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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The HOX code - a nightmare for proponents of Evolution

In order to know what mechanisms eventually provoke change and if unguided evolution of an organism is a viable explanation, it must be known what mechanisms do form phenotype,  body architecture, organs, various cell types, cell migration etc. Development biology ( Evo-devo ) is a rather new branch of biology, but, yesterday, I gave a look at the book   Development biology, Gilbert / Barresi. 11th ed 2018. Despite studying biology for years, I had the impression to know almost nothing of what is described there. Development biology might be the most complex branch of biology, and many open questions remain.

Homeoboxes have been found in fungi, plants and animals. In each "kingdom" homeobox genes occupy a key position in the genetic control of either cell differentiation, morphogenesis and or body plan specification.

All Hox genes and many other developmental transcription factors contain the homeobox,  known for their colinearity: conserved arrangement on chromosomes that is the same as their order of activation along the body axis. The regulation is very precise.  The degree of sequence conservation of the homeodomain is extremely high indicating strong functional constraints leading to a high pressure to retain the homeobox sequences constant.

What the Hox code represents is a somewhat digital mechanism for regulating axial patterning. By mixing and matching combinations of the expression of a small number of Hox genes, organisms generate a greater range of morphological possibilities.

It is obvious that not any arrangement of Homeobox genes will give rise to functional body architecture. The precise arrangement is key to have functional body plans.  Mutations in hox genes do produce aberrant body plans..like legs where there should be antennae in fruit flies. But it is a mistake to assume that this is evidence that hox genes causally lay out the body plan, just like it would be a mistake to assume that a fault in a TV, causing a disruption in the reception of the signal, shows that the TV box produces the signal itself. Linear DNA cannot produce 3D form. There is a higher orchestration, which directs the correct linear arrangement of Homeobox genes in the genome.

Hox Genes in Development: The Hox Code
https://www.nature.com/scitable/topicpage/hox-genes-in-development-the-hox-code-41402

This colinearity, arrangement, order of activation and precise regulation of Hox gene clusters indicates there is a HOX Code, which sets the right pattern of Hox gene cluster arrangement for correct sequential expression of segments and rhombomeres in the embryo.  

There is uncertainty in our understanding of homeobox gene cluster evolution at present. This relates to our still rudimentary understanding of the dynamics of genome rearrangements and evolution over the evolutionary timescales being considered when we compare lineages from across the animal kingdom.

The mechanisms responsible for the synchronous regulation of Hox genes and the molecular function of their colinearity remain unknown. Despite 35 years of active research, the mechanisms of Hox gene regulation have remained elusive. It has been argued that chromatin structure and histone demethylation play important roles in activation of Hox genes, but the mechanism precisely directing chromatin modifications to specific loci at the right time remains mysterious.

What does this elucidate? Life is not only composed of organic carbon-based matter but essentially, instructional information. Not any kind of information, but complex, specifying information, blueprints, which precisely orchestrates and directs how to develop, build, adopt animals, plants, fungi, bacterias, and perpetuate life in all its various forms.

1. Cells store codified information in DNA, and at least 18 epigenetic codes, which are complex instructional informational blueprints, essential for cells to make copies of themselves, animal development, adaptation, and body architecture
2. All Codes, and blueprints we know the origin of come from an intelligent mind. Evolution is a non-directed, non-intelligent process and does not suffice to explain the origin of biodiversity and body architecture.
3. Therefore we have 100% inference that DNA comes from an intelligent mind and 0% inference that it is not.

The various codes in the cell
http://reasonandscience.catsboard.com/t2213-the-various-codes-in-the-cell

The Genetic Code
The Splicing Codes
The Metabolic Code
The Signal Transduction Codes
The Signal Integration Codes
The Histone Code
The Tubulin Code
The Sugar Code
The Glycomic Code
The non-ribosomal code
The Calcium Code
The RNA code
A domain substrate specificity code of Nonribosomal peptide synthetases (NRPS)
The DNA methylation Code
The coactivator/corepressor/epigenetic code
The transcription factor code
The post-translational modification code for transcription factors
The HOX Code

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152 Re: My articles on Wed Nov 07, 2018 4:19 am

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Charles Darwin attended a Church of England school. With the aim of becoming a clergyman, he went to the University of Cambridge and studied Anglican theology.

As a non-conformist, he, like many apostates, and founders of sects, invented a branch of the religion called natural atheology

Natural Atheology
https://www.cambridge.org/core/books/darwinian-heresies/natural-atheology/61E8212A6EAC59F908A6D83F6ADA7B82

becoming its Pope, high-priest, bishop, and main evangelist and propagandist. A true all-in-one job. He is the author of the naturalists Bible, the famous book On the Origin of Species by means of natural selection, published on 24 November 1859.

Today, after almost 160 years, his religion is wide-spread, in special amongst evolutionary biologists and biochemists, atheists and agnostics, and widely taught in public schools, and has still resisted the growing evidence provided by scientific inquiry and advance, demonstrating that the real mechanisms that guide speciation, evolution, grow, phenotype formation, body architecture, development and biodiversity at large depend on guided pre-programming, various genetic and epigenetic codes and languages, sophisticated information selection, encoding, transmission, decoding, and interdependent biological principles - specialization, messaging, stigmergy and apoptosis.

As such, his hypothesis of mindless mutations and natural selection, and later, genetic drift and gene flow have been shown to be demonstrably false, and his postulates remain in the realm of blind faith, and his followers follow his footsteps as Popes, pastors, evangelists, propagandists influencing many, infesting the minds of the incautious and uneducated, which firmly believe that natural causes have the capacity to replace intelligence of the highest order to implement the most complex Uber computers, and veritable High-tech factory complexes, more complex than any factory made by man: biological Cells.

Hosea 4.6: My people are destroyed from lack of knowledge.

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153 Re: My articles on Thu Nov 08, 2018 6:50 pm

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Despite the common attacks from the atheist camp, we need to learn, to be more gracious, that we respond their insults by either remain quiet, or leave the debate when it fits, without lower the level, and show them that we adopt a spirit of love ( and as such, be morally superior to them ). But we need to demonstrate also strength and courage, being bold and fearless, secure and convinced of what we believe, and that we adopt reason and logic in our thinking. And that strength comes from showing them that we can both: believe in the supernatural, and miracles, but at the same time well understand the natural world and its inner workings, as far as science permits. And show, that the natural world points, yeah, breaths, even screams out in all its levels and dimensions, from the extreme precision and fine-tuning of the atoms and its forces to the formidable engineering in the molecular world and the sophisticated language employed in DNA, to the colorful beauty of nature, to the whole universe and its extreme tuning: design !!

They might not understand the language of the natural world, and what it transmits to us because their mind is darkened by their will to deny God. But God does, when he wills so and draws the unbeliever to him, and when the atheist's eyes are open, he suddenly sees differently. His blinkers fall off. Our worldview grows and takes form by putting the pieces of information together, bit by bit. One information here, another there. When an atheist finally permits the truth to reach him, his intellectual cognitive dissonance is removed, and an aha moment is the starting point to get things straight. That's when intellectual satisfaction comes to his mind and his heart. That's when his soul begins to breathe, and God begins to shine in his heart, and the warmth of his love to give him peace.

John 1:3 Through him ( Christ) all things were made; without him nothing was made that has been made.

Psalm 19:1-4“ The heavens declare the glory of God; the skies proclaim the work of his hands. Day after day they pour forth speech; night after night they display knowledge. There is no speech or language where their voice is not heard. Their voice goes out into all the earth, their words to the ends of the world.”

Nehemiah 9:6 "You alone are the LORD You have made the heavens, The heaven of heavens with all their host, The earth and all that is on it, The seas and all that is in them You give life to all of them And the heavenly host bows down before You.

Isaiah 66:2 "For My hand made all these things, Thus all these things came into being," declares the LORD "But to this one I will look, To him who is humble and contrite of spirit, and who trembles at My word.

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154 Re: My articles on Sun Nov 11, 2018 7:00 am

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Origins - what cause explains best our existence, and why? Philosophy and theology

Some time ago I posted at my timeline that it was my intention to write a book on origins. In the last few days, I realized, that if I wait, until I advance to cover all relevant issues on how biological Cells work, it will take years to finally start format and transform the collected information into book form. So I decided to start transferring the information that I have already at hand into book form through Scribus. That part is rather fast. In less than a day, I can write over 40 pages. The first 42 pages are ready, free for download. Please share with your friends and in special, with unbelievers.

At this stage, I have not added the information of all sources and links yet. So - please do not argue that I am plagiarizing. Most information is collected from third parties, and I inform the source. Later, I will insert and link to the sources.

The first three chapters are :

Chapter 1: Science only? Is science the only way to find truth?
Chapter 2: The God hypothesis
Chapter 3: The Theory of Intelligent Design

This is the link for download. The format is PDF:
https://ln.sync.com/dl/aecf30f00/7g99fwx5-6kt8y2mx-7427w6dd-nxwd5ep9

you will find the same information as well at my library::
http://reasonandscience.catsboard.com/t2742-origins-what-cause-explains-best-our-existence-and-why-philosophy-and-theology

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155 Re: My articles on Sun Nov 11, 2018 8:37 pm

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Thermodynamics and science predictions

It is often praised, how science based on methodological naturalism serves to make accurate predictions. Let's imagine that we would be aliens, being part of a super-intelligent civilisation. visiting early earth four billion years ago with a spaceship. We would find a hostile environment, no life, just spewing volcanoes etc.

We would leave, returning to our own planet, run a computer simulation, and make a prediction of how the earth would look like, 4 billion years later, and trying to simulate the effects that the four known forces of physics would have on every atom and every subatomic particle on our planet.

If we ran such a simulation out to the present day, would it predict that the basic forces of Nature would reorganize the basic particles of Nature into libraries full of encyclopedias, science texts and novels, nuclear power plants, aircraft carriers with supersonic jets parked on deck, and computers connected to laser printers, CRTs and keyboards?

If we graphically displayed the positions of the atoms at the end of the simulation, would we find that cars and trucks had formed, or that supercomputers had arisen? Certainly, we would not, and adding sunlight to the model would not help much.

The argument of thermodynamics was popular and often used by creationists, over a decade ago, but has gone a little bit abandoned in more recent Facebook times. The standard answers by atheists were that the earth is not closed, but an open thermodynamic system, receiving constantly energy through sunlight, which could decrease rather than increase entropy, so the argument is moot.

The Earth is an open system, it receives energy from the sun and entropy can decrease in an open system, as long as it is ‘‘compensated’’ somehow by a comparable or greater increase outside the system.

Isaac Asimov replied through an article at the Smithsonian journal:
You can argue, of course, that the phenomenon of life may be an exception [to the second law]. Life on earth has steadily grown more complex, more versatile, more elaborate, more orderly, over the billions of years of the planet’s existence. From no life at all, living molecules were developed, then living cells, then living conglomerates of cells, worms, vertebrates, mammals, finally Man. And in Man is a three-pound brain which, as far as we know, is the most complex and orderly arrangement of matter in the universe. How could the human brain develop out of the primeval slime? How could that vast increase in order (and therefore that vast decrease in entropy) have taken place?

Asimov concludes that the second law is not really violated, because: Remove the sun, and the human brain would not have developed . . . . And in the billions of years that it took for the
human brain to develop, the increase in entropy that took place in the sun was far greater; far, far greater than the decrease that is represented by the evolution required to develop the human brain.

Similarly, Peter Urone, in College Physics, wrote:
Some people misuse the second law of thermodynamics, stated in terms of entropy, to say that the existence and
evolution of life violate the law and thus require divine intervention. . . . It is true that the evolution of life from inert
matter to its present forms represents a large decrease in entropy for living systems. But it is always possible for the
entropy of one part of the universe to decrease, provided the total change in entropy of the universe increases.

The Theism VS Atheism debate is ALL about probability.

The reason natural forces can turn a computer or a spaceship into rubble and not vice versa is probability: of all the possible
arrangements atoms could take, only a very small percentage could add, subtract, multiply and divide real numbers, or fly
astronauts to the moon and back safely.

If an increase in order is extremely improbable when a system is closed, it is still extremely improbable when the system is
open, unless something is entering which makes it not extremely improbable.

The claim that the second law does not apply to open systems was invented in an attempt to avoid the evident implications and logical inference of a creator.

The missing ingredient is information.

Norbert Weiner - MIT Mathematician - Father of Cybernetics

"Information is information, not matter or energy. No materialism which does not admit this can survive at the present day."

Life is permeated by codified information. Not only genetic but mostly, epigenetic information. Complex blueprints, which direct how the most complex high-tech factory complex of the universe, biological cells, have to be built, and how to error check and repair themselves all along the production process of higher molecular machines, how to generate energy in the form of ATP molecules, how to import the basic, life-essential elements, purify them, use them to  build the basic building blocks of life like RNA, DNA, amino acids, carbohydrates and fatty acids, how to create a homeostatic ambiance permitting information exchange and signaling networks to operate, how to react to ecological cues, how to develop, and how to respond to nutritional demands. And it had all to be pre-programmed and set up in advance for life to kick off - without evolution.

This coincides with the REMARKABLE, awe -, well, actually the God-inspired beginning of the Gospel of John:

1 In the beginning was the Word, and the Word was with God, and the Word was God. 2 He was with God in the beginning. 3 Through him all things were made; without him nothing was made that has been made.

Science and religion are not at war, but actually complementary. One informs the other, and vice-versa. They are the same coin, one side showing the face, and the other side the numbers. Both point to God. A God that does not hide himself, but made himself known to us. John continues in verse 14:

The Word became flesh and made his dwelling among us. We have seen his glory, the glory of the one and only Son, who came from the Father, full of grace and truth.

What a remarkable revelation !! Praise the Lord.

What is remarkable as well about the above text is that it was essentially formatted as a scientific paper.

The article, ‘‘A Second Look at the Second Law,’’ by Dr. Granville Sewell, Professor of Mathematics at University of Texas at El Paso, was submitted on October 21, 2010 to the Journal of Applied Mathematics Letters. Dr. Sewell’s article was peer-reviewed and accepted for publication on January 19, 2011.

On March 2, 2011, the Editor-in-Chief of Applied Mathematics Letters, Dr. Ervin Rodin, decided to withdraw the article without consultation with the author, not because of any errors or technical problems found by the reviewers or editors, but because the Editor-in-Chief subsequently concluded that the content was more philosophical than mathematical and, as such, not appropriate for a technical mathematics journal such as Applied Mathematics Letters.

Truth is, the REAL problem was that it was Intelligent Design-friendly. Then , afterwards:

Applied Mathematics Letters, which agreed to apologize to Intelligent Design-friendly Texas professor Granville Sewell and have its publisher, Elsevier, pay $10,000 in legal fees, has posted the text of its apology

http://retractionwatch.com/2011/06/13/applied-mathematics-letters-posts-apology-for-retracting-intelligent-design-friendly-paper/

The Journal of Applied Mathematics Letters and its Editor-in-Chief, Dr. Rodin, provide their sincere and heartfelt apologies to Dr. Sewell for any inconvenience or embarrassment that may have been caused by their unilateral withdrawal of his article, and wish Dr. Sewell the best in the future and welcome Dr. Sewell’s submission of future articles for possible publication.

Dr. Sewell’s article as accepted by Applied Mathematics Letters can be viewed at:

http://www.math.utep.edu/Faculty/sewell/AML_3497.pdf

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156 Re: My articles Yesterday at 4:08 am

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" There is no evidence of God ". Really?
That's one of the arguments most frequently brought forward by unbelievers. What they, however, want to say is: There is no evidence that points ( in his view ) to God. The problem is the lens and a priori assumption someone adopts, and what someone wishes to be true. The evidence is for all of us the same. The observable world. The tool to make rational conclusions, too: Our mind. The conclusion we make on how everything came to be, depends on the interpretation of the evidence and reality. While some are gullible towards the claim that natural mechanisms created everything, the theist is incredulous towards that view.

The theist is incredulous towards the claim that :
Ignorance about origins is justified. The universe exists without beginning or was made from nothing.  Randomness produced cosmological and biochemical fine-tuning. Chaos produced order. Non-life produced life.  Matter produced codes, and instructional blueprints, signalling, and information transmission networks. Computers, computer networks, molecular machines, assembly lines, and high-tech factory parks, consciousness, and objective moral values.  

  

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