Intelligent Design, the best explanation of Origins

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126 Re: My articles on Wed Oct 10, 2018 3:06 am

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Confirmation bias & willful ignorance: How to deal with it.

Atheists, in most, if not all cases, aren't looking for evidence of Gods existence or proof. They are looking to find reasons that confirm what they want to be true. They look for validation. What they want, is to avoid God and find relief to justify to themselves what they want to be true. They aren't interested in arguments, but when a theist makes them, the only aim is to find ways to refute and reject what points to a creator. It is called confirmation bias. Wiki: Confirmation bias, also called confirmatory bias or myside bias is the tendency to search for, interpret, favor, and recall information in a way that confirms one's preexisting beliefs or hypotheses. It is a type of cognitive bias and a systematic error of inductive reasoning. People display this bias when they gather or remember information selectively, or when they interpret it in a biased way. The effect is stronger for emotionally charged issues and for deeply entrenched beliefs.

Many unbelievers find it intellectually more justified or defendable not to declare themselves openly as ( strong ) atheists. They do want to avoid the burden of proof - they know it would bring their position into trouble. They know that all no - God hypotheses are intellectually bankrupt and easy to shut down. There are no good reasons to apply Occam's Razor to God. So they either duck cowardly and say: I do not hold an epistemologically elaborated position - I just do not believe yours. They try to sell their fish like this: "

We replace God with honesty by saying "we don't know". The fact that we don't currently know does not mean we will never know because we have science, the best method we have for answering questions about things we don't know. Simply saying "God did it" is making up an answer because we are too lazy to try to figure out the real truth."

Sounds nice, but engaging a theist just to try to bring him down to unbelief without offering a better alternative, without any real intention to actually honestly consider and evaluate his beliefs means to waste his time and behaving egoistically, to use him to solidify his unbelief in God. What he does not realize, that, by doing so, all he is doing, is a way of self-delusion. We, believers in the promises of Christ, know, that our efforts make sense, independently if the counterpart considers our light of truth, or not, because of 1. Our words can germinate one day. Atheists do not forget, and in a particular, future situation, when they are more open, they can remember, and the information can help them to come to God. And 2. The ones that reject the truth and die without coming to Christ, cannot justify that they did not be called to come to repentance. If they get lost, it's their fault. Not Gods, or his servants which did not follow Christs calling to go to the world to preach the gospel.

Then, besides the weak atheists, we have the " We don't know-ists. ". They proudly do put on display their willful ignorance like the adornment of a peacock and feel that trumpet it to the world how little they know about origins is not only a beautiful but intellectually very scholar and worth of admiration. They put things upside down and don't realize that their position is a sublime admittance of brainlessness, laziness, and irrational blindness, not smart, but on the contrary: intellectually disturbing. But their real motivations are clear. They express just another form of confirmation bias and use another tactic to justify their unbelief. Their cognitive dissonance which they obviously do not admit is obvious, we are not ignorant of it.

For this reason, not rarely, when an atheist or agnostic has exposed, what his motivations are, it makes no sense for a theist to engage such a person for much time. I have a long list of people that I blocked, because, they cannot handle the fact that their motivations have been exposed, and not rarely, they lowered the level to personal attacks. My way to deal with it is either blocking, or saying goodbye, and not engaging further. Our time is precious.

There are many out there that need their faith to be strengthened. And providing evidence in Creation that points to God is a formidable way.

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127 Re: My articles on Thu Oct 11, 2018 10:39 am

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Do we need to see architects, engineers, programmers, coordinators, instructors, managers, specialists, regulators, fine-tuners, interpreters etc. in action, building factories,  to conclude a factory was made by intelligent professionals? Or can we conclude design and intelligent setup as the best explanation when we see a factory in operation?

Engineering requires an engineer
Architecture requires an architect
An orchestra requires a Director
Organization requires an organizer
Setting up a programming language requires a programmer
Setting up Information selection programs require Search and Selection Programming engineers
Setting up translation programs requires translation programmers
Creating communication systems require  Network engineers
Electrical networks require electrical engineers
Logistics require a logistic specialist
Modular organization requires a Modular project manager
Setting up recycling systems require a recycling technician
Setting up power plants requires Systems Engineers of Power Plants
Nanoscale technology requires Nano Process Development Engineers
Product planning and control require a Production Control Coordinator
Establishing product Quantity and Variant Flexibility require product management engineers
Waste management require a waste logistics manager
Creating a language requires intelligence
Creating Instructional information requires an Instructor
Coordination requires a coordinator
Setting up strategies requires a strategist
Regulation requires a regulator
Controlling requires intelligence that sets up and programs the automatic control functions
Recruiting requires intelligence which instructs autonomous programs how to do it.
Interpretation requires intelligence which creates an interpretation program.
Switch mechanisms with on and off states require intelligent setup.
Setting up transport highways requires  Transportation Development engineers
Controlled factory implosion programming requires an Explosive Safety Specialist

Biological Cells do all above described, but no intelligence to set up all these things is required?

Objection: We have never observed a being of any capacity creating biological systems and life.  
Answer: We do not need direct observed empirical evidence to infer design. As anyone who has watched TV's Crime Scene Investigation knows, scientific investigation of a set of data (the data at the scene of a man's death) may lead to the conclusion that the event that produced the data (the death) was not the product of natural causes not an accident, in other words but was the product of an intelligence a perpetrator.
But of course, the data at the crime scene usually can't tell us very much about that intelligence. If the data includes fingerprints or DNA that produces a match when cross-checked against other data fingerprint or DNA banks it might lead to the identification of an individual. But even so, the tools of natural science are useless to determine the I.Q. of the intelligence, the efficiency vs. the emotionalism of the intelligence, or the motive of the intelligence. That data, analyzed by only the tools of natural science, often cannot permit the investigator to construct a theory of why the perpetrator acted.  Sherlock Holmes can use chemistry to figure out that an intelligence a person did the act that killed the victim, even if he can't use chemistry to figure out that the person who did it was Professor Moriarty, or to figure out why Moriarty did the crime.
Same when we observe the natural world. It gives us hints about how it could have been created. We do not need to present the act of creation to infer creationism / Intelligent design.

Atheists err when asking for material evidence to prove God's existence
http://reasonandscience.catsboard.com/t2256-atheists-err-when-asking-for-material-evidence-to-prove-god-s-existence

Question for an atheist. Are you a non-believer because you cannot see, hear or touch God? or is it for other reasons?
If it is because you cannot prove there is a God, I want to propose another question.
But first, try this out.
Say "I love tasty food," but don't actually try to physically make an effort to say it. Use your mind to say it.
Okay, what exactly did you just do and how is it that you can hear yourself so clearly in your own mind. There is an action (you saying the statement) and its existence is clear to you, but to us that sentence that you just said "out loud" in your head doesn't exist to us.
Matter of fact I will ask you, right now, to prove to me that you just said, "I love tasty food," in your head.
Telling me you said that statement isn't showing me evidence as to its existence. Some of you may say, "Hey, well it is dumbass." Ok, I understand how that can be a compelling argument. Now lets consider that I may lie to you and tell you that I did say I love tasty food consciously, but I actually didn't. Well then, the physical act of telling someone you thought something isn't the most viable way of showing evidence as to what you actually thought. Therefore isn't proving anything.
To get to the point, I want to say that there are probably lots of things that don't physically exist in our world, but have an existence. Just because you can't prove something doesn't mean it doesn't exist.
hopefully food for thought.

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128 Re: My articles on Fri Oct 12, 2018 4:03 am

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Creation of the Earth vs Heaven

Exodus 20:11
"For in six days the LORD made the heavens and the earth, the sea and all that is in them, and rested on the seventh day; therefore the LORD blessed the sabbath day and made it holy.

John 14:2
“Do not let your hearts be troubled. You believe in God; believe also in me. My Father’s house has many rooms; if that were not so, would I have told you that I am going there to prepare a place for you? And if I go and prepare a place for you, I will come back and take you to be with me that you also may be where I am.

1 Corinthians 2
“What no eye has seen, what no ear has heard, and what no human mind has conceived”—the things God has prepared for those who love him
If God created the universe and the earth in six days, can you imagine how beautiful for Christ's bride, the redeemed Church, you and me, the place he is preparing for us, will be? Christ resurrected and went to heaven two thousand years ago, and said, while he is not returning to take us home to heaven ( the Earth is just a passage place for all of us, but in special for the redeemed Church and all that belong to HIM) , he is preparing a place for us to stay with him - forever. That is, 730000 days, he is already preparing !!! He is already now, preparing 120 thousand times longer than he was when he made the earth !! - and what amazingly beautiful world that must have been prior the fall - we have still today a glimpse of it - and he still working on our heavenly place !! Yup - great plans God has for us - little unfaithful sinners that transgress his will with such ease, and so often demonstrate so little love for him.

His care and incomprehensible love for us should humble us to stay and seek more his face, and aim to do his will, and demonstrate our love towards the one that came to suffer and give his Life on our behalf, to save us from the torment that God deniers and God haters face in eternity - what great salvation - he had truly all reasons to exclaim before the moment he was to give up his spirit and died: It's done !!

His sacrifice is truly incomprehensible for us. The Almighty One, the great I AM, Supreme Creator Over All, the King of Kings, Lord of all, Lion of the Tribe of Judah, the ruler, the lofty one, the one reigning for all eternity, nobody above him, the Alpha and Omega, the first and the last, the all-powerful, the holy and just God, creator of the heavens and the earth, billions of angels serving him day and night, became our Redeemer, the Lamb of God, a humble man, being born in nobody land, Nazareth, a small place of no importance in the Roman Empire.

http://www1.cbn.com/…/five-things-you-didnt-know-about-naza…
Nazareth was the original small town. in Jesus' day, only 120-150 people lived in Nazareth. In John 1:46, Nathanael asked the famous question, "Can anything good come out of Nazareth?" This tiny farming village, high on a hill and far from the main trade routes, was the last place anyone would look for the Messiah of Israel. Unless they were smart enough to figure out the following prophecy....
Isaiah prophesied that the Messiah would come from Nazareth about 600 years before the village existed.
In the 8th century before Christ's birth, Isaiah prophesied that "a shoot will spring from the stem of Jesse, and a branch from his roots will bear fruit" (Isaiah 11:1). The word "branch" in Hebrew is netzer, the same root word from which the name "Nazareth" comes. Some historians have suggested that Nazareth was named as "the town of the branch," meaning "the place where the Branch of David lives." In the New Testament, Matthew connects Nazareth with the prophecy in Isaiah 11:1: "And came and resided in a city called Nazareth, that what was spoken through the prophets might be fulfilled, ‘He shall be called a Nazarene’" (Matthew 2:23).

Nazareth was a small town, disdained by others, and the Messiah grow in a humble and poor family, walked amongst us, and to die naked ( yes, in order to humiliate they were crucified naked )

As J. Vernon McGee (Thru the Bible) says:
He was crucified naked. It is difficult for us in this age of nudity and pornography to comprehend the great humiliation He suffered by hanging nude on the cross. They had taken His garments and gambled for ownership. My friend, He went through it all, crucified naked, that you might be clothed with the righteousness of Christ, and so be able to stand before God throughout the endless ages of eternity.
He was humiliated and exposed to the most painful torture invented by man.

https://theologyarchaeology.wordpress.com/…/06/12/crucifix…/
• Cicero described crucifixion as “the cruelest and most terrible punishment” (Verr. 2.5.165).
• Josephus called it “the most pitiable of deaths” (J.W. 7.203).
Ancients also considered crucifixion to be the ultimate shame. For example, Celsus, the second-century ad detractor of Christianity, wrote that Jesus had been executed in a “dishonorable and shameful way” (Origen, Cels. 6.10). The author of Hebrews wrote that Jesus “endured the cross, disregarding the shame” (Heb 12:2). In crucifixion, everything was done to humiliate and dishonor the victim in addition to torturing him or her to death.
Christ went through all this, to take your sins my sins, all our sins, of all humanity, and pay the price of sin: death. The just and sinless, dying for sinners.
Seek him more and love him more. Lift up your face and contemplate his goodness - he is good and good-hearted - despite all our rebellious ways, he loves and keeps loving us.
But he is not weak, but strong and powerful - and just. A courageous warrior - if you make HIM your enemy - he is the worst you can imagine.

Hebrew 10.31:
For we know him who said, “It is mine to avenge; I will repay,” and again, “The Lord will judge his people.” It is a dreadful thing to fall into the hands of the living God.
His justice will always prevail, and his enemies will all perish, soon or later.

Psalm 94:15
For justice will prevail,
and all the morally upright will be vindicated.

There is no more foolish behavior than to deny and reject him - just to seek living without someone above that wants to direct our lives and orient us - to the better. To live a meaningful and blessed life. Better you make peace and surrender before its too late !! If you walk on the street today and cross the street, and a car does not see you, you can suffer an accident, the car hits you, and die. Where will you go? How can you face eternity without making peace with your creator, here - before its too late? - he is not asking you to start doing miraculous things - he just wants that you surrender to his grace, repent, and start following HIM, and orient your ways towards HIS direction - his will for us is always the best way. He is all-knowing and has a plan for us. For me, and for you. He deserves our trust. If he made life and all that surrounds us, do you think he does not know better than you, what is good for you? Why insisting on living a meaningless egoistic rebellious life, outside of the will of your creator - the only end station will the death ??

1 Chronicles 16:23-31
Sing to the LORD, all the earth; proclaim his salvation day after day. Declare his glory among the nations, his marvelous deeds among all peoples. For great is the LORD and most worthy of praise; he is to be feared above all gods. For all the gods of the nations are idols, but the LORD made the heavens. Splendor and majesty are before him; strength and joy are in his dwelling place. Ascribe to the LORD, all you families of nations, ascribe to the LORD glory and strength. Ascribe to the LORD the glory due his name; bring an offering and come before him. Worship the LORD in the splendor of his holiness. Tremble before him, all the earth! The world is firmly established; it cannot be moved. Let the heavens rejoice, let the earth be glad; let them say among the nations, “The LORD reigns!”
Come and let us sing the Lord together. Hallelujah !! Maranatha.

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129 Re: My articles on Sat Oct 13, 2018 8:13 pm

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We all are subdued to the inescapable fact that we depend on faith to make sense of the reality which surrounds us.
There are no unbelievers.
There are believers which are correct, and believers that are incorrect in regards to our origins.
There are believers in God, and there are believers that the natural world is all there is.
Agnosticism as a state of constant being is not justified.
To know anything someone needs to have faith.
Faith in sensory perception,
faith in rational ability,
faith in the uniformity of nature.
Without faith, we couldn't function in society.

Gödel's incompleteness theorem

http://reasonandscience.catsboard.com/t1298-godel-s-incompleteness-theorem

Nearly all scientific laws are based on inductive reasoning. These laws rest on an assumption that the universe is logical and based on fixed discoverable laws. You cannot PROVE this. (You can’t prove that the sun will come up tomorrow morning either.) You literally have to take it on faith. In fact most people don’t know that outside the science circle is a philosophy circle. Science is based on philosophical assumptions that you cannot scientifically prove. Actually, the scientific method cannot prove, it can only infer. (Science originally came from the idea that God made an orderly universe which obeys fixed, discoverable laws.) Now please consider what happens when we draw the biggest circle possibly can – around the whole universe. (If there are multiple universes, we’re drawing a circle around all of them too):

There has to be something outside that circle. Something which we have to assume but cannot prove
The universe as we know it is finite – finite matter, finite energy, finite space and finite time
The universe is mathematical. Any physical system subjected to measurement performs arithmetic. (You don’t need to know math to do addition – you can use an abacus instead and it will give you the right answer every time.)
The universe (all matter, energy, space and time) cannot explain itself
Whatever is outside the biggest circle is boundless. By definition it is not possible to draw a circle around it.
If we draw a circle around all matter, energy, space and time and apply Gödel’s theorem, then we know what is outside that circle is not matter, is not energy, is not space and is not time. It’s immaterial.
Whatever is outside the biggest circle is not a system – i.e. is not an assemblage of parts. Otherwise we could draw a circle around them. The thing outside the biggest circle is indivisible.
Whatever is outside the biggest circle is an uncaused cause, because you can always draw a circle around an effect.

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130 Re: My articles on Sun Oct 14, 2018 7:37 am

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Why is there.....

Why are there bipedals, if there are still quadrupeds?
Why are there still tetrapods, if there are quadrupeds?
Why are there still tetrapods, if there are still lobe-finned fishes?
Why are there lobe-finned fishes, if there are ray-finned fishes?
Why did paired fins derive and evolve from gill structures?
Why do gills in jawless animals such as lampreys form from the embryo's innermost layer of cells, or 'endoderm', whereas in jawed vertebrates, including many fish species, from the outermost layer, or 'ectoderm'?
Why are there skeletons, if there are still crustaceans with exoskeletons?
How could there have been a transition from invertebrates to vertebrates, if bone formation is an irreducibly complex process?
Why are there still marine worms, if there are crustaceans?
Why are there still annelid worms, if there are still Arthropods?
If there are hominoids, why are there still fish?

Its co-option, lateral gene transfer, parallel evolution, convergent evolution, genetic drift, gene flow, natural selection, antigenic drift, and a sprinkle of imagination, dude !! If you didn't know, go and learn how evolution works !!

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A walk through the epigenetic landscape which regulates Gene expression points to the requirement of intelligent setup and design

Following article is better read here:
http://reasonandscience.catsboard.com/t2061p125-my-articles#6169

The gene regulatory network
http://reasonandscience.catsboard.com/t2590p25-origins-what-cause-explains-best-our-existence-and-why#6153

Life is built upon an instructional blueprint stored in the Genome, through DNA, but also higher order epigenetic codes and languages ( various information layers, one above the other ) signaling and information transmission networks, which regulate which information in the genome has to be expressed or repressed, and when. Each gene section has a start and stop - promoter sequence, which informs the transcription machinery ( RNA polymerase ) when to start, and when to stop transcribing a specific gene. The regulation, when and where to do so, depends on the Gene regulation network.

The ultracomplex cellular machinery, responsible for it, has been traditionally a little bit less in focus than everything that happens in genomics because of evolution. Science is still pretty much, in the beginning, to unravel how epigenetic regulatory networks work. The complexity is just phenomenal, and nothing short of amazing - and shifting the make of phenotypes to higher - epigenetic, rather than only genetic information, and as such, the mechanisms that govern the making of bodies, depend on various molecular processes and protein complexes, signaling and information networks, which are best described through structuralism, which is an umbrella name for different mechanisms that guide the formation of body plans, in the center of all, EPIGENETIC INFORMATION AND VARIOUS EPIGENETIC CODE SYSTEMS AND LANGUAGES.

Epigenetics is one of the hottest fields in the life sciences. It’s a phenomenon with wide-ranging, powerful effects on many aspects of biology. Epigenetics is essentially additional information layered on top of the sequence of letters (strings of molecules called A, C, G, and T) that makes up DNA. If you consider a DNA sequence as the text of an instruction manual that explains how to make a human body, epigenetics is as if someone's taken a pack of highlighters and used different colors to mark up different parts of the text in different ways. For example, someone might use a pink highlighter to mark parts of the text that needs to be read the most carefully, and a blue highlighter to mark parts that aren't as important.

Genes are regulated by epigenetic networks, which includes heritability, as it defines a nongenetic memory of function that is transmitted from generation to generation.

Epigenetic information very much defines how bodies are built, and that shifts the quest of biodiversity from genes, and genetic information, to epigenetics. One gene section can be expressed upon different splicing through the spliceosome machinery, for example in human cells, 300 times differently, that means the product of 300 different functional proteins species can be and are produced. 20 thousand genes in the human genome can synthesize 6 million different protein species !! Where did the instruction come from to generate the splicing code and language which governs and directs the right gene splicing?

Back to gene regulation. 
Regulation of gene expression includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA),  Sophisticated programs of gene expression are widely observed in biology, and they need to be able to permit:

Developmental pathways
- Developmental pathways are networks of genes that act coordinately to establish the body plan. Disruptions of genes in one pathway can have effects in related pathways and may result in serious dysmorphogenesis or cancer.

Cells can change dramatically, following a definite developmental pathway: that’s what happens in cell differentiation, for example from a hematopoietic stem cell to differentiated blood cells like lymphocytes, monocytes, neutrophils, and so on. The end of the differentiation is the final differentiated cell, which is in a sense more “stable”, having reached its final intended “form”.

Respond to environmental stimuli
- The ability to change over time in response to the environment is fundamental and is determined by the organism's genetics. A living organism must be able to respond appropriately to external/environmental stimuli; A response can take many forms, from the contraction of a unicellular organism to external chemicals to complex reactions involving all the senses of multicellular organisms. An example of responding to stimuli is a bacterium forming an endospore when exposed to tough, unfavorable conditions to protect itself

Adapt to new food sources
- All organisms need to adapt to their habitat to be able to survive.

Those “stable” differentiated cells, however, are still in a continuous flow of informational change, which is still drawn by continuous modifications in the transcriptome/proteome and in chromatin configurations. Even if these changes are less dramatic, and do not change the basic identity of the differentiated cell, still they are necessary to allow adaptation to different contexts, for example varying messages from near cells or from the rest of the body, either hormonal, or neurologic, or other, or other stimuli from the environment (for example, metabolic conditions, stress, and so on), or even simply the adherence to circadian (or other) rhythms.  "Stable"cells are not stable at all: they change continuously while retaining their basic cell identity, and those changes are, again, drawn by continuous modifications in the transcriptome/proteome and in the chromatin configurations of the cell.

These are requirements for all life forms, and cells must be able to deal with all three requirements. If they cannot respond to environmental stimuli - no life. If they cannot adapt to new food sources - no life. If they have no programmed development pathways - no life.

The result of this machinery and of its workings is that thousands of proteins are transcribed and translated smoothly at different times and in different cells

Any step of gene expression may be modulated, from the DNA-RNA transcription step to post-translational modification of a protein. The following is a list of stages where gene expression is regulated, the most extensively utilized point is Transcription Initiation:

- Chromatin domains
- Transcription
- Post-transcriptional modification
- RNA transport
- Translation
- mRNA degradation

The mechanisms upon which gene expression relies, that is Gene repression or activation, the basis of the epigenetic landscape of a cell encompasses

- DNA methylation
- histone modifications
- histone variants
- nucleosome positioning

Epigenetic plasticity is further regulated by the three-dimensional and higher-order chromatin structure, including nucleosome repositioning, DNA looping, and long-range chromatin interactions.

The above different mechanisms that control these epigenetic changes do not stand alone, and there are a clear interconnection and interdependency between them.

Interdependence means, if one of the three mechanisms is not present, the others cannot function properly. And if the modifications do not occur as they should, cancer and other diseases are the consequence. Which demonstrates that a gradual stepwise increase in complexity was not possible. These mechanisms are interlocked and had to emerge fully developed and properly functioning right from the beginning. 

The interaction between transcriptome/proteome and chromatin configuration is an interaction. The transcriptome/proteome determines the chromatin configuration in many ways: for example, changing the methylation of DNA (DNA methyltransferases); or modifying the post-transcriptional modifications (methylation, acetylation, ubiquitination and others) of histones (covalent histone-modifying complexes), or creating new loops in chromatin (transcription factors); or directly remodeling chromatin itself (ATP-dependent chromatin remodeling complexes). In the same way, any modification of the chromatin landscape immediately influences what the existing transcriptome/proteome is and can do, because it directly changes the transcriptome/proteome as a result of the changes in gene transcription. Of course, this can modify the availability of genes, promoters, enhancers, and regulatory regions in general at chromatin level.

Remarkable is, that all these molecular systems depend on epigenetic languages, and the ability to interpret signals. That means cells must be able to interpret, react, transmit, and receive both, internal and external information and stimuli, and a signaling network must be fully set up. Receptors on the Cell membrane ( there are many different ones ) receive external information, and signals are transmitted to the machinery which receives, interprets, understands, and activates various responses. Corepressor/coactivator exchange complexes are targets of multiple extracellular and intracellular signaling pathways.

In communication, by definition, four things need to exist:

1. A code
2. An encoder that obeys the rules of a code
3. A message that obeys the rules of the code
4. A decoder that obeys the rules of the code

These four things—language, the transmitter of language, message, and receiver of language—all have to be precisely defined in advance before any form of communication can be possible at all. This is an interdependent irreducible system.

DNA methylation depends on the DNA methylation code and language. Histone modifications depend on the Histone Code, which is governed by protein readers, writers, editors, and erasers, and there is even combinatorial readout of and cross-talk between post-translational modifications ( PTMs ) of histone tails. That can occur between the eight histone tails of a nucleosome which protrude out of the nucleosome ( One histone core of eight histone subunits and the DNA molecule is wrapped twice around a Histone Octamer is a nucleosome), or between different, neighboring nucleosomes, or even distant ones.

The interplay between such effectors, readers and writers generate a multifaceted network of intertwined contacts that can provide a high degree of specificity. Furthermore, many nuclear complexes are not static and undergo component swapping, a powerful mechanism for altering their chromatin-targeting capabilities. Beyond mediating specific chromatin anchoring, PTM cross-talk can also trigger a cascading series of writing, erasing and reading events.

Access to the DNA within chromatin involves the cooperative action of DNA sequence, site-specific transcription factors, histone modification enzymes, and a set of chromatin remodeling complexes.

These mechanisms activate transcription through transcription factors, which bind on regulatory sequences on the Genome, and start gene expression. Transcription activation depends on six sequential steps, and is EXTREMELY COMPLEX, depending on hundreds of specialized proteins, where, if one is missing or malfunctioning, the result is disease, cancer, and Cell death.

How do secular science papers explain the origin of gene regulatory networks? You can guess - of course - evolution !!

Eugene Koonin: The origin of eukaryotes and multicellularity involved invention of several fundamentally new functional systems. The eukaryotic chromatin remodeling machinery is such a major eukaryotic innovation, which does not appear to have direct prokaryotic predecessors analogs.

Another paper claims:
Nucleosome-remodeling enzymes may thus have evolved directly from ancestral helicase-type motors, and peripheral domains have furnished regulatory capabilities that bias the remodeling reaction toward different structural outcomes.

Coordinated actions, regulation, and strategic interactions are crucial and must be pre-programmed by intelligence and require foreknowledge of distant needs. Were these peripheral domains not precisely structured and specialized to perform the task right from the beginning, they could not perform properly.  Random, unguided non-intelligent natural processes would need to promote a future functional outcome with intermediate non-functional stages, and evolving the right physical properties of these peripheral domains, finely tuned to perform a conjoined co-operative action and correct regulation tasks once the system was fully set up. Furthermore, transcription activation is life-essential and could not occur, if the process was not fully implemented.   Even more, coordination and regulation are required for these biological processes since it indicates that when both are not existent or fully implemented, the life-essential processes like transcription activation cannot occur properly, and in cases of malfunction, causing cancer.

Eugene Koonin attributes its origin to a momentous evolutionary transition. This scenario indicates however rather that a set up through gradual evolutionary mechanisms is not possible. The requirement of fine tuning and extreme regulation of the whole process, its management, and control, certainly require all or almost all the components. 

Davidson gives the death strike: 
No subcircuit functions are redundant with another, and that is why there is always an observable consequence if a dGRN subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.







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132 Re: My articles Yesterday at 5:18 am

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"Irreducible complexity has been debunked?
There is no irreducible complexity? I see it ALL OVER in molecular biology. If someone tells you that IC has been debunked, he just signed a declaration of HAVING NO CLUE about the issue.
What emerged first: Gene repression, or activation?
Life would not exist without both...."


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133 Re: My articles Yesterday at 8:13 am

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Adaptation of cells to new environments

Several life-essential EPIGENETIC mechanisms respond to environmental stress. 

- heat shock factors (HSFs)
- The unfolded protein response (UPR)
- nonhomologous end-joining and homologous recombination
- The DNA Damage Response
- The Response to Oxidative Stress

Evolution takes supposedly thousands of years to gain an environmental advantage. So what environmental benefit would evolution supposedly provide, if adapting and responding to environmental stimuli is not only a life-essential process which had to be fully implemented when life began but, furthermore, a pre-programmed process based on information through signaling networks?


Cells have many mechanisms to modulate the signaling pathways at transcriptional, post-transcriptional and post-translational levels.

Organisms respond to short-term environmental changes by reversibly adjusting their physiology to maximize resource utilization while maintaining structural and genetic integrity by repairing and minimizing damage to cellular infrastructure, thereby balancing innovation with robustness. The cell’s initial response to a stressful stimulus is geared towards helping the cell to defend against and recover from the insult. 2 The fact that the cell’s survival critically depends on the ability to mount an appropriate response towards environmental or intracellular stress stimuli can explain why this reaction is highly conserved in evolution. The adaptive capacity of a cell ultimately determines its fate.

One of the reasons behind the evolutionary success of mammals (and other multicellular organisms) is their extraordinary capacity to adapt to changing environmental conditions. 3

Maybe the authors should ask himself, how the Cell could have survived without the mechanism implemented from day one !!

If the stress stimulus does not go beyond a certain threshold, the cell can cope with it by mounting an appropriate protective cellular response, which ensures the cell’s survival. One of the main prosurvival activities of cells, the heat shock response, was originally described as the biochemical response of cells to mild heat stress (i.e., elevations in temperature of C above normal) During initiation of the heat shock response general protein transcription and translation is halted, presumably to alleviate the burden of misfolded proteins in the cell. However, transcription factors that enhance expression of a specific subset of protective genes are selectively activated under these conditions; these are the heat shock factors (HSFs) Vertebrate cells have three different HSFs: HSF1 is essential for the heat shock response and is also required for developmental processes, HSF2 and HSF4 are important for differentiation and development, while HSF3 is only found in avian cells and is probably redundant with HSF1 .

Secretory and membrane proteins undergo posttranslational processing, including glycosylation, disulfide bond formation, correct folding, and oligomerization, in the ER. In order to effectively produce and secrete mature proteins, cellular mechanisms for monitoring the ER environment are essential. Exposure of cells to conditions such as glucose starvation, inhibition of protein glycosylation, disturbance of Ca2+ homeostasis and oxygen deprivation causes accumulation of unfolded proteins in the ER (ER stress) and results in the activation of a well-orchestrated set of pathways during a phenomenon known as the unfolded protein response (UPR)

Upon cellular stress conditions that are caused by exposure to chemotherapeutic agents, irradiation, or environmental genotoxic agents such as polycyclic hydrocarbons or ultraviolet (UV) light, damage to DNA is a common initial event DNA double-strand breaks (DSBs) and single-strand breaks (SSBs) are considered as key lesions that initiate the activation of the DNA damage response. Damage to DNA engages DNA repair processes to ensure the cell’s survival in the case of sublethal damage. Depending on the type of lesion, DNA damage initiates one of several mammalian DNA repair pathways, which eventually restore the continuity of the DNA double strand. There are two main pathways for the repair of DSBs, that is, nonhomologous end-joining and homologous recombination

Cell survival requires appropriate proportions of molecular oxygen and various antioxidants. Reactive products of oxygen are amongst the most potent and omnipresent threats faced by cells. These include ROS such as

superoxide anion
hydrogen peroxide (H2O2)
singlet oxygen
hydroxyl radical (OH•)
peroxy radicals
the second messenger nitric oxide (NO•) which can react with O2 to form peroxynitrite (ONOO−)

Infectious agents can drive a plethora of stress responses by activating pattern recognition receptors. In the initiation of innate immune responses against pathogens, pattern-recognition receptors (PRRs) have an essential role in recognizing specific components of microorganisms and triggering responses that eliminate the invading microorganisms. However, inappropriate activation of PRRs can lead to prolonged inflammation and even to autoimmune and inflammatory diseases. Thus, PRR-triggered responses are regulated through the degradation or translocation of the innate receptors themselves and through the involvement of intracellular regulators or amplifiers. In addition, a complex interplay between PRRs and/or other immune pathways finely tunes the outcome of host immune defense responses. 4

Considerable evidence has now accumulated indicating that the intracellular mechanisms that are activated in response to different stresses — which include the DNA damage response, the unfolded protein response, mitochondrial stress signalling and autophagy — as well as the mechanisms ensuring the proliferative inactivation or elimination of terminally damaged cells — such as cell senescence and regulated cell death — are all coupled with the generation of signals that elicit microenvironmental and/or systemic responses. Such mechanisms of cellular adaptation to stress contribute to the formidable resilience of the organism but can also contribute to its degeneration over time. 3

Normally in cells there exists equilibrium between pro-oxidant species and antioxidant defense mechanisms such as ROS-metabolizing enzymes including catalase, glutathione peroxidase, and superoxide dismutases (SODs) and other antioxidant proteins such as glutathione (GSH)

For the preservation of organismal homeostasis, as severely damaged, irreversibly infected, functionless and/or potentially oncogenic cells are destined for persistent inactivation or elimination, respectively.

It has become apparent that most (if not all) mechanisms of cellular response to stress are also associated with paracrine and endocrine signals that communicate a potential threat to the organism and hence contribute to the maintenance of systemic homeostasis. 


Signaling pathways and regulators of PRRs. 
Pattern-recognition receptors (PRRs) share intracellular pathways that lead to the production of pro-inflammatory cytokines and type I interferons (IFNs). 
a | All the Toll-like receptors (TLRs), except for TLR3, interact with MYD88 to induce the activation of nuclear factor-κB (NF‑κB) and mitogen-activated protein kinases (MAPKs), which induce the transcription factor activator protein 1 (AP-1), for the induction of pro-inflammatory cytokine expression. The TIR domain-containing adaptor protein inducing IFNβ (TRIF) pathway is shared by TLR4 and TLR3, and induces the activation of interferon regulatory factors IRF3–IRF7 for the production of type I IFNs.
b | Retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5) first interact with mitochondrial antiviral signaling protein (MAVS) and then activate signaling cascades through stimulator of interferon genes (STING) and TANK-binding kinase 1 (TBK1), leading to the expression of type I IFNs. MAVS also signals through receptor-interacting serine/threonine protein kinase 1 (RIPK1) for AP‑1 activation. 
c | Many cytosolic DNA and RNA sensors, including cyclic GMP–AMP synthase (cGAS), double-strand break repair protein MRE11, IFNγ-inducible protein 16 (IFI16), DNA-dependent protein kinase (DNA‑PK), the probable ATP-dependent RNA helicases DDX41 and DDX60, leucine-rich repeat flightless interacting protein 2 (LRRFIP2) and protein kinase RNA-activated (PKR), recognize intracellular DNA or RNA and converge on STING to drive type I IFNs and cytokine production. The ATP-dependent RNA helicases DHX9 and DHX36 recognize CpG-containing DNA and induce the MYD88‑dependent signalling pathway. 
d | NOD-like receptors (NLRs) are activated upon cellular infection or stress, and engage innate immune responses via RIPK2–NF‑κB signalling activation. Some NLRs, such as NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3), ICE protease-activating factor (IPAF) and NLR apoptosis inhibitory protein 5 (NAIP5), form inflammasomes that contain the apoptosis-associated speck-like protein containing a CARD (ASC) and caspase 1, and trigger the maturation of interleukin-1β (IL-1β). 4


1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3081528/
2. https://www.hindawi.com/journals/ijcb/2010/214074/
3. http://sci-hub.tw/https://www.nature.com/articles/s41580-018-0068-0
4. http://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/26711677

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134 Re: My articles Yesterday at 4:24 pm

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Who created God? And how did he create the universe?

One of the most common ways atheists conduct and continue a debate, once they have no escape and every objection of the watchmaker argument has been refuted, is, to move goalposts, and to ask either: Who created God, or how he created the world.

Question: Would God not cease to be God, if he depended on someone or something else to be God? Is God not the highest being, nothing above him, and as such, the first, or necessary cause?

On an “Anselmian” conception of God, God is the greatest possible being; it is in the very nature of God that he essentially (and necessarily) possess all compossible perfections.

Are these questions not a sign about how philosophically ill-informed many atheists are? And need to be spoon fed 101 on the very basics? unfortunately yes.

Who or what created God?
http://reasonandscience.catsboard.com/t77-who-created-god

The creator is a self-existing power. He is not created; He is eternal. He is the One who brought time, space, and matter into existence. Since the concept of causality deals with space, time, and matter, and since God is the one who brought space, time, and matter into existence, the concept of causality does not apply to God since it is something related to the reality of space, time, and matter. The cause of the universe must have been non-material because if the cause was material/natural, it would be subject to the same laws of decay as the universe. That means it would have to have had a beginning itself and you have the same problem as cycles of births and deaths of universes. So the cause of the universe’s beginning must have been supernatural, i.e. non-material or spirit—a cause outside of space-matter-time. Such a cause would not be subject to the law of decay and so would not have a beginning. That is, the cause had to be an eternal spirit.

5 Easy Steps to refute naturalism
http://reasonandscience.catsboard.com/t1877-easy-steps-to-refute-naturalism

Either the cosmos
(1) had no beginning, or
(2) it had a beginning.
(1) If the cosmos had no beginning, then there must be an infinite series of past events. However, it is impossible to traverse an actual infinite. Therefore, the universe cannot be infinitely old. Besides that, If the cosmos was infinitely old, it would have reached maximum entropy a long, long, time ago. Since it has not reached maximum entropy, it cannot be infinitely old without violating the second law of thermodynamics.
(2) If the cosmos had a beginning, then it must have come from (A) nothing or (B) something.
2.A. Although physicists such as Krauss and Hawking talk about "the universe creating itself from nothing," they are using the word "nothing" to mean the vacuum energy, which is not a true nothing. To be more precise, being cannot emerge from non-being.
2.B. If the entire cosmos came from something, that thing must transcend our cosmos, that is, it must exist beyond the limits of our space/time continuum. We may call it the First Cause.

What's the Mechanism of Intelligent Design?
http://reasonandscience.catsboard.com/t1794-how-exactly-did-god-create-the-universe-and-the-world-what-process-was-involvedwas-involved

We don't know how exactly a mind might can act in the world to cause change. Your mind, mediated by your brain, sends signals to your arm, hand and fingers, and writes a text through the keyboard of the computer I sit here typing. I cannot explain to you how exactly this process functions, but we know, it happens. Consciousness can interact with the physical world and cause change. But how exactly that happens, we don't know. Why then should we expect to know how God created the universe? The theory of intelligent design proposes an intelligent mental cause as origin of the physical world. Nothing else.

An intelligent designer creates through power, information input ( words ), wisdom, and will. But how exactly does this work?

Ann Gauger: It's still worth considering how a mind might act in the world to cause change. The answer is we don't know. I sit here typing. My mind, mediated by my brain, is putting words into a computer program (designed by other minds, by the way), using my fingers to type. But how does it happen, really? Where does the impulse to press one key instead of another come from? And how do these words, products of my mind, communicate to others through their computer screens? We can't really say how our own minds work to interact with the world, yet we know they do. It is our universal, repeated, personal experience that shows us that our consciousness interacts with our bodies to produce information, but exactly how it works is not known. So why should we expect to know how the agent(s) responsible for the design of life or the universe may have worked? The theory of intelligent design does not propose a mechanism (a strictly or necessarily materialistic cause) for the origin of biological information. Rather, it proposes an intelligent or mental cause. In so doing, it does exactly what we want a good historical scientific theory to do. It proposes a cause that is known from our uniform and repeated experience (to borrow a phrase) to have the power to produce the effect in question, which in this case, is functional information in living systems.

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