to make factories, and interdependent factory parks made upon those instructions are of intelligent origin. Biological cells are therefore the result of Intelligent design.

The Factory maker argument
1. Living Cells store very complex genetic and epigenetic information through the genetic code, and over fourty epigenetic languages, translation systems, and signaling networks. These information systems instruct the making and operation of cells and multicellular organisms. The operation of cells is close to thermodynamic perfection, and its operation occurs analogously to computers. Cells ARE computers in a literal sense, using boolean logic. Each cell hosts millions of interconnected molecular machines, production lines and factories analogous to factories made by man. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks. Cells operate robot-like,  autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advance and sophistication.
2. The origin of blueprints containing the instructional complex information, and the fabrication of complex machines and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup.
3.  Herschel 1830 1987, p. 148: “If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.” A metaphor (“A biological cell is like a production system”) demonstrates that similar behaviors are driven by similar causal mechanisms. Therefore, the origin of biological information and self-replicating cell factories is best explained by the action of a brilliant super powerful intelligent designer, who created life for his own purposes.

Devolution indicates the impossibility of random assembly to get complex macromolecules to kick-start life
1. At least 1300 proteins are required as building blocks for the simplest living cell to come to existence
2. Proteins are highly complex structures. The probability of random creation of complex proteins, the assemblage of the needed 1300 in one place in nature without any control is less than 10^722.000 or impossible.
3. According to the science paper: Paradoxes of life, Steve Benner reports: Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”.  The literature reports (to our knowledge) exactly  ZERO CONFIRMED OBSERVATIONS where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. it is IMPOSSIBLE for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. 
4. Such impossibility of chance indicates the necessity of an intelligent designer.

1. Biological cells are factories
2. Factories are the result of intelligent design
3. Therefore, biological cells are designed.

1. Either high levels of complexity seen in the living is due to a designer, or random chance.
2. The enemy of the arise of complex self-replicating energy demanding physico-chemical structures is entropy
3. Therefore, it is far more likely that an intelligent designer did setup life, rather than chance.

1. The implementation and construction of factory parks for specific goals always depends on planning, elaborating blueprints and codified specified instructions.
2. The make and development of cells that are literally self-replicating factories are due to blueprints, genetic instructions,  stored in DNA.
3. All information storage devices, code languages, blueprints, information transmission systems, translation ciphers, with the purpose to make factories, are of intelligent origin. Biological cells are therefore the result of Intelligent design.

1. The basic building blocks of life have never been synthesized in the lab. Evidence has demonstrated that prevital unguided origin of each of the four classes is not possible.
2. Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. Either the basic building blocks of life were created, or the result of unguided prebiotic events.
3. Since prebiotic synthesis is not possible by unguided natural means, most likely they were created by an intelligent designer.

1. The origin and construction of machines, computers, and factories is best explained through the action of intelligent designers.
2. Cells host molecular machines, production lines, and are literally computers and factories, made and controlled by instructional information.  
3. Therefore, the origin of living systems functioning and controlled based on instructional information is best explained by creation through an intelligent designer.  

Biological Cells are irreducibly complex:
1. Cell subunits and compartments form a complex system that is useful only in the completion of a much larger system that is able to keep the basic functions of life. A minimal Cell, in order to permit life, according to an article in Science magazine, from 2016, requires a minimal genome of about 473 gene products, and at least 438  proteins, each fully set up and functional for specific tasks. A discrete minimal size of each individual protein complex formed by multiple subunits and cofactors is required in order to be functional. And it only operates when interconnected and in a joint venture similar to a robot in a production line, and precise energy supply.
2. Cells must be created and be functional, all at once. As Graham Cairns-Smith noted, this system has to be fixed in its essentials through the critical interdependence of subsystems. Irreducibly complex and interdependent systems cannot evolve but depend on intelligence with foreknowledge on how to build discrete parts with distant goals.
3. Therefore, intelligent design is the best explanation of the origin of living, self-replicating cells.

Cells are made analogously to how humans make machines and factories
1. The cell coordinates its functions by virtue of a ‘genetic program’ encoded in the DNA that directs and controls the expression of a specific set of RNA's and proteins, which assemble deterministically into stable ‘molecular machines’ that reliably and efficiently execute predetermined operations according to the mechanisms of cell division, endocytosis, signal transduction, etc.
2. This is analogous to engineers, which produce blueprints, which prescribe and instruct the making and assembly of machines for specific purposes. 
3. Herschel 1830 1987, p. 148: “If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.” A metaphor (“A biological cell is like a production system”) demonstrates that similar behaviors are driven by similar causal mechanisms.
4. Since there was no human mind present when life started, we can conclude that a nonhuman higher intelligent agency must have created life. 


1.Cells contain high information content that directs and controls integrated metabolic pathways which by significant alterations are inevitably damaged or destroys their function. They also require regulation and are structured in a cascade manner, similar to electronic circuit boards.
2. There is always an observable consequence if a circuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the circuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin and set up of information (instructional prescribing complex information), integrated complex circuits with little tolerance of change.
4. Therefore, intelligent design constitutes the best explanation for the origin of these systems. 

1. Biological cells operate based on the storage and transmission of information, genetic and epigenetic landscapes, the principles of communication which are in a cause and effect relationship with mechanical engineering. In other words, biosemiotics on a systems-level is the controlling principle of biomechanics.
2. To assign the rise of such controlling principles to a selective process of evolution leaves serious difficulties. The growth of a blueprint into the complex machinery that it describes seems to require a system of causes not specifiable in terms of physics, chemistry, and the laws of inanimate nature. This missing principle which builds a bodily structure on the lines of an instruction given by DNA and epigenetic codes must be an integrative power at work, which goes beyond physical and chemical principles. Entire complex multicellular systems cannot be explained in terms of their individual, constituent parts and their interactions.
3. Envisioning potential shapes,  the emergence of higher-level features that arise from the parts requires foresight. The phenomena of life can only be understood by the action of a divine extraordinarily brilliant and powerful mind which transcends physics and chemistry, capable to bring forward algorithms, biosemiotics, computation, and information that directs the making of machine-like structures of extraordinary complexity seen on a molecular scale, and unseen in the macroscopic world.



Last edited by Otangelo on Thu Jan 14, 2021 8:38 am; edited 28 times in total

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Otangelo


Admin
Arguments based on biocomplexity and biodiversity

Error check and repair mechanisms
1 a)The genetic code is at or very close to a global optimum for error minimization. Only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors. That would be expected if the code were the product of intelligent selection. 
b)The assignment during translation of 64 codons ( 1 codon = 3 RNA nucleotides, where each can be one of the four used in life) 4x4x4=64 is assigned to only 20 ( in some cases 22) puts in question, why not attempting to accomodate just 2 codons with 4x4=16 possible positions to 16 amino acids. Or 64 codons to 61 amino acids. This “redundancy” was initially interpreted as an inefficient artifact of natural, sometimes messy trial-and-error processes. Since then, however, we have discovered that the redundancy is actually vital. The apparent overkill minimizes reading and transmitting errors so that the same amino acid is transferred to each generation.
c)The genetic information is transmitted by over 25 extremely complex interconnected and interdependent molecular machines. This communication system encodes, sends, and decodes genetic texts, which requires as well error check and repair mechanisms along the way to maintain low genetic mutation rate, and minimizing replication, transcription, and translation errors, and permit organisms to pass accurately genetic information to their offspring, and survive. This system had to be set-up prior to when life began because it depends on it. During replication, nucleotides, which compose DNA, are copied. When E coli makes a copy of its DNA, it makes approximately one mistake for every billion new nucleotides. It can copy about 2000 letters per second, finishing the entire replication process in less than an hour.  Compared to human engineering, this error rate is amazingly low. coli makes so few errors because DNA is proofread in multiple ways. 
d) Proteins,marvelous pieces of chemical nanoengineering, in order to become functional, must fold from linear, to specific 3-D forms. Properly folded proteins are essential for life because they conduct most of the necessary functions in a cell. If it folds into the wrong shape, a protein is useless. If the first proteins fell into these death valleys, life on Earth would never have appeared. Spontaneous folding is quite rapid (milliseconds to seconds) for many proteins, but many large, critical proteins fail to find by themselves the right shape and, without help, would become only so much molecular waste.So when a protein misfolds, other proteins, named chaperonins, help proteins fold into the right shape. They have been shown to interact with up to 30% of the cell’s proteins, so their importance is real. Now, amazingly, even these very own proteins, named GroEL, which help misfolded proteins to fold properly, can also misfold. And it has been  shown that GroES, a co-chaperone assists in folding GroEL. Amazing. Machines, that help other machines to assemble properly, are by themselves subject to errors, and life has inbuilt mechanisms to fix as well these machines that help fixing other machines !! 




Regulation is essential in biology
1. Regulation is ubiquitous in biology, and a fundamental property of living systems. Keeping a stable internal cellular environment requires constant adjustments as conditions change inside and outside the cell. The adjusting of systems within a cell is called homeostatic regulation. Because the internal and external environments of a cell are constantly changing, adjustments must be made continuously to stay at or near the set point (the normal level or range). Regulation of biological processes occurs when any process is modulated in its frequency, rate or extent. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. While Gene expression in prokaryotes is regulated primarily at the transcriptional level, in eukaryotic cells, it is regulated at many levels (epigenetic, transcriptional, post-transcriptional, translational, and post-translational). Metabolism or intracellular signaling also requires regulation. Gene regulation is a dynamical process composed of a number of steps, for example the binding of Transcription Factors to DNA, recruitment of transcription machinery and the production of the messenger RNA, post-transcriptional regulation, splicing and transport of mRNA, translation, maturation and possible localization of proteins. 
2. Regulation requires a distinctive architecture of functional relationships, and specifically the action of a dedicated subsystem whose activity is dynamically decoupled from that of the constitutive regime. Regulate means control or maintain the rate or speed of (a machine or process) so that it operates properly. Regulation is the management of complex systems according to a set of rules and trends. It is a rule or directive made and maintained by an authority. Regulating is always either a) a preprogrammed action by an intelligent agency, or b) an action where an intelligent agent is directly actively involved. 
3. Setting rules, giving directives for specific purposes or functions is always the result of a mental action. It is logical to conclude that biological regulation requires intelligent set up.


Waste management in biology points to design
1. Waste management (or waste disposal) includes the activities and actions required to manage waste from its inception to its final disposal. This includes the collection, transport, treatment, and disposal of waste, together with monitoring and regulation of the waste management process, and is always preceded by careful planning and foresight of the entire process by waste management engineers,  and implemented virtually simultaneously. 
2. Biological cells have cleverly engineered mechanisms that grind molecular protein garbage ( Proteasome Garbage Grinders ), coordinate loading and translocation of the waste products ( by superb Multisubunit peptide-loading complexes (PLC) ) to the waste disposal site, where the waste products are processed and sorted out (Histocompatibility complex class I (MHC-I) with 1,6 million atoms that to work with atomic precision ), and the final products are transported to the surface of the cell through the exquisite secretory pathway. There, T-Cells scan the MHC-I with receptors, and recognize when the cell was infected by foreign invaders, and induce their apoptosis ( cell suicide)
At least 9 macromolecular complexes need to work together in a joint venture, which communicates with each other to orchestrate this masterfully information-based process through signaling languages. If one of the complexes in the pathway is missing, no deal, the immune system cannot do its job, and the organism cannot survive and dies. Of course, all this incredible marvel of molecular engineering had to be born fully set up. No stepwise evolutionary process would lead to such a system. 
3. Therefore, the intelligent design theorist is justified to posit an unfathomably clever intelligent designer with foresight, who knew how to implement such a masterfully crafted waste management system on a molecular scale. 

The Ribosome
1. Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.
2. The set up of a language, and upon it, the programming of a completely autonomous communication network, which directs the operation of a complex factory, which during operation error checks and performs repairs, to make specific purposeful products, is always the product of an intelligent agency.
3. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder does science confesses that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: an intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.

Evidence of design in the ribosome
1. Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. For example, the functional group A2451, one single ribonucleotide which is not only of vital importance for peptide bond catalysis ( yeah, how did unguided events "discover" hot to place this one tiny molecule in the right place amongst 2900 of its peers ) but when the translation process is stalled, it signals to a dynamically coupled group in the exit tunnel of the product, the polypeptide chain: " we have a problem here" !! and the ribosome takes action. Ribosomes form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, they can halt the translation process on the fly, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential. Even more strikingly amazing, ribosomes occasionally get stalled when faulty messenger RNA molecules are read, for instance, for a messenger RNA that has broken and is thus is missing its stop codon. The ribosome uses an incredible piece of bio-engineering to rescue a stalled situation when they get stuck at the end of the truncated chain. They use a mechanism called Trans-translation. It is a ubiquitous bacterial mechanism for ribosome rescue in the event of translation stalling. This mechanism is a key component of multiple quality control pathways in bacteria that ensure proteins are synthesized with high fidelity in spite of challenges such as transcription errors, mRNA damage, and translational frameshifting. This so-called Trans-Translation is performed by a ribonucleoprotein complex.
2. The set up of a language, and upon it, the programming of a completely autonomous communication network, which directs the operation of a complex factory, which during operation error checks and performs repairs, to make specific purposeful products, is always the product of an intelligent agency. 

3. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder does science confesses that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: an intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.

Evidence of design in the ribosome
1. Ribosomes have the purpose to translate genetic information into proteins. According to Craig Venter, the ribosome is “an incredibly beautiful complex entity” which requires a minimum of 53 proteins. It is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products…  They are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They can halt the translation process on the fly, and coordinate extremely complex movements. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.
2. For the assembly of this protein-making factory, consisting of multiple parts, the following is required: genetic information to produce the ribosome assembly proteins, chaperones, all ribosome subunits, and assembly cofactors. a full set of tRNA's, a full set of aminoacyl tRNA synthetases, the signal recognition particle, elongation factors, mRNA, etc. The individual parts must be available,  precisely fit together, and assembly must be coordinatedA ribosome cannot perform its function unless all subparts are fully set up and interlocked. 
3. The making of a translation machine makes only sense if there is a source code, and information to be translated. Eugene Koonin: Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage is extremely difficult even within a speculative scheme let alone experimentally. Speaking of ribosomes, they are so well structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working.  Design some machinery which behaves like this and I personally will build a temple to your name! Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. The origin of the ribosome is better explained through a brilliant intelligent and powerful designer, rather than mindless natural processes by chance, or/and evolution since we observe all the time minds capabilities producing machines and factories.

Translation through the ribosome is an irreducible, integrated complex process

1. The ribosome is the 3D printer of proteins. A human-made 3D printer is made of several functional parts, like the nozzle, the extruder, cooling fan, heated be, the painter's tape, etc. The 3D extruder has no use on its own. But only, when working inside the 3D printer in the right place. A bacterial cell depends upon a translation and coding system consisting of 106 distinct but functionally integrated proteins as well several distinct types of RNA molecules (tRNAs, mRNAs, and rRNAs). This system includes the ribosome (consisting of fifty distinct protein parts), the twenty distinct tRNA synthetases, twenty distinct tRNA molecules with their specific anticodons, about 200 ribosome assembly proteins and 75 co-factors, chaperones, free-floating amino acids, ATP molecules (for energy), and—last, but not least—information-rich mRNA transcripts for directing protein synthesis. Many of the proteins in the translation system perform multiple functions and catalyze coordinated multistep chemical transformations.
2. In the same sense, as an engineer would not project, invent, create and make a blueprint of a 3D printer extruder with no use by its own, but only conjoined, and together with all other parts while projecting a whole printer, envisioning its end function and use, its evident that unguided random natural events without foresight would not come up with an assemblage of tiny molecular machines, enzymatic structures with unique contours, which bear no function by their own, but only when inserted as part of the ribosome with higher ends, being essential for cells to translate DNA information into proteins, and being a key part participating to perpetuate life. Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. In other words: Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overarching design goal. A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (instructed complex information), irreducible complexity, and the setup of complex machines with little tolerance of change.   Therefore, intelligent design constitutes the best explanations for the origin of the information guiding the making of the irreducible and integrated complex ribosome protein factory.

1. High information content (or specified complexity), irreducible complexity, and the setup of exquisitely integrated circuits, which by significant alterations are inevitably damaged or destroys the function,   constitute strong indicators or hallmarks of (past) intelligent design.
2.The high information content and biological irreducible metabolic pathways which also require regulation and structured in a cascade manner, similar to electronic circuit boards, utilizing proteins and enzymes that manifest by themself irreducible complexity, constitute strong indicators or hallmarks of (past) creation through intelligent intervention,  and design.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (instructed complex information), irreducible complexity, and the setup of complex circuits with little tolerance of change. 
4. Therefore, intelligent design constitutes the best explanation for the origin of information and irreducible complexity in metabolic biological circuits. 


Evidence of design in the ribosome
1.  Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. For example, the functional group A2451, one single ribonucleotide which is not only of vital importance for peptide bond catalysis ( yeah, how did unguided events "discover" hot to place this one tiny molecule in the right place amongst 2900 of its peers ) but when the translation process is stalled, it signals to a dynamically coupled group in the exit tunnel of the product, the polypeptide chain: " we have a problem here" !! and the ribosome takes action. Ribosomes form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, they can halt the translation process on the fly, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential. Even more strikingly, ribosomes occasionally get stalled when faulty messenger RNA molecules are read, for instance, for a messenger RNA that has broken and is thus is missing its stop codon. The ribosome uses an incredible piece of bio-engineering to rescue a stalled situation when they get stuck at the end of the truncated chain. They use a mechanism called Trans-translation. It is a ubiquitous bacterial mechanism for ribosome rescue in the event of translation stalling. This mechanism is a key component of multiple quality control pathways in bacteria that ensure proteins are synthesized with high fidelity in spite of challenges such as transcription errors, mRNA damage, and translational frameshifting. This so-called Trans-Translation is performed by a ribonucleoprotein complex.
2. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder does science confesses that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: 
3. An intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.

Within an embryo, several processes play out at the cellular and tissue level to create an organism. These processes include cell proliferation, differentiation, and cellular movement
1. Cell fate determination depends on various kinds of codified information, communication and feedback systems, signaling, and bar-code marking.  These information systems prescribe, drive, direct, operate, control, and induce reacting to stimuli, provide patterning cues, regulation, determine and permit the making of decisions based on memory, control transcription, remodel chromatin structure and state, control cell-cell interactions, differential gene expression, regulate which genes are transcribed in a cell ( which genes are turned on and off ), influence the arrangement of different cell types during embryological development, give cues to cleavage patterns, create asymmetry from homogeneity, induce concentration gradients, cell positioning, and many more. 
2. These are not simply chemical reactions, but actions directed by prescribed, instructional complex information input.  This orchestration depends on a network of logic interactions programmed into the DNA sequence, epigenetic information, and signaling networks that amount essentially to a hardwired biological computational device. Animal forms depend on tightly integrated networks of genes, proteins, and other molecules to regulate their development.
3. Neither proponents of "evo-devo," nor proponents of other proposed materialistic theories of evolution, have identified a mutational mechanism capable of generating anything even remotely resembling a complex integrated circuit. In our experience, the functional integration of parts in complex systems generally—are known to be produced by intelligent agents—specifically, by engineers. Intelligence is the only known cause of such effects. Developing animals employ a form of integrated circuitry, and certainly one manifesting a tightly and functionally integrated system of parts and subsystems, and intelligence is the only known cause of these features. Once established, the complexity of integrated circuits and signaling networks makes them stubbornly resistant to mutational change. Disarming any one of these hierarchically structured systems produces some abnormality in expression.

The cell is a factory - adios materialism.
1.  Computer hard-drives with high capacity of digital data storage, software programs based on languages using statistics, syntax, semantics, pragmatics, and apobetics, and the elaboration of complex instructional blueprints through those software programs, and data transmission systems (encoding, sending, decoding), all operated through computers and interlinked computer networks, which prescribe, drive, direct, operate and control interlinked compartmentalized factory parks making products for specific purposes, full of autonomous, robotlike high-tech production lines, high-efficiency power plants, complex high-tech robots with autoregulation and feedback loops, producing products with minimal error rates, that are transported through GPS driven transport carriers to their destination, all driven through energy made by high rotative turbines and power plants,  are always set up by intelligent agents designing those things for purposeful goals.
2. Science has unraveled, that cells, strikingly, contain, and operate through all those things. Cells are cybernetic, ingeniously crafted cities full of factories. Cells contain information, which is stored in genes (books), and libraries (chromosomes). Cells have superb, fully automated information classification, storage, and retrieval programs ( gene regulatory networks ) that orchestrate strikingly precise and regulated gene expression. Cells also contain hardware - a masterful information-storage molecule  ( DNA ) - and software, more efficient than millions of alternatives ( the genetic code ) - ingenious information encoding, transmission, and decoding machinery ( RNA polymerase, mRNA, the Ribosome ) - and highly robust signaling networks ( hormones and signaling pathways ) - awe-inspiring error check and repair systems of data ( for example mind-boggling Endonuclease III which error checks and repairs DNA  through electric scanning ). Information systems, which prescribe, drive, direct, operate, and control interlinked compartmentalized self-replicating cell factory parks that perpetuate and thrive life. Large high-tech multimolecular robotlike machines ( proteins ) and factory assembly lines of striking complexity ( fatty acid synthase, non-ribosomal peptide synthase ) are interconnected into functional large metabolic networks. In order to be employed at the right place, once synthesized, each protein is tagged with an amino acid sequence, and clever molecular taxis ( motor proteins dynein, kinesin, transport vesicles ) load and transport them to the right destination on awe-inspiring molecular highways ( tubulins, actin filaments ). All this, of course, requires energy. Responsible for energy generation are high-efficiency power turbines ( ATP synthase )- superb power generating plants ( mitochondria ) and electric circuits ( highly intricate metabolic networks ). When something goes havoc, fantastic repair mechanisms are ready in place. There are protein folding error check and repair machines ( chaperones), and if molecules become non-functional, advanced recycling methods take care ( endocytic recycling ) - waste grinders and management ( Proteasome Garbage Grinders )
3. Chemist Wilhelm Huck, professor at Radboud University, Netherlands: A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity. Cells, containing all those things are irreducibly complex. Without energy, information, or the basic building blocks fully synthesized, there would be no life. All this is best explained as a product of a super-intellect, an agency equipped with unfathomable intelligence - through the direct intervention, creative force, and activity of an intelligent cognitive agency, a powerful creator.

1. Cell fate determination depends on various kinds of codified information, communication and feedback systems, signaling, and bar-code marking.  These information systems prescribe, drive, direct, operate, control, and induce reacting to stimuli, provide patterning cues, regulation, determine and permit the making of decisions based on memory, control transcription, remodel chromatin structure and state, control cell-cell interactions, differential gene expression, regulate which genes are transcribed in a cell ( which genes are turned on and off ), influence the arrangement of different cell types during embryological development, give cues to cleavage patterns, create asymmetry from homogeneity, induce concentration gradients, cell positioning, and many more.
2. These are not simply chemical reactions, but actions directed by prescribed, instructional complex information input.  This orchestration depends on a network of logic interactions programmed into the DNA sequence, epigenetic information, and signaling networks that amount essentially to a hardwired biological computational device. Animal forms depend on tightly integrated networks of genes, proteins, and other molecules to regulate their development.
3. Neither proponents of "evo-devo," nor proponents of other proposed materialistic theories of evolution, have identified a mutational mechanism capable of generating anything even remotely resembling a complex integrated circuit. In our experience, the functional integration of parts in complex systems generally—are known to be produced by intelligent agents—specifically, by engineers. Intelligence is the only known cause of such effects. Developing animals employ a form of integrated circuitry, and certainly one manifesting a tightly and functionally integrated system of parts and subsystems, and intelligence is the only known cause of these features. Once established, the complexity of integrated circuits and signaling networks makes them stubbornly resistant to mutational change. Disarming any one of these hierarchically structured systems produces some abnormality in expression.

Information directing the make of factories has always mental origin
1. Cells are cybernetic, ingeniously crafted cities full of interlinked fully autonomous chemical nano factories. They host large high-tech macromolecular machines, superb power plants, and striking nano-robots. Wonderful arrays of fully automated manufacturing production lines, transport carriers, generate energy through incredibly efficient turbines, neuron transistors, miniaturized Computers. All those things are made based on algorithmic specified instructional complex information, which prescribes how all those things have to be made, controlled, assembled, and work together in an integrated fashion.  
2. The emergence of cities full of interlinked factories full of computer directed machines, assembly lines made of a series of robots working in a joint venture,  energy turbines, transistors, circuit boards, logic gates for specific purposes,directed by prescribed, instructional complex assembly information have only been observed to come from intelligent minds.  Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process. This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic codes, and upon it, instructional information, is like suggesting that a rainbow can write poetry... it is never going to happen!
3. Therefore, most probably, cell factories containing all those things are the product of an intelligent designer.

1. A transistor can be considered an artificial Neuron. Every living cell within us is a hybrid analog–digital supercomputer. The brain is like 100 billion computers working together.
2. Biological cells are programmed to be experts at taking inputs, running them through a complicated series of logic gates through circuit-like operations and producing the desired programmed output.
3. The origin of programs, logic gates, and complex circuits to obtain a purposeful specific outcome is always tracked back to intelligent implementation.

1. The more statistically improbable something is, the less it makes sense to believe that it just happened by blind chance.
2. Statistically, it is practically impossible, that the primordial genome, proteome, and metabolome of the first living cell arose by chance.
3. Furthermore, we see in biochemistry purposeful design.  
4. Therefore, an intelligent Designer is by far the best explanation for the origin of life.

1. The mechanisms required to build complex organismal form are preprogrammed instructional complex information encoded in various genetic and at least 41 epigenetic codes and languages and communication by various signaling codes through various physicochemical signaling networks.
2. Science has demonstrated, that evolution by mutations and natural selection genetic drift, and gene flow result in entropy, deteriorate the genome, rather than increasing information and organismal complexity.
3. The origin of instructional complex information ( analogous to blueprints ) and signaling networks is always tracked back to intelligence setting them up with specific purposes.
4. Therefore, biodiversity and organismal architecture are better explained by an intelligent creator, rather than mindless evolution.

1. Regulating, governing, controlling, recruiting, interpreting, recognizing, orchestrating, choreographing, elaborating strategies, guiding, instructing, fine-tuning, monitoring, organizing, are all tasks of the gene regulatory network, which are ultrasophisticated communication networks, analogous to electric circuits in man-made devices.
2. In the same sense as copper, plastic, basic electronic parts do not turn into a  printed circuit board randomly, molecular regulators, transcription factors, on/off switches, feedback loops do not turn into a gene regulatory network by unguided processes. Communication networks and signal transmission systems, similar as seen in gene regulatory networks, highly flexible, and able to rapidly reconfigure to deliver different outputs can only be implemented and pre-programmed by intelligence.
3. Therefore, most probably, the gene regulatory network was implemented and programmed by an intelligent agency.

1. Regulation, governing, controlling, recruiting, interpretation, recognition, orchestrating, elaborating strategies, guiding, instruct are all tasks of the gene regulatory network.
2. Such activity can only be exercised if no intelligence is present if the correct actions were pre-programmed by intelligence.
3. Therefore, most probably, the gene regulatory network was programmed by an intelligent agency.


1. Complex multicellular lifeforms depend on gene regulatory networks (dGRN's) which are a collection of molecular regulators that interact with each other and with other substances in the cell to orchestrate the expression of DNA. 
2. dGRN's operate based on logic gates and their networks process chemical input signals similar to computers. These encoded instructions are based on boolean logic.
3. Logic depends on reason. Reason depends on intelligence. Only an intelligent mind can think rationally, and implement a system based on conceptual laws of logic. Therefore, the best and most reasonable explanation for the existence of complex gene regulatory networks based on boolean logic, essential for the making of complex multicellular organisms, is the creative action of a powerful, transcendent, intelligent Creator. 

1. The setup of functional Information retrieval systems, like a library classification system, is always tracked back to intelligence
2. The gene regulatory network is a fully automated, pre-programmed, ultra-complex gene information extraction system
3. Therefore, its origin is best explained through the intelligent setup

1. The genomic program for development operates primarily by the regulated expression of genes encoding transcription factors and components of cell signaling pathways.
2. A program can always be traced back to a programmer.
3. Therefore, the genomic program of development most probably was programmed by a programmer. That programmer is God.

1. A transistor can be considered an artificial Neuron. Every living cell within us is a hybrid analog-digital supercomputer. The brain is like 100 billion computers working together. 
2. Biological cells are programmed to be experts at taking inputs, running them through a complicated series of logic gates through circuit-like operations and producing the desired programmed output.
3. The origin of programs, logic gates, and complex circuits to obtain a purposeful specific outcome is always tracked back to intelligent implementation.


The oxygen-evolving complex (OEC) of photosystem II is irreducible complex.
1. One of the most important and fundamental biochemical reactions on which all advanced life-forms depend is performed by the oxygen-evolving complex (OEC) in oxygenic photosynthesis, responsible for catalyzing the light-driven oxidation of water to molecular oxygen in plants, algae, and cyanobacteria. It is also described as "undoubtedly one of the most remarkable inventions in all of biology." OEC is surrounded by 4 core proteins of photosystem II at the membrane-lumen interface.  It remains a fundamental mystery of how this complicated, four-electron transfer process originated. Enigmatic is how the precise geometry and unique mechanism of the OEC came about. Key differences exist between oxygenic and anoxygenic photosynthetic machinery with no apparent homologs or transitional forms that would provide clues to their development. Foremost among these differences is the presence and key role of manganese at the site of water oxidation in photosystem II. This is distinct from bacterial anoxygenic reaction centers, which rely on redox-active periplasmic proteins as electron donors.
2. According to peer-reviewed scientific papers, each of the four extrinsic proteins, (PsbO, PsbP, PsbQ, and PsbR)  of plants are ESSENTIAL, and each was tested upon mutated form, and the mechanism was found inefficient and compromising the OEC function. Furthermore, a water network around the Mn4CaO5 cluster and D1 protein subunit of PSII is also indispensable, and irreducible.  Site-directed mutants show severe impairment of the water oxidation cycle and fail to grow photoautotrophically.
3. That means evolutionary intermediates are non-functional. There is a precise fit and size matching of the residues with the individual atoms of the clusters. This is evidence, that this most fundamental biochemical reaction could not have emerged by evolutionary, step-wise mechanisms, and therefore, Darwin's theory has been falsified and refuted. The only plausible alternative to darwinian evolution is intelligent design.


1. The grand overarching scheme of the morpho-genesis and formation of single eukaryotic cell form, shape, architecture, function, structure, following the formation of tissues and higher order of biological structures  is that information conveyed through codified signaling directs intracellular molecular actors. It is due to at least 36 different signaling molecules & mechanisms which direct at least 15 force-generating molecules, through least 38 different mechanisms. They are classified into two groups: 
a) Semantophoretic molecules ( carry genetic and epigenetic information) that provide complex instructional cues of action through signaling which is fundamental to coordinate any common behavior and organize the division of labor. The following activities are performed in an integrated, orchestrated, interdependent manner by at least 36 different signaling molecules & mechanisms in following different ways: 8 molecules signal, 4 orient, 5 activate,  2 direct, 3 promote, 2 regulate, 1 guide, 3 organize, 1 inform, 1 coordinate, 1 specify, 1 modulate, 1 provide position cues, 2 mediate, 1 provoke change.
b) At least 15 force-generating actors, molecules that are directed through those signals and instructions, are responsible for cell morpho-genesis,that is: Filaments, microtubules, lamellopodia, crosslinkers, motors, protein complexes, the centrosome, adhesion proteins, force generators, the extracellular matrix, intra-cellular modules, key regulators, protein gradients,  the mitotic spindle, mechanical signals which act in at least 38 different ways, to name: activating, binding, breaking, coordinating, conferring positional information, directing, forcing transmission, generating, guiding, helping to organize, inducing, informing, mediating, modulating, organizing, orienting, providing positioning rules, provoking changes, promoting, regulating, signaling, stretching, specifying. 
2.The molecules, acting upon the instructional signals received,  form patterns, force change, stretch, change and induce cell shape, move positions, orient, provoke ingress, express, align, deform, accumulate molecules, invaginate, extend, form a web, concentrate, hold together, give mechanical support, stiffen, promote stabilization, form geometry, polarity, form division-plane positioning, phosphorylate, dephosphorylate, force transmission,  couple molecules physically, form gradients, deform, pull forces, promote cell rounding, transduce, specify cell-fate, extend, provide structural links, form aspect ratio and size, form filament ends, etc.
3.Codified signals and information directing the make of machines ( proteins) and factories ( cells)  have only been observed to come from intelligent minds.  Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process.
This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic codes, and upon it, instructional information, is like suggesting that a rainbow can write poetry... it is never going to happen!  Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating a conceptual semiotic information is a conscious intelligent mind. Life is no accident, the vast quantity of semiotic information in life provides powerful positive evidence that we have been designed.

1. Single cell to man evolution is not a scientific theory. Science, observational science, begins with . . . observation. No human being anywhere ever saw any of the proposed steps from amoeba to multicellular invertebrates, to chordates, to fish, to amphibians to reptiles and birds, and to mammals and man. It is all speculation about what might have occurred in the unobserved, unobservable, unrepeatable and untestable past. You cannot do a controlled experiment on events of history.Modern molecular biology would suggest that any naturalistic origin of life from dirty pond water theory is nonsense.
2. Evolution is speculation based on naturalism, that everything must be required to have a natural cause, nothing supernatural can exist, and materialism. that matter and energy is absolutely all there is was, or ever can be amen.
3. Abductive reasoning permits the inference that life and biodiversity was created by the Creator of this Universe, and of man, which is extraordinarily brilliant and powerful.

1. Pre-programming and prescription of information to get an intended purposeful outcome requires foresight.
2. Foresight comes always from an intelligent agent.
3. Therefore, biodiversity is the result rather of divine intelligent design, than unguided evolution.

1. The term 'evolution' is an equivocation fallacy that attempts to define two different proposed processes under the same definition. It is a violation of the logical reasoning process to conclude that the genetic variation we can observe within and around species explains the creation of complex body plans, organs, and other complex systems. Darwin's theory is illogical, serendipitous, and unproven.
2.. Complex life by complete accident over billions and trillions of successive serendipitous accidents is an incredulous claim without evidence.
3.. Calculations of the time necessary to evolve from goo-to-you reveal such a low probability of macro-evolution happening that the odds are beyond the threshold of 'impossible'. Hitchen's was correct - "What can be asserted without evidence can be dismissed without evidence"...

Molecular Machines point to intelligent design
1. Living cells are full of Molecular machines, rotors, and engines, and they are made upon the same design principles as big machines. They are a pre-requisite for DNA replication. Life, according to a science paper from 2016,  needs a minimum of 438  different, in part interdependent proteins in order to start, and they require to be fully in place before natural selection can be considered as a driving force to produce evolutionary novelties.
2. The emergence of machines for specific purposes, and assembly lines of machines working in a joint venture, have never been observed to emerge by lucky accidents, spontaneously through self-organization by unguided natural events in an orderly manner without external direction,  purely physicodynamic processes, and reactions, but always through the direct intervention and creative force of an intelligent agency, a powerful creator.
3. Therefore, the origin of molecular machines is best explained by the ( past )creative act of an intelligent designer.


The organization of the genome dictates protein assembly
1.  Proteins are synthesized in specific orders to assemble large protein complexes, such as microtubule, proteasome, ribosomes, and cellulosome. These protein complexes are assembled both inside and outside cells through the coordination of gene expression, protein transport, and binding processes. Protein complexes can compose of different cofactors and post-translational modifications. Multiple protein subunits have to come together to form protein complexes that play critical functional roles in a cell. There is a remarkable correspondence between gene order and protein assembly order. The gene order has a significant effect and helps in the protein subunit assembly. Operon gene order is optimized to match the order in which protein subunits assemble. There is a significant benefit from tightly coordinating gene expression and protein assembly. Genetic circuits, physical transport, and binding kinetic rates all modulate the distribution of protein complexes. The interplay between the circuit architecture and the genetic and physical rate kinetics together determine the protein assembly structure. 
2. Foreknowledge is required for the protein multisubunit assembly that has to be performed and involving ordering principles which are known to come from an intelligent mind.  Subunits confer no function unless their use is known in the heterogeneous organization, formed from multiple distinct protein subunits, and completed into the much larger system.  There has to be a corresponding order. If gene sequences were  formed stochastically by mutations, and if trial and error explored protein assembly space possibilities until a particular sequential functional order and finally functional heteromeric subunit combination of protein complexes was "discovered", the cell would have been producing a considerable number of nonfunctional proteins assembled in the wrong way. In that process, deleterious genetic mutations would probably be eliminated by selection, long before a new protein assembly sequence would be explored and become functional.
3. Therefore, evolutionary principles and mutations are an inadequate explanation for the specific genetic order and genetic circuits. An intelligent designer instantiating protein assembly is the more case-adequate explanation.


Dinoflagellates with multi-barrel Gatling guns
1. Nematodinium Dinoflagellates are the coolest cells. They are among the most complex single-celled organisms we know of.They have ballistic "nematocyst" organelles. The weaponry is complicated, savage, and unlike what’s seen in animals. These bugs are basically the battle tanks of the microbial world, with armor-piercing, multi-barrel Gatling guns capturing them with their harpoon-like weapons that pierce the prey and drag them in to be consumed. They have  intricate weapons—including a microscopic version of a Gatling gun—to harpoon their dinners.    They are hunters that eat other dinoflagellates, which themselves are bristling with armor, microscopic munitions and even chemical weapons.  The tiny weapons are a unique invention
2. In order for their ballistic organelle to function, a capsule or nematocyst is required, which is composed of 9 essential elementary parts that compose the Gatling gun. This is an integrated interdependent system, where all parts must be in place in order to reach the higher end, that is to catch prey.
3. The origin of these sophisticated ballistic organelles that exceed those of animals in complexity are best explained through intelligent design.
https://reasonandscience.catsboard.com/t3055-a-dinoflagellate-protist-which-has-eyes-like-in-vertebrates-and-ballistic-multi-barrel-guns-for-taking-out-prey-by-design-or-evolution



Last edited by Otangelo on Tue Feb 16, 2021 5:28 am; edited 28 times in total

https://reasonandscience.catsboard.com

8Syllogistic - Arguments of Gods existence based on positive evidence Empty Arguments based on morality Fri Nov 27, 2020 8:40 am

Otangelo


Admin
Arguments based on morality

1. If objective moral values exist, then God exists.
2. Objective moral values exist.
3. Therefore, God exists.

1. If there is no God, there are no objective moral values, since they are prescribed " ought to be's". Then moral values are just a matter of personal opinion, and as such, no objectively or universally valid at all.
3. If that is the case, unbelievers have no moral standard to judge anything as morally good or bad.
4. But torturing babies for fun is always bad, no exception, therefore, objective moral values exist, and God exists. 


1. If objective moral values exist, then God exists.
2. Objective moral values exist. It is always wrong to torture, rape, and kill little babies for fun.
3. Therefore, God exists.

The Argument from Moral Truth
1. There exist objective moral truths. (Slavery and torture and genocide are not just distasteful to us, but are actually wrong.)
2. These objective moral truths are not grounded in the way the world is but, rather, in the way the world ought to be.
3. The world itself—the way it is, the laws of physics, or physical being can not account for the way the world ought to be.
4. The only way to account for morality is that God established morality.
5. Therefore, God exists.

1. If there is no God, there are no objective moral values, since they are prescribed " ought to be's".
2. If there is no God, then moral values are just a matter of personal opinion, and as such, no objectively or universally valid at all.
3. If that is the case, unbelievers have no moral standard to judge anything as morally good or bad.
4. Therefore, in order to criticize God, they need to borrow from the theistic worldview, and as such, their criticism is self-contradicting and invalid.
5. Even IF they could make a case to criticize God's choices, that would not refute his existence.



Last edited by Otangelo on Thu Dec 03, 2020 2:47 pm; edited 1 time in total

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9Syllogistic - Arguments of Gods existence based on positive evidence Empty Argument from logic Fri Nov 27, 2020 8:41 am

Otangelo


Admin
Argument from logic

1. Minds exist which have and use objective logic.
2. Objective logic cannot be based on our subjective minds, a non-static universe or immaterial abstractions outside of a mind.
3. Objective logic depends and can only derive from a pre-existing necessary first mind with objective logic. 

1. Logical absolutes exist.  Logical absolutes are conceptual by nature--are not dependent on space, time, physical properties, or human nature.  
2. They are not the product of the physical universe (space, time, matter) because if the physical universe were to disappear, logical absolutes would still be true.  
3. Logical Absolutes are not the product of human minds because human minds are different--not absolute.  
4. But, since logical absolutes are always true everywhere and not dependent upon human minds, it must be an absolute transcendent mind that is authoring them.  
5. This mind is called God. 

1. Flowering plants of the genus Musa will always only generate Bananas. Citrus species will always only produce citrus fruits like Orange, lemon etc.
2. Only an intelligent mind, capable of logical reasoning, is an adequate cause to create other minds able to reason. If we as humans possess the capability to intellectually understand and to know, then the cause must have the same or better capabilities of the same sort.
3. Arguing that matter can produce a mind, consciousness, intelligence, and the capability of logical reasoning is special pleading.

1. Without laws of logic, we could not make an argument.
2. We can make an argument.
3. Therefore, there must be laws of logic.

While this argument is circular, it is a non-fallacious use of circular reasoning. Since we couldn’t prove anything apart from the laws of logic, we must presuppose the laws of logic even to prove they exist. In fact, if someone were trying to disprove that laws of logic exist, he’d have to use the laws of logic in his attempt, thereby refuting himself.

Argument for God from Mind, Logic, Truth, Reality...
1. If Something exists, We must exist (we cannot have an illusion of an illusion)
2. If We exist, Reality must exist
3. If Reality exists, Truth must exist
4. If Truth exists, Laws of truth, (Logic) must exist
5. If Logic exists, a First Eternal Cause and a contingent Minds must exist.
6. If a contingent Minds exist. an eternal Mind must exist (infinite regress is impossible)
7. If an eternal Mind, Logic, and Truth, exist, then the eternal Immaterial, transcendent, personal Being (God),First Cause must exist
Conclusion: God must absolutely necessary, exist, because Reality, an eternal Mind Logic, and Truth exist.
The existence of God and it’s logically derived attributes are deducted Logically and are absolute conceptual truths


The rules of reason and logic are universal and unchanging.
Only reason can discern between true and false.
Communicating truthfully has more value.

 
https://carm.org/atheism/transcendental-argument



Last edited by Otangelo on Fri Jan 01, 2021 8:44 am; edited 8 times in total

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10Syllogistic - Arguments of Gods existence based on positive evidence Empty Argument from consciousness Mon Nov 30, 2020 2:22 pm

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Argument from consciousness

1. Minds are composed of intentional states
2. Intentional states are normative states that create the possibilities of failure
3. Good or bad are not natural states

Argument from consciousness 
1. Consciousness englobes the mind, "qualia", intellectual activity, calculating, thinking, forming abstract ideas, imagination, introspection, cognition, memories, awareness, experiencing, intentions, free volition, free creation, invention, generation of  information. It classifies, recognizes and judges behavior, good and evil. It is aware of beauty, and feels sensations and emotions.
2.  Hard objects are never observed spontaneously to transform themselves into abstract ideas.  To ascribe to the electrons in our brain the property to generate consciousness, and not to ascribe the same property to the electrons moving in a bulb, is in contradiction with quantum physics, which establishes that all electrons are equal and indistinguishable, that is they have all exactly the same properties. The mind is to the brain what a pianist is to a piano. The former (the pianist) is not reducible to the latter (the piano).
3. Those are all fundamental discrete indivisible non-quantifiable qualities of substance, which has a different identity from hard physical objects, matter and space. It is immaterial   Perception, understanding, and evaluation of things adds a quality beyond and absent from natural physical matter and states, and can, therefore, not be reduced to known physical principles.The mind cannot be an emergent property of the brain. Existing fundamentals—space, time, mass, charge can’t explain consciousness, which itself is something fundamental, and essentially different than physical things. Therefore, dualism is true, and since the universe had a beginning, the mind precedes and exists beyond the universe. That mind is God.

Syllogistic - Arguments of Gods existence based on positive evidence Body-m10



Last edited by Otangelo on Fri Jan 22, 2021 6:08 am; edited 4 times in total

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The origin of genetic information, genetic code, and ribosome point to a designed set up

https://reasonandscience.catsboard.com/t2895-syllogistic-arguments-of-gods-existence-based-on-positive-evidence#8245

1. D
2. D -> A & B & C
3. A & B & C -> requires Intelligence
4. Therefore Intelligence

A: Information, Biosemiotics ( instructional complex mRNA codon sequences transcribed from DNA )
B: Translation mechanism ( adapter, key, or process of some kind to exist prior to translation = ribosome )
C: Genetic Code
D: Functional proteins

1. Life depends on proteins ( molecular machines ) (D). Their function depends on the correct arrangement of a specified complex sequence of amino acids.
2. That depends on the translation of genetic information (A) through the ribosome (B) and the genetic code (C), which assigns 61 codons and 3 start/stop codons to 20 amino acids
3. Instructional complex Information ( Biosemiotics: Semantics, Synthax, and pragmatics (A)) is only generated by intelligent beings with foresight. Only intelligence with foresight can conceptualize and instantiate complex machines with specific purposes, like translation using adapter keys (ribosome, tRNA, aminoacyl tRNA synthetases (B)) All codes require arbitrary values being assigned and determined by agency to represent something else ( genetic code (C)).  .
4. Therefore, Proteins being the product of semiotics/algorithmic information including translation through the genetic code, and the manufacturing system ( information directing manufacturing ) are most probably the product of a divine intelligent designer.


The problem of translation through the Ribosome is threefold:

1. The origin of Information stored in the genome.

1. Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process.
2. This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry... it is never going to happen!  Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind.
3. Since life depends on vast quantity of semiotic information, life is no accident, and provides powerful positive evidence that we have been designed. A scientist working at the cutting edge of our understanding of the programming information in biology, he described what he saw as an “alien technology written by an engineer a million times smarter than us”

2. The origin of the adapter, key, or process of some kind to exist prior to translation = ribosome

1. Ribosomes have the purpose to translate genetic information into proteins. According to Craig Venter, the ribosome is “an incredibly beautiful complex entity” which requires a minimum of 53 proteins. It is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products…  They are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They can halt the translation process on the fly, and coordinate extremely complex movements. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.
2. For the assembly of this protein making factory, consisting of multiple parts, the following is required: genetic information to produce the ribosome assembly proteins, chaperones, all ribosome subunits and assembly cofactors. a full set of tRNA's, a full set of aminoacyl tRNA synthetases, the signal recognition particle, elongation factors, mRNA, etc. The individual parts must be available,  precisely fit together, and assembly must be coordinated. A ribosome cannot perform its function unless all subparts are fully set up and interlocked.
3. The making of a translation machine makes only sense if there is a source code, and information to be translated. Eugene Koonin: Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage is extremely difficult even within a speculative scheme let alone experimentally. Speaking of ribosomes, they are so well-structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working.  Design some machinery which behaves like this and I personally will build a temple to your name! Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. The origin of the ribosome is better explained through a brilliant intelligent and powerful designer, rather than mindless natural processes by chance, or/and evolution since we observe all the time minds capabilities producing machines and factories.

3. The origin of the genetic code

1. A code is a system of rules where a symbol, letters, words, etc. are assigned to something else. Transmitting information, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan.  In cells,  the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
2. Assigning meaning of characters through a code system, where symbols of one language are assigned to symbols of another language that mean the same, requires a common agreement of meaning. The assignment of triplet codons (triplet nucleotides) to amino acids must be pre-established by a mind.
3. Therefore, the origin of the genetic code is best explained by an intelligent designer.

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1. Cells are cybernetic, ingeniously crafted cities full of interlinked fully autonomous chemical nano factories. They host large high-tech macromolecular machines, superb power plants, and striking nano-robots. Wonderful arrays of fully automated manufacturing production lines, transport carriers, generate energy through incredibly efficient turbines, neuron transistors, miniaturized Computers. All those things are made based on algorithmic specified instructional complex information, which prescribes how all those things have to be made, controlled, assembled, and work together in an integrated fashion.  
2. To assign the rise of such controlling principles to a selective process of evolution leaves serious difficulties. The growth of a blueprint into the complex machinery that it describes seems to require a system of causes not specifiable in terms of physics, chemistry, and the laws of inanimate nature. This missing principle which builds a bodily structure on the lines of an instruction given by DNA and epigenetic codes must be an integrative power at work, which goes beyond physical and chemical principles. Entire complex multicellular systems cannot be explained in terms of their individual, constituent parts and their interactions.
3. 
 Envisioning potential shapes,  the emergence of higher-level features that arise from the parts requires foresight. The phenomena of life can only be understood by the action of a divine extraordinarily brilliant and powerful mind which transcends physics and chemistry, capable to bring forward algorithms, biosemiotics, computation, and information that directs the making of machine-like structures of extraordinary complexity seen on a molecular scale, and unseen in the macroscopic world. Therefore, most probably, cell factories containing all those things are the product of an intelligent designer.

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13Syllogistic - Arguments of Gods existence based on positive evidence Empty Syllogisms about irreducible complexity Sun Jan 10, 2021 6:08 am

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Syllogisms about irreducible complexity

https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact#8349

1. In biology, there are many complex elementary components necessary to build large integrated macromolecular systems like multi-protein complexes (RNA polymerase), 3D printers (the ribosome), organelles (mitochondria), etc., where their making requires complex multistep enzyme-catalyzed biosynthesis pathways. These elementary components are only useful in the completion of that much larger system. Not rarely, these biosynthetic pathways produce intermediate products, that left without further processing, are either a) nonfunctional, or b) harmful and kill the cell (for example, Reactive Oxygen Species (ROS), in the biosynthesis pathway of Chlorophyll b.
2. A minimal amount of prescribed, pre-programmed, instructional complex information stored in genes is required to instruct the making of a) functional elementary components and b) the assembly instructions to integrate them into complex macromolecular systems. Natural selection would not fix an allele variant that would instruct the making of an intermediate, nonfunctional, or harmful elementary component, and play no role in guiding its evolution. Foreknowledge is required to get a complex biological system through implementing a biosemiotic information system (which is irreducibly complex), directing the making of functional elementary components, and assembly into the entire complex integrated system.
3. Therefore, the origin of biological systems based on biosemiotic instructions are best explained by a brilliant, super-powerful mind with foresight and intent, and not undirected evolutionary pressures.

The histone Information system is irreducibly complex
1. In living cells, information is encoded through the histone code which is a set of rules, stored in amino acid sequences in the histone tail. They are used to orchestrate gene expression. And so, the information which is sent through the system, as well as the communication channels that permit encoding, sending, and decoding, which in gene expression is done through the orchestration of histone code readers, writers, erasers, and permit the loosening and tightening chromatin, and in consequence, the RNA polymerase machinery to express specific genes. 
2. A codified information transmission system depends on: a) A code as a system of rules where a symbol, letters, words, or even sounds, gestures, or images, are assigned to something else. Assigning meaning of characters through a code system requires a common agreement of meaning. Statistics, Semantics, Synthax, and Pragmatics,  b) Information encoded through that code, c) An information storage system, and d) an information transmission system, that is encoding, transmitting, and decoding.This system had to be set-up all at once. That is the software - the histone code "language", as well as the hardware, that is the histone tails upon which the "message" is written, the readers, writers, and erasers.
3.  The assignment of codified meaning to combinatorial amino acid sequences must be pre-established by a mind.The origin of such complex communication systems is best explained by an intelligent designer. Since no humans were involved in creating these complex computing systems, a suprahuman super-intelligent agency must have been the creator. 

Many systems in biology are irreducibly complex
1. There are many systems and parts in biology, that can be named, that require to be integrated to work. They work interdependently, only in a joint venture, and can be classified as irreducibly complex. A few examples are:
No glycine amino acids, no pyrimidines, no DNA - no life. No Watson Crick base pair fine-tuning, no DNA - no life. No Topoisomerase II or helicase proteins, no DNA replication - no life perpetuation. No peripheral stalk, a subunit in ATP synthase Nano turbines, no energy supply trough ATP for biological cells, no advanced life. No cleavage of tRNA during its biosynthesis, tRNA's will not be useful for the cell, no life. No Nitrogenase enzymes to fix nitrogen in an energy-demanding, triple bond-breaking process, no ammonia, required to make amino acids - no nitrogen cycle - no advanced life. No chlorophyll, no absorption of light to start photosynthesis, no starch and glucose - cells will have no food supply to sustain complex organisms - no advanced life on earth. No water evolving complex in photosynthesis, no oxygen, no advanced life. No carotenoids quenching heat in chlorophyll in the antenna complex, the surrounding membrane would be burned - no advanced life.   No Rubisco, no fix of CO2, no hydrocarbons - no advanced life. No counterion in retinal, and Rhodopsin could not receive visible light - and there would be no vision on earth by any organism.
2. It's like having a gigantic jigsaw puzzle of millions of pieces that trigger a knob. If not ALL puzzle pieces are brought together to complete it, the knob does not switch, and light does not turn on. None of the above-mentioned proteins has any function if not interconnected and inserted at the right place like a sub-part in a machine or production line. In the same manner, as a robot has no function by itself and by its own, and outside a factory unless placed at the right production line, getting the right substrate from another robot, processing it in the right manner, and handing it over to the next processing step - which also has to have its right function and manufacturing proceeding pre-programmed- nothing is done and achieved. Often, if in a production line, just one robot goes havoc, the entire production lines stop functioning. If you have a fully working car, but lose the key, you cannot turn it on, and it will not start. Sometimes, a tiny cable goes oxidized, or breaks and the car stop to function.  
3. Life is an unimaginable balancing act, beginning with the setup of physical laws upon which the properties and operation of the physical universe depend, fine-tuning of the universe, the fundamental forces, our galaxy, the earth, and its life-permitting conditions, but, if helicase, just ONE protein that unwinds DNA, is not here, our universe would be lifeless.
4. This is evidence of planned design by a powerful creator, that knows how, and not a lifeless magic trick blindly believed by so many atheists.

The cell is irreducibly complex
1. A strand of RNA can make one simple chemical reaction occur, but that’s not all what is needed. Even a most primitive cell needs essential molecules of life to replicate and thus to continue to exist. If there is no quality control, no inspections, no checks and balances, no feedback, no networks in the system of the cell, what will happen? Only entropy.
2. In order for life to begin there is need of an irreducible complex system even within the simplest cell.
3. Therefore, a supreme intelligent designer of irreducible complex cell factories system most likely exists. 

The irreducible complexity of the cell
1. On the one side, we have the putative prebiotic soup with the random chaotic floating around of the basic building blocks of life, and on the other side,  the first living self-replicating cell ( LUCA ), a supposed fully operational minimal self-replicating cell, using the highly specific and sophisticated molecular milieu with a large team of enzymes which catalyze the reactions to produce the four basic building blocks of life in a cooperative manner, and furthermore, able to maintain intracellular homeostasis, reproduce, obtaining energy and converting it into a usable form, getting rid of toxic waste, protecting itself from dangers of the environment, doing the cellular repair, and communicate.  
2. The science paper: Structural analyses of a hypothetical minimal metabolism proposes a minimal number of 50 enzymatic steps catalyzed by the associated encoded proteins. They don't, however, include the steps to synthesize the 20 amino acids required in life. Including those, the minimal metabolome would consist of 221 enzymes & proteins. A large number of molecular machines, co-factors, scaffold proteins, and chaperones are not included, required to build this highly sophisticated chemical factory.
3. There is simply no feasible viable prebiotic route to go from a random prebiotic soup to this minimal proteome to kick-start metabolism by unguided means. This is not a conclusion by ignorance & incredulity, but it is reasonable to be skeptic, that this irreducibly complex biological system, entire factory complexes composed of myriads of interconnected highly optimized production lines, full of computers and robots could emerge naturally defying known and reasonable principles of the limited range of random unguided events and physical necessity. Comparing the two competing hypotheses, chance vs intelligent design, the second is simply by far the more case-adequate & reasonable explanation.

1. High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.
2. Biological systems have high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
4. Therefore, intelligent design constitutes the best explanation for the origin of information and irreducible complexity in biological systems.

Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information, irreducible, and interdependent biological systems. 
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information, irreducible and interdependent systems of all sorts. 
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information and irreducible complexity in the cell, and interdependence of proteins, organelles, and body parts, and even of animals and plants, aka moths and flowers, for example.  

The argument by the impossibility of gradual development
1. Proponents of neo-Darwinism try to prove that the eye, ear, blood clotting, and heart could develop in small steps.
2. But in this gradualistic concept, each change has to provide some advantage.
3. Natural selection selects only for functional advantage.
4. Natural selection eliminates things that have no function and can even harm the organism.
5. Thus, the half functional blood clotting; flagellum of E. coli; heart, etc are impossible scenarios.
6. These must have already existed in their full functionality to facilitate the survival of the living being.
7. Therefore, a creator exists.

1. Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eight last steps are used by specific enzymes uniquely in this pathway.
2. The pathway must go all the way through, otherwise, chlorophyll is not synthesized.
3. Therefore, the Chlorophyll biosynthesis pathway is irreducibly complex.


The blood clotting system
1. Professor Doolittle argued that new laboratory work showed two components of the blood-clotting cascade could be eliminated (“knocked-out”) from mice and the mice got along fine without them. However, Doolittle misread the laboratory work: the double knock-out mice have severe problems and have no functioning blood clotting system. They are not models of evolutionary intermediates.
Although anyone can misread a paper, in my opinion, the fact that an expert cited a recent and contradictory journal article, instead of a publication directly addressing the evolution of blood clotting, shows that there are indeed no detailed explanations for the evolution of blood clotting in the literature and that, despite Darwinian protestations, the irreducible complexity of the system is a significant problem for Darwinism.
2. Although embedded in a lengthy description of how blood clotting and other systems work, Professor Miller’s actual explanation for how the vertebrate clotting cascade evolved consists of one paragraph. It is a just-so story that doesn’t deal with any of the difficulties the evolution of such an intricate system would face. Even so, in the one paragraph, Miller proposes what looks like a detrimental or fatal situation, akin to the knock-out mice (above) that lack critical components.
3. Keith Robinson proposed that a cascade might begin with a single enzyme with three different properties. Upon duplication of the gene for the enzyme, the duplicate loses several of the properties, resulting in a two-component cascade. Repetition of the scenario builds cascades with more components. Although intriguing, the scenario starts with a complex, unjustified situation (the enzyme with multiple abilities) that already has all the necessary activities. What’s more, the proposed gene duplication and several steps needed to lose function are “neutral,” unselected mutations. Stringing together several very specific neutral mutations to build a complex system is vastly improbable and amounts to intelligent design.
http://www.trueorigin.org/behe03.asp


The irreducible interdependence of information generation and transmission systems
1. Codified information transmission system depends on: 
a) A language where a symbol, letters, words, waves or frequency variations, sounds, pulses, or a combination of those are assigned to something else. Assigning meaning of characters through a code system requires a common agreement of meaning. Statistics, Semantics, Synthax, and Pragmatics are used according to combinatorial, context-dependent, and content-coherent rules. 
b) Information encoded through that code,
c) An information storage system, 
d) An information transmission system, that is encoding, transmitting, and decoding.
e) Eventually translation ( the assignment of the meaning of one language to another )
f)  Eventually conversion ( digital-analog conversion, modulators, amplifiers)
g) Eventually transduction converting the nonelectrical signals into electrical signals
2. In living cells, information is encoded through at least 30 genetic, and almost 30 epigenetic codes that form various sets of rules and languages. They are transmitted through a variety of means, that is the cell cilia as the center of communication, microRNA's influencing cell function, the nervous system, the system synaptic transmission, neuromuscular transmission, transmission b/w nerves & body cells, axons as wires, the transmission of electrical impulses by nerves between brain & receptor/target cells, vesicles, exosomes, platelets, hormones, biophotons, biomagnetism, cytokines and chemokines, elaborate communication channels related to the defense of microbe attacks, nuclei as modulators-amplifiers. These information transmission systems are essential for keeping all biological functions, that is organismal growth and development, metabolism, regulating nutrition demands, controlling reproduction, homeostasis, constructing biological architecture, complexity, form, controlling organismal adaptation, change,  regeneration/repair, and promoting survival. 
3. The origin of such complex communication systems is best explained by an intelligent designer. Since no humans were involved in creating these complex computing systems, a suprahuman super-intelligent agency must have been the creator of the communication systems used in life. 

The software and hardware of the cell are irreducibly complex
1. The cell contains a complex information storage medium through DNA.
2. The cell has a complex information processing system ( through  RNA polymerase, transcription factors, a spliceosome, a  ribosome,  chaperone enzymes, specialized transport proteins, and ATP
3. The cell contains a genetic code that is at or very close to a global optimum for error minimization across plausible parameter space
4. The cell stores complex, specified, coded information ( the software )
5. The cell has a complex translation system through a universal cipher, which assigns 61 codons (4x4x4=64-3 stop and start=64) to 20 amino acids and permits the translation of the genetic code into functional proteins
6. This constitutes a logical structure of information processing: DNA>>RNA>>>Protein, based on software and hardware. Both aspects must be explained.
7. There is no reason for information processing machinery to exist without the software, and vice versa.
8. Systems of interconnected software and hardware are irreducibly complex.
9. A irreducible complex system can not arise in a stepwise, evolutionary manner.
10. Only minds are capable to conceptualise and implement  instructional information control systems transformed into molecular dynamics
11. Therefore, an intelligent designer exists.


Translation through the ribosome is an irreducible, integrated complex process
1. A bacterial cell depends upon a translation and coding system consisting of 106 distinct but functionally integrated proteins as well several distinct types of RNA molecules (tRNAs, mRNAs, and rRNAs). This system includes the ribosome (consisting of fifty distinct protein parts), the twenty distinct tRNA synthetases, twenty distinct tRNA molecules with their specific anticodons, about 200 ribosome assembly proteins and 75 co-factors, chaperones, free-floating amino acids, ATP molecules (for energy), and—last, but not least—information-rich mRNA transcripts for directing protein synthesis. Many of the proteins in the translation system perform multiple functions and catalyze coordinated multistep chemical transformations.
2. The ribosome is the 3D printer of proteins. A human-made 3D printer is made of several functional parts, like the nozzle, the extruder, cooling fan, heated be, the painter's tape, etc. The 3D extruder has no use on its own. But only, when working inside the 3D printer in the right place. In the same sense, as an engineer would not project, invent, create and make a blueprint of a 3D printer extruder with no use by its own, but only conjoined, and together with all other parts while projecting a whole printer, envisioning its end function and use, its evident that unguided random natural events without foresight would not come up with an assemblage of tiny molecular machines, enzymatic structures with unique contours, which bear no function by their own, but only when inserted as part of the ribosome with higher ends, being essential for cells to translate DNA information into proteins, and being a key part participating to perpetuate life. Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. In other words: Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overarching design goal. A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (instructed complex information), irreducible complexity, and the setup of complex machines with little tolerance of change.   Therefore, intelligent design constitutes the best explanations for the origin of the information guiding the making of the irreducible and integrated complex ribosome protein factory.

1. High information content (or specified complexity), irreducible complexity, and the setup of exquisitely integrated circuits, which by significant alterations are inevitably damaged or destroys the function,   constitute strong indicators or hallmarks of (past) intelligent design.
2.The high information content and biological irreducible metabolic pathways which also require regulation and structured in a cascade manner, similar to electronic circuit boards, utilizing proteins and enzymes that manifest by themself irreducible complexity, constitute strong indicators or hallmarks of (past) creation through intelligent intervention,  and design.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (instructed complex information), irreducible complexity, and the setup of complex circuits with little tolerance of change. 
4. Therefore, intelligent design constitutes the best explanation for the origin of information and irreducible complexity in metabolic biological circuits.



The oxygen-evolving complex (OEC) of photosystem II is irreducibly complex.
1. One of the most important and fundamental biochemical reactions on which all advanced life-forms depend is performed by the oxygen-evolving complex (OEC) in oxygenic photosynthesis, responsible for catalyzing the light-driven oxidation of water to molecular oxygen in plants, algae, and cyanobacteria. It is also described as "undoubtedly one of the most remarkable inventions in all of biology." OEC is surrounded by 4 core proteins of photosystem II at the membrane-lumen interface.  It remains a fundamental mystery of how this complicated, four-electron transfer process originated. Enigmatic is how the precise geometry and unique mechanism of the OEC came about. Key differences exist between oxygenic and anoxygenic photosynthetic machinery with no apparent homologs or transitional forms that would provide clues to their development. Foremost among these differences is the presence and key role of manganese at the site of water oxidation in photosystem II. This is distinct from bacterial anoxygenic reaction centers, which rely on redox-active periplasmic proteins as electron donors.
2. According to peer-reviewed scientific papers, each of the four extrinsic proteins, (PsbO, PsbP, PsbQ, and PsbR)  of plants are ESSENTIAL, and each was tested upon mutated form, and the mechanism was found inefficient and compromising the OEC function. Furthermore, a water network around the Mn4CaO5 cluster and D1 protein subunit of PSII is also indispensable, and irreducible.  Site-directed mutants show severe impairment of the water oxidation cycle and fail to grow photoautotrophically.
3. That means evolutionary intermediates are non-functional. There is a precise fit and size matching of the residues with the individual atoms of the clusters. This is evidence, that this most fundamental biochemical reaction could not have emerged by evolutionary, step-wise mechanisms, and therefore, Darwin's theory has been falsified and refuted. The only plausible alternative to Darwinian evolution is intelligent design.


The argument of the zip-codes within the cell
1.  Michael Denton compared the cell to a city.  He writes: “To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometers in diameter and resembles a giant airship large enough to cover a great city like London or New York.  What we would then see would be an object of unparalleled complexity and adaptive design.... a world of supreme technology and bewildering complexity.”
2. This has become more then true by discovering new details in the mind-boggling complex life of the cell. Proteins are the workhorses of the cell, but to get the most work out of them, they need to be in the right place.  In neurons, for example, proteins needed at axons differ from those needed at dendrites, while in budding yeast cells, the daughter cell needs proteins the mother cell does not.  In each case, one strategy for making sure a protein gets where it belongs is to shuttle its messenger RNA to the right spot before translating it. The destination for such an mRNA is encoded in a set of so-called “zipcode” elements, which loop out of the RNA string to link up with RNA-binding proteins.  In yeast, these proteins join up with a myosin motor that taxis the complex to the encoded location.
3. All the above speaks about amazing, irreducible complexity and intelligent design of one of the simplest cells, the yeast. How this complex system evolved was not explained. This complexity found in the simple cell of yeast is one more example out of innumerable complex systems that are necessary for the existence of the cell. 
4. The irreducible complex systems are evidence of an intelligent design that could have been made only by a super-intelligent person all men call God.


Proteasomes
1. The disposal of protein “trash” in the cell is the job of a complex machine called the proteasome.  What could be lower than trash collection?  Here also, sophisticated mechanisms work together. 
2. PhysOrg described a new finding that shows that “two different mechanisms are required to determine which targets to destroy.” The “recognition tag” and “initiator tag.”
3. Both mechanisms have to be aligned properly to enter the machine’s disposal barrel.  “The proteasome can recognize different plugs1, but each one has to have the correct specific arrangement of prongs1,” said a researcher at Northwestern University.
4. This is another example of interdependent irreducible complex systems. One can’t argue for evolution; that first only one system existed.
5. The work of a designer is again obvious and all men call him God.

The argument of increasing knowledge about the complexity of the cell 
1. Almost 30 years ago, in 1985 Michael Denton in his book Evolution: A Theory in Crisis, p. 328 compared a cell to a large city, filled with “supreme technology and bewildering complexity.”  Nowadays we have not only much more detailed information about the complexity of the cell and how life works but also every week in the reports/writings of science, new findings are made about regulators, teams, quality controls, checkpoints, conductors, players with starring roles. Let’s see a few examples:
a. Bricks that build:  “Researchers have found in mice that supporting cells in the inner ear, once thought to serve only a structural role, can actively help repair damaged sensory hair cells, the functional cells that turn vibrations into the electrical signals that the brain recognizes as sound.”
b. Master regulator: Whether or not a cell grows is decided by a remarkable protein kinase enzyme called mTOR. As part of two complexes, mTORC1 and mTORC2, mTOR integrates and interprets all sorts of factors that influence cell growth — including nutrients, stressors (=agents that causes stress to an organism), and the outputs of signal-transduction networks (=biological circuits that pass along information) — by targeting a multitude of substrates that drive processes such as protein translation, metabolism, and cell division. Research into mTOR-mediated signaling has taken on added urgency since it was discovered that most cancers contain mutations that inappropriately activate this protein.
The newly-uncovered structure of mTOR, made up of 1,500 amino acids, shows that it has a “gatekeeper mechanism that controls substrate access to the active site.”
c. Checkpoint Charlies:  “MTBP acts with Treslin/TICRR to integrate signals from cell cycle and DNA damage response pathways to control the initiation of DNA replication in human cells.”
d. Damage repair: One latest study, performed on yeast cells, describes cooperation between translesion DNA synthesis (TLS), single-stranded DNA repair (ssDNA), and homologous recombination, which rebuilds a damaged strand from the intact strand.  “These findings suggest that ssDNA that might originate during the repair of closely opposed lesions or of ssDNA-containing lesions or from uncoupled replication may drive recombination directly in various species, including humans.”
2. All these examples indicate the irreducibly complex system of the cell’s life and structure. If not assembled all together at the same time even the simplest cell could not survive. There would be no life on this earth.
3. Intelligent design and creation by a brilliant intelligent person all men call God is most likely true.

Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.
In other words: Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overarching design goal.
A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution. 



Last edited by Otangelo on Tue Jan 19, 2021 6:54 am; edited 4 times in total

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Argument: There is no empirical proof of God's existence. Extraordinary claims require extraordinary evidence. 
Answer: There is no empirical proof of God's existence. But there is neither, that the known universe, the natural physical material world is all there is. 
The burden of proof cannot be met on both sides.  Consequently, the right response does not need an empirical demonstration of Gods existence
but we can elaborate philosophical inferences to either affirm or deny the existence of a creator based on circumstantial evidence, logic, and reason.

The first question to answer is not which God, but what cause and mechanism best explain our existence. There are basically just two options.
Either there is a God/Creator, or not. Either a creative conscious intelligent supernatural powerful agency above the natural world acted and was involved, or not.
That's it.  All answers can be divided into these two basic options, worldviews, and categories. 

Design can be tested using scientific logic.  How? Upon the logic of mutual exclusion, design and non-design are mutually exclusive( it was one or the other) so we can use eliminative logic: if non-design is highly improbable, then the design is highly probable.  Thus, evidence against non-design
(against production of a feature by undirected natural process) is evidence of design.  And vice versa. The evaluative status of non-design 
(and thus design)  can be decreased or increased by observable empirical evidence, so a theory of design is empirically responsive and is testable.

God is "the light of being itself", the answer to the question of why there's existence to begin with.
… according to the classical metaphysical traditions of both the East and West, God is the unconditioned cause of reality – of absolutely everything that is – from the beginning to the end of time. Understood in this way, one can’t even say that God "exists" in the sense that my car or Mount Everest or electrons exist. God is what grounds the existence of every contingent thing, making it possible, sustaining it through time, unifying it, giving it an actuality. God is the condition of the possibility of anything existing at all.

Cosmological arguments:

Being cannot come from non-being.
Since we exist, then being has always been in one form or another.
Since the universe had a beginning, a non-physical being must have existed beyond the universe, causing the universe into existence.
That being is God.

1. Being cannot come into existence from absolutely nothing.  If there ever would have been a state of absolutely nothing, then that state would not change, but remain so.  Since there is existence, being has always been.  
3. Since the physical universe had a beginning, and infinite regress of  physical causes is not possible. the cause must be non-physical and eternal.  
3. That “being” must have existed without beginning, eternally, and be spiritual in nature. This being, we call God.
 
1. Something cannot come into existence from absolutely nothing.
2. The universe had a beginning. The present moment cannot be reached by adding individual events together from eternity. The second law of thermodynamics refutes the hypothesis of an eternal universe.
3. Therefore an eternal & necessary first cause is the best explanation of our existence.
4. An agent endowed with free will can have a determination in a timeless dimension to operate causally at a (first) moment of time and thereby to produce a temporally first effect.
 
1. If there ever was nothing at all, then there would still be absolutely nothing.
2. Since something does exist, one must logically conclude that something has always existed.
3. That “something” must be either physical or non-physical. If it were physical, we would have to ask, what caused that 
4. Since the physical universe began to exist, the cause must be non-physical.  Another term for the “non-physical” would be “spirit.”
5. Therefore, that “something” must have existed eternally, and be and spiritual in nature. This being, we call God.

1. Something cannot come into existence from absolutely nothing.
2. The universe had a beginning, therefore, it had a cause. So the existence of the universe depends on the existence of that cause.
3. The present moment cannot be reached by adding individual events together from eternity.
4. The second law of thermodynamics refutes the hypothesis of an eternal universe.
5. Therefore an eternal & necessary first cause is the best explanation of our existence.
6. An agent endowed with free will can have a determination in a timeless dimension to operate causally at a (first) moment of time and thereby to produce a temporally first effect.


1. Contingent or non-necessary beings depend on an external cause that made them come into existence - the physical universe – is also contingent.
2. Since that external cause has to be outside the whole aggregate of contingent things, it cannot itself be contingent. So it is necessary.
3. Hey presto, we’ve demonstrated that there is a necessarily existent, uncreated, non-contingent being which causes all other things! And this, of course, is God.

6. Since the physical universe came into existence at a finite time ago, the cause must be non-physical.
7. Another term for the “non-physical” would be “spirit.”
8. Therefore, that “something” must have existed eternally, and be and spiritual in nature. This being, we call God.

The Thomistic Cosmological Argument
There are dependent beings.
If something is a dependent being, then its continued existence must be sustained by something else.
If a dependent being is sustained by something else, then either the chain of sustained beings regresses infinitely or terminates in an independent being that is not itself sustained.
The chain of sustained beings cannot regress infinitely.
Therefore, the chain of sustained beings must terminate in an independent being that is not itself sustained.

1. The universe is either eternal, or it had a beginning. Most probably it had a beginning, based on philosophical and scientific considerations. 
2. Everything which has a beginning has a cause.
3. Therefore, the Universe had a cause.

1. The universe obeys laws and rules of mathematics and physics, a specific set of equations, upon which it operates with stability, Constance and regularity.
2. The implementation of laws of mathematics and physics depends on the action of an intelligent rational agency.
3. Therefore, the physical universe which operates in an interdependent manner with the laws of physics was with high certainty implemented by an intelligent creator. 

1. The universe obeys laws and rules of mathematics and physics, a specific set of equations, upon which it can exist and operate. That includes Newtonian Gravity of point particles, General Relativity and Quantum Field Theory. Everything in the universe is part of a mathematical structure. All matter is made up of particles, which have properties such as charge and spin, but these properties are purely mathematical.
2. The implementation of laws of mathematics and physics depends on the action of an intelligent rational agency.
3. Therefore, most probably, an intelligent creator of the universe exists.

1. Physical laws are descriptive of what has never been observed. But there is no particular reason or physical necessity for why they are the way they are, and making a life-permitting universe possible. In fact, these sets could take any value, and be different.
2. The explanation of why the universe obeys in specific these life-permitting laws and set of equations can be due to either the existence of an infinite set of laws in an infinite number of universes, each obeying a different set of physical laws, which are not life-permitting, or the set-up by a powerful intelligent creator.
3. Multiverses are undetectable and unobservable, and there is no evidence of their existence. Furthermore, it would take  10^123 attempts to fine-tune the cosmological constant, to have a universe, either life-permitting or non-life permitting. There are about 10^80 atoms in the known universe. And either our universe or a set of multiverses had to have a beginning, so a cause cannot be avoided.  So the multiverse proposal is not only entirely unscientific but disregarding Occam's razor, where the least speculation is usually better.

1. The physical universe is governed by physical laws. Both are interdependent and irreducible. There would not be one without the other.
2. Laws and require a lawgiver. And interdependent systems a creator
3. Therefore, nature, the laws of nature, and their interdependence require a creator.

1. The initial conditions of the universe, subatomic particles, the Big Bang, the fundamental forces of the universe, the Solar System, the earth and the moon, are finely tuned to permit life. Over 150 fine-tuning parameters are known.
2. Finetuning is either due to chance, necessity or design.
3. Finetuning is extremely unlikely due to chance or necessity. Therefore, it is most probably due to a powerful creator which did set up the universe in the most precise exact fashion to permit life on earth.

Arguments for the origin of life

1. Either life is due to natural processes, or intelligent design.
2. Life is not due to natural processes,
3. Therefore it is due to intelligent design.

1. Factories are the result of intelligent design
2. Biological cells are factories
3. Therefore, biological cells are designed. 

1. Either high levels of complexity seen in the living is due to a designer, or random chance.
2. The enemy of the arise of complex self-replicating energy-demanding Physico-chemical structures is entropy
3. Therefore, it is far more likely that an intelligent designer did setup life, rather than chance.

1. The origin of blueprints containing the information to fabricate complex machines and interlinked factories which produce goods for specific purposes are both always the result of intelligent setup.
2. Living Cells store very complex genetic and epigenetic information through the genetic code, and over twenty epigenetic languages, translation systems, and signaling networks. These information systems instruct the making and operation of cells and multicellular organisms. Each cell hosts millions of interconnected molecular machines, production lines and factories analogous to factories made by man. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks. Cells operate robot-like,  autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advance and sophistication.
3. Therefore, the origin of biological information and self-replicating cell factories is best explained by the action of an intelligent designer, who created life for his own purposes.

1. Cell subunits and compartments form a complex system that is useful only in the completion of a much larger system that is able to keep the basic functions of life. A minimal Cell, in order to permit life, requires a minimal genome of about 200 genes, and at least 560 interconnected proteins, each fully set up and functional for specific tasks. A discrete minimal size of each individual protein complex formed by multiple subunits and cofactors is required in order to be functional. And it only operates when interconnected and in a joint venture similar to a robot in a production line, and precise energy supply.
2. Cells must be created and be functional, all at once. Irreducibly complex and interdepend systems cannot evolve but depend on intelligence with foreknowledge on how to build discrete parts with distant goals. 
3. Therefore, intelligent design is the best explanation of the origin of living, self-replicating cells. 

1. DNA stores information based on a code system, and codified, complex, instructional information, with the same function as a blueprint.  
2. All codes and blueprints come from intelligence.
3. Therefore, the genetic code and the instructions to build cells and complex biological organisms, stored in DNA, were most likely created by an intelligent agency.

1. Protein domains appear analogous to words in natural languages in which the rules of word association are dictated by linguistic rules or grammar.
2. The set up of words, languages, rules of association and linguistic rules, and grammar come always from intelligence
3. Therefore the set up of rules existing for protein domains is best explained by an intelligent designer

1. Cells use sophisticated information selection ( the Gene regulatory network ) encoding and transcription ( DNA & RNA polymerase machines ) transmission (mRNA), and decoding ( Ribosome ) systems.
2. Setup of information transmission systems, aka.  Selection, encoding, transmission, and decoding are always a deliberate act of intelligence
3. The existence of the genetic information transmission system is best explained by the implementation of an intelligent designer.    

1. Blueprints, instructional information and master plans, and the make of complex machines and factories upon these are both always tracked back to an intelligent source which made both for purposeful, specific goals. 
2. The Blueprint and instructional information stored in DNA, which directs the making of biological cells and organisms - the origin of both is, therefore, best explained by intelligent design. 

1. The implementation and construction of factory parks for specific goals depends always on planning, elaborating blueprints and codified specified instructions.
2. The make and development of cells that are literally self-replicating factories are due to blueprints, genetic instructions,  stored in DNA. 
3. All information storage devices, code languages, blueprints, information transmission systems, translation ciphers, with the purpose to make factories, are of intelligent origin. Biological cells are therefore the result of Intelligent design.


1. The basic building blocks of life have never been synthesized in the lab. Evidence has demonstrated that prevital unguided origin of each of the four classes is not possible.
2. Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. Either the basic building blocks of life were created, or the result of unguided prebiotic events.
3. Since prebiotic synthesis is not possible by unguided natural means, most likely they were created by an intelligent designer.  

Arguments based on biocomplexity and biodiversity

1. The mechanisms required to build complex organismal form is preprogrammed instructional complex information encoded in various genetic and at least 23 epigenetic codes and languages and communication by various signaling codes through various physicochemical signaling networks.
2. Science has demonstrated, that evolution by mutations and natural selection genetic drift, and gene flow result in entropy, deteriorate the genome, rather than increasing information and organismal complexity.
3. The origin of instructional complex information ( analogous to blueprints ) and signaling networks is always tracked back to intelligence setting them up with specific purposes.
4. Therefore, biodiversity and organismal architecture are better explained by an intelligent creator, rather than mindless evolution.

1. Regulation, governing, controlling, recruiting, interpretation, recognition, orchestrating, elaborating strategies, guiding, instruct are all tasks of the gene regulatory network.
2. Such activity can only be exercised if no intelligence is present if the correct actions were pre-programmed by intelligence.
3. Therefore, most probably, the gene regulatory network was programmed by an intelligent agency.

1. Complex multicellular lifeforms depend on gene regulatory networks (dGRN's) which are a collection of molecular regulators that interact with each other and with other substances in the cell to orchestrate the expression of DNA. 
2. dGRN's operate based on logic gates and their networks process chemical input signals similar to computers. These encoded instructions are based on boolean logic.
3. Logic depends on reason. Reason depends on intelligence. Only an intelligent mind can think rationally, and implement a system based on conceptual laws of logic. Therefore, the best and most reasonable explanation for the existence of complex gene regulatory networks based on boolean logic, essential for the making of complex multicellular organisms, is the creative action of a powerful, transcendent, intelligent Creator. 

1. The setup of functional Information retrieval systems, like a library classification system, is always tracked back to intelligence
2. The gene regulatory network is a fully automated, pre-programmed, ultra-complex gene information extraction system
3. Therefore, its origin is best explained through the intelligent setup

1. The genomic program for development operates primarily by the regulated expression of genes encoding transcription factors and components of cell signaling pathways.
2. A program can always be traced back to a programmer.
3. Therefore, the genomic program of development most probably was programmed by a programmer. That programmer is God.

Arguments based on morality

1. If objective moral values exist, then God exists.
2. Objective moral values exist.
3. Therefore, God exists.

1. If there is no God, there are no objective moral values, since they are prescribed " ought to be's". Then moral values are just a matter of personal opinion, and as such, no objectively or universally valid at all.
3. If that is the case, unbelievers have no moral standard to judge anything as morally good or bad.
4. But torturing babies for fun is always bad, no exception, therefore, objective moral values exist, and God exists. 


Argument from logic

1. Minds exist which have and use objective logic.
2. Objective logic cannot be based on our subjective minds, a non-static universe or immaterial abstractions outside of a mind.
3. Objective logic depends and can only derive from a pre-existing necessary first mind with objective logic. 

Matter-antimatter pair production ratio 1 in 10 billion of “leftover particles” happens to be the exact amount of mass necessary for the formation of stars, galaxies, and planets. The number of electrons (in the universe) is equivalent to the number of protons to an accuracy of one part in 10 to the 37th power. If it were not so, galaxies, stars, and planets would never form. Upon the finetuning by a happy accident of the cosmological constant,  the probability that our universe contains galaxies is akin to exactly 10^123. That is 1 possibility in 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000, 000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 . During one orbit around the Sun, Earth actually rotates about its own axis 366.3 times. The Moon orbits the Earth in 27.3 days. Of course, a day is one Earth rotation on its own axis. 366.3 x 27.3 = 9999.99 At the same time, the Earth is 366.3% the diameter of the Moon and the Moon is 27.3% the diameter of Earth. 366.3% x 27.3% = .999999. The combined diameter of all the planets in our solar system is 10 times greater than the Earth’s circumference. This has astonishingly high accuracy at 99.99%. The distance between the moon and the sun is 400 times greater than the distance from the earth and the moon. The Sun happens to be 400 times the Moon’s diameter, and 400 times as far away. This means the Sun and Moon appear to be the same size when viewed from Earth. The circumference of the earth at the equator is 24,901.55 miles. The earth’s rotation speed is 1037.5646 mph. If you divide 24,901.55 by 1037.5646 you get 24. Which is the number of hours in a complete day. Just enough rotation speed compared to it’s size to equal a perfect exposure to both sunlight and darkness so that life could exist here.

Concluding a Creator as the best explanation of our existence is not an argument based on gaps of knowledge and ignorance or circular reasoning, but on a solid epistemological framework and sound scientific, philosophical and theological reasoning, and what we do know, discovered and observed in the natural world.
 
From absolutely nothing, nothing comes. Creation demands an Intelligent Designer. If there were no creator, there would still be nothing. The universe had a beginning and requires, therefore, a cause. The universe cannot be past eternal. This present moment in time can't represent an actually infinite number of events added one to another proceeding from the past. Time has proceeded forward from the past as one event is added onto another to get us to today.  But we know that whenever you pause in the count as we've done today, that you can't have an infinite number of events.  This means that there is not an infinite number of events that go backward from this point in time. Which means the universe is not eternal. The physical laws require a lawmaker. The physical universe and its laws are interdependent.

There are over 150 finely-tuned constants of the universe that must be all just right to the extreme. The expansion rate of the Big bang, the cosmological constant, the four fundamental forces,  and the earth, are fine-tuned and require a tuner. It is astonishing to say the least, that the number of electrons (in the universe) is equivalent to the number of protons to an accuracy of one part in 10 to the 37th power. If it were not so, galaxies, stars, and planets would never form. Quarks and anti-quarks form via matter-antimatter pair production. Because of their nature, these particles instantly annihilate each other. However, during the Big Bang, a slight asymmetry in this pair production resulted in approximately 1 extra particle of matter for every 10 billion produced. It turns out that this 1 in 10 billion ratios of “leftover particles” happens to be the exact amount of mass necessary for the formation of stars, galaxies, and planets. As much as 2 in 10 billion, and the universe would have just been filled with black holes. As little as 0.5 in 10 billion, and there wouldn’t have been enough density for galaxies to form.

Life comes only from life.  How is the origin of these things best explained? Supercomputers, hardware, software based on a language using signs and codes like the alphabet, an instructional blueprint, complex machines, factory assembly lines, error check and repair systems, recycling methods, waste grinders and management, power generating plants, power turbines, and electric circuits? Randomly, by unguided, accidental events, or intelligent invention, planning, design, and implementation?  Chance is the ONLY causal alternative, once the design is excluded, to explain the origin of biological Cells, which are literally miniaturized, ultracomplex, molecular, self-replicating factories. Conscience,  free will, morality, human values, logic, speech, the mind, and beauty are also all best explained through design. Based on evidence and observation, it makes the most sense, and it is rational to conclude that the probability is far far higher, that the natural world was created, rather than not. That is not an argument of ignorance but based on positive scientific evidence.

The day when scientists discovered that the universe most probably a beginning, it was doomsday for naturalism. Even more, when unprecedented evidence elucidated the shocking and incredible fact that the universe, from the quantum to the macro scale, was adjusted in the extreme to make life possible on earth.
When it became clear, that DNA stores codified information, as well. When it became clear, that biological Cells are miniaturized factories, the funeral bells for a worldview without God were ringing. And so, when science became slowly to realize that Darwin's idea was a fluke.

Nonetheless, atheists are singing, mocking, rattling their instruments, blowing their trumpets, organizing marches for humanism and secularism, celebrate their stars, open temples to express their unbelief, name-calling who defies them, express their unbelief in the Bible and think it was debunked, and doing nothing else than expressing their brainless blindness. What a strange world in which we live.....

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1. Things with specific purposes are always first the product of a creative mind, and then physically instantiated. With the end in mind, a blueprint is made which permits the implementation of the desired result.
2. DNA, the blueprint of life, instantiates the making of the cell, its operation and  processes.
3. Therefore, life is the product of Gods mind.

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