Intelligent Design, the best explanation of Origins

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201My articles - Page 9 Empty Re: My articles on Mon Feb 25, 2019 3:32 pm


Intelligent design arguments, based on ignorance or incredulity?

The more knowledge we gain about the natural world, and the more obvious it is that a creator is behind this space-time continuum, the more responsible we are to respond based on that knowledge about how we position ourselves towards God. If it was unjustifiable not to believe in God when knowledge about the natural world was a fraction of what it is today, how much more are we responsible today?

Let us suppose someone presents you a blueprint to make a factory with 500 complex, interlinked machines, but you have no idea about the origin of that blueprint, do you think its rather rational to suppose that very intelligent people made the planning and project of the blueprint of the factory, or trial and error of ink randomly splashing on the paper trillions of times, and suddenly, somehow, the blueprint emerged on the paper ?

If we calculate an astronomically high number of random trial and error attempts to make a minimal proteome for a first hypothetical cell, which I mentioned, is a theoretically lucky occurrence of one in 10"150000 trials, this is just a fraction of the picture. The odds are far far greater if we consider the probability to connect everything in the right order, like an electric circuit.

A minimal metabolic network for a first Cell is enormously complex. Following link gives an idea.

How Cellular Enzymatic and Metabolic networks  point to design

If an atheist wants to tell me that my reasoning is based on ignorance or incredulity, i have to ask, where that person learned about the basics of logic.

God of the gaps and incredulity, a justified refutation of ID arguments?

1. if there is no money in the wallet
2. It's an argument of knowledge to say: There is no money in the wallet after you check.
3. The same happens in molecular biochemistry. We checked, and scientists discovered that DNA stores specified complex information, which is a blueprint, instructing the precise sequence of amino acids to make proteins. Such information has never been observed to emerge by chance, and therefore, we have evidence that something is extremely unlikely (e.g., that chance could inform the correct instructions to make proteins). Indeed, scientists will often debate whether an experiment's result should be considered evidence of absence. Something has proven not to be the result of X ( as chance, for example )
4. Intelligence can act towards achieving specific goals, and knows how to create codified language, and use that language to create blueprints, used to make complex machines, production lines, and factories. It can finely tune and arrange things to work in a precise fashion. it can shape and form parts that perform tasks by interacting like lock and key. None of all this has been observed to be achieved by any alternative non-intelligent mechanism. if anyone wants to propose an alternative to replace intelligence, it should meet the burden of proof, and falsify the claim based on empirical testing and falsification.
5. Hence, the argument of Intelligent Design as best explanation of origins is based on experiments and observation, gained knowledge and experience. Not from ignorance.

Sorry. NO. I have not enough faith to be an atheist.

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How to recognize the signature of (past) intelligent actions

Creation is evidence of a Creator. But not everybody ( is willing ) to see it.

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
- something purposefully made for specific goals
- systems and networks functioning based on logic gates
- specified complexity, the instructional blueprint or a codified message  
- irreducible complex and interdependent systems or artefacts 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
- Fine-tuning
- objective moral laws

When we say something is “designed,” we mean it was created intentionally and planned for a purpose. Designed objects are fashioned by intelligent agents who have a goal in mind, and their creations reflect the purpose for which they were created. We infer the existence of an intelligent designer by observing certain effects that are habitually associated with conscious activity. Rational agents often detect the prior activity of other designing minds by the character of the effects they leave behind. A machine is made for specific goals and organized, given that the operation of each part is dependent on it being properly arranged with respect to every other part, and to the system as a whole. Encoded messages and instructional blueprints indicate an intelligent source. And so does apply mathematical principles and logic gates.

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.

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203My articles - Page 9 Empty The factory maker argument on Sun Mar 10, 2019 9:55 am


The factory maker argument

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 them for purposeful, specific goals.  

2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signalling networks.

2. The Blueprint and instructional information stored in DNA and epigenetics, which directs the make of biological cells and organisms - the origin of both is, therefore, best explained by an intelligent designer which created life for his own purposes.

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.”

DNA - the instructional blueprint of life

DNA Is Called The Blueprint Of Life: Here’s Why
OCTOBER 26, 2017
DNA is called the blueprint of life because it is the instruction manual to create, grow, function and reproduce life on Earth similar to a blueprint of a house. 10

Biological Cells are equal to a complex of millions of interlinked factories

The Molecular Fabric of Cells  BIOTOL, B.C. Currell and R C.E Dam-Mieras (Auth.)
Cells are, indeed, outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products. The range of products is quite remarkable and encompass chemically simple compounds such as ethanol and carbon dioxide as well as the extremely complex proteins, carbohydrates, lipids, nucleic acids and secondary products. Furthermore: Self-replication is the epitome of manufacturing advance and achievement, far from being realized by man-made factories.  

Self-replication had to emerge and be implemented first, which raises the unbridgeable problem that DNA replication is irreducibly complex. Evolution is not a capable driving force to make the DNA replicating complex, because evolution depends on cell replication through the very own mechanism we try to explain. It takes proteins to make DNA replication happen. But it takes the DNA replication process to make proteins. That’s a catch 22 situation.

Chance of intelligence to set up life: 
100% We KNOW by repeated experience that intelligence does elaborate blueprints and constructs complex factories and machines with specific purposes.

Chance of unguided random natural events doing it:

Chance of random chemical reactions to setup amino-acid polypeptide chains to produce  functional proteins on early earth external to cellular biosynthesis:
1 in 10^200.000 That's virtually the same as 0%. There are 10^80 atoms in the universe.

Peptide Bond Formation of amino acids in prebiotic conditions: an insurmountable problem of protein synthesis on early earth:

1. The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of pre-biological ( chemical) evolution.
2. The formation of amide bonds without the assistance of enzymes poses a major challenge for theories of the origin of life. 
3. 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.
4. Polymerization is a reaction in which water is a product. Thus it will only be favoured in the absence of water. The presence of precursors in an ocean of water favours depolymerization of any molecules that might be formed.
5. 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.
6. 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. 1

Now let us suppose that all these problems would be overcome, and random shuffling would take place:

Calculations of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events

Proteins are the result of the DNA blueprint, which specifies the complex sequence necessary to produce functional 3D folds of proteins. Both improbability and specification are required in order to justify an inference of design.
1. According to the latest estimation of a minimal protein set for the first living organism, the requirement would be about 560 proteins, this would be the absolute minimum to keep the basic functions of a cell alive.  
2. According to the Protein-length distributions for the three domains of life, there is an average between prokaryotic and eukaryotic cells of about 400 amino acids per protein. 8
3. Each of the 400 positions in the amino acid polypeptide chains could be occupied by any one of the 20 amino acids used in cells, so if we suppose that proteins emerged randomly on prebiotic earth, then the total possible arrangements or odds to get one which would fold into a functional 3D protein would be 1 to 20^400 or 1 to 10^520. A truly enormous, super astronomical number. 
4. Since we need 560 proteins total to make a first living cell, we would have to repeat the shuffle 560 times, to get all proteins required for life. The probability would be therefore 560/10^520.  We arrive at a probability far beyond  of 1 in 10^200.000  ( A proteome set with 239 proteins yields odds of approximately 1/10^119.614 ) 7
Granted, the calculation does not take into consideration nor give information on the probabilistic resources available. But the sheer gigantic number os possibilities throw any reasonable possibility out of the window. 

If we sum up the total number of amino acids for a minimal Cell, there would have to be 560 proteins x 400 amino acids  =  224.000 amino acids, which would have to be bonded in the right sequence, choosing for each position amongst 20 different amino acids, and selecting only the left-handed, while sorting out the right-handed ones. That means each position would have to be selected correctly from 40 variants !! that is 1 right selection out of 40^224.000 possibilities !! Obviously, a gigantic number far above any realistic probability to occur by unguided events. Even a trillion universes, each hosting a trillion planets, and each shuffling a trillion times in a trillionth of a second, continuously for a trillion years, would not be enough. Such astronomically unimaginably gigantic odds are in the realm of the utmost extremely impossible. 

We can take an even smaller organism, which is regarded as one of the smallest possible, and the situation does not change significantly:
The simplest known free-living organism, Mycoplasma genitalium,  has the smallest genome of any free-living organism, has a genome of 580,000 base pairs. This is an astonishingly large number for such a ‘simple’ organism. It has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451. If we calculate the entire proteome, then the odds are 470 x 347 = 163090 amino acids, that is odds of 20^164090 , if we disconsider that nature had to select only left-handed amino acids and bifunctional ones. 

Science confirms:

Abiogenesis is virtually impossible

Lynn Margulis:
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.

No scientific experiment has been able to come even close to synthesize the basic building blocks of life, and reproduce a self-replicating Cell in the Laboratory through self-assembly and autonomous organization. Scientists do not have even the slightest clue as to how life could have begun through an unguided naturalistic process absent the intervention of a conscious creative agency. The total lack of any kind of experimental evidence leading to the re-creation of life; not to mention the spontaneous emergence of life… is the most humiliating embarrassment to the proponents of naturalism and the whole so-called “scientific establishment” around it… because it undermines the worldview of who wants naturalism to be true.

“There’s a huge chasm between the origins of life and the last common ancestor,”

Scientists are learning that what is required for life seems to be much greater than what is possible by natural process. This huge difference has motivated scientists to creatively construct new theories for reducing requirements and enhancing possibilities, but none of these ideas has progressed from speculation to plausibility. The simplest "living system" we can imagine, involving hundreds of components interacting in an organized way to achieve energy production and self-replication, would be extremely difficult to assemble by undirected natural process. And all of this self-organization would have to occur before natural selection (which depends on self-replication) was available.

Eugene Koonin, advisory editorial board of Trends in Genetics, writes in his book: The Logic of Chance:  page 351:
The origin of life is the most difficult problem that faces evolutionary biology and, arguably, biology in general. Indeed, the problem is so hard and the current state of  the art seems so frustrating that some researchers prefer to dismiss the entire issue as being outside the scientific domain altogether, on the grounds that unique events are not conducive to scientific study.

125 reasons to believe in God

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204My articles - Page 9 Empty Re: My articles on Mon Mar 18, 2019 4:06 am


The odds, to get a Universe,  hosting Stars, and Life

The cosmological constant acts as a repulsive force, causing space to expand and, when negative, acts as an attractive force, causing space to contract. This constant must be right amongst 10^123 possibilities. if not set up right, there would be no Universe.

Now let's suppose there was a multiverse generator.  He would have made 10^18 attempts after 30 billion years.

The universe produced the number of electrons 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 (because electromagnetic forces would so overwhelm gravitational forces).

Quarks and anti-quarks form via matter-antimatter pair production. Because of their nature, these particles instantly annihilate each other. However, during the creation of the universe, 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 ratio 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.

Lee Smolin:
If there was a multiverse, there would have to be 10^229 of them then one would by chance contain stars. The part of the universe we can see from earth contains about 10^22 stars which together contain about 10^80 protons and neutrons. These numbers are gigantic, but they are infinitesimal compared to 10^229. A probability this tiny is not something we can let go unexplained. Luck will certainly not do here; we need some rational explanation of how something this unlikely turned out to be the case.

The chance of a minimal protein set to kick-start life, 560 proteins, average each: 400 amino acids in length, is one positive occurrence in 20^224.000 attempts.

The diameter of the observable universe is 93 billion light-years, 8.8×10^26 metres or 5.5×10^26 miles

I have not enough faith to be an atheist.

Fine-tuning of the universe

Calculations of life beginning through unguided, natural, random events.

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205My articles - Page 9 Empty Re: My articles on Sat Apr 06, 2019 7:29 pm


The transition from RNA to DNA, a major enigma in Origin of life research

DNA (Deoxyribonucleic acid) is the core of life on Earth, every known living organism is using DNA to store information. DNA is so precious and vital to eukaryotic cells that its kept packaged in the cell nucleus, it's being copied but never removed because it never leaves the safety of nucleus. The structure of RNA nucleotides is very similar to that of DNA nucleotides, with the main difference being that the ribose sugar backbone in RNA has a hydroxyl (-OH) group that DNA does not. This gives DNA its name: DNA stands for deoxyribonucleic acid. When a protein is " energized", that is, when it "charged", it is ready to perform work, in biochemistry terms, it is in a so-called  "reduced" state.  The requirement of transforming RNA's into DNA's is that the hydroxyl (-OH) group at position 2 on the pentose ribose sugar needs to be removed, and only a hydrogen atom remains. The removal is called " reduction " ( that's from where the enzyme has its name ) The name Hydroxyl comes from a combination of a Hydrogen atom with an Oxygen atom. In the reaction, the oxygen atom is separated and removed, and hydrogen remains. So RNA is deoxygenized, the oxygen atom is removed.

The transition of RNA to DNA is one of the great enigmas of Origin of Life research. One of the key steps is to replace the OH group at C2′ of the ribose moiety of the four common ribonucleotides with hydrogen, This apparently tiny difference is essential to give DNA the stability which RNA lacks, and so the information can remain preserved over generations. Many steps are required in the transition  This exchange is performed by a extraordinary protein complex, Ribonucleotide reductase, a truly marvellous molecular machine.

Uracil is also replaced with Thymine, which is another amazing molecular venture with life-essential significance and amazing logic, which only a being with foresight and incredible power, knowledge, and intelligence could know, a Chemist par excellence, and implement the solution of the problem. In this post, i want to outline Ribonucleotide reductases.  

RNRs are essential enzymes to sustain life in all free-living cells, providing the only known de novo pathway for the biosynthesis of deoxyribonucleotides (dNTPs), the immediate precursors for DNA synthesis and repair.  RNRs are tightly controlled through transcriptional and allosteric regulation, subcellular compartmentalization and small protein inhibitors.  There are three classes of RNR enzymes which have the same catalytic activity, but different amino acid sequences to reach the same result.

De novo synthesis of deoxyribonucleotides is a chemically demanding reaction, which proceeds via a carbon-centred free radical.  The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA to DNA-encoded genomes.

The second class ,Class II requires a coenzyme, called adenosylcobalamin (vitamin B12 ). Vitamin B12 is one of eight B vitamins; it is the largest and most structurally complicated vitamin.  It contains the biochemically rare element cobalt (chemical symbol Co) positioned in the center of a corrin ring.  Vitamin B12 is exceptional in comparison to other vitamins and coenzymes for several reasons. Firstly, there is its structural complexity, which is also reflected in its biosynthetic requirements such that somewhere around thirty genes are necessary for its complete de novo synthesis. Remarkable is as well, that Organisms synthesize the complex organometallic framework of cobalamin ( Cbl )  using nearly 30 enzymatic steps in one of nature’s largest characterized biosynthetic pathways.

How could the first synthesis of B12 have occurred and emerged prebiotically?

In fact, the entire class of Vitamins required for the origin of life finds no explanation whatsoever in science, how they could have synthesized prebiotically:

Coenzymes are essential across all domains of life. B vitamins (B1-thiamin, B2- riboflavin, B3-niacin, B5-pantothenate, B6-pyridoxine, B7-biotin, and B12-cobalamin) represent the largest class of coenzymes, which participate in a diverse set of reactions including C1-rearrangements, DNA repair, electron transfer, and fatty acid synthesis.

Another paper describes B12 synthesis as follows: The biochemical steps required for the transformation of uroporphyrinogen III into AdoCbl are one of the most mesmerizing and at times bewildering pathways operated in nature. It is outside the scope of this paper to cover aspects of control and regulation or to delve too deeply into how this intricate network of enzymes may have arisen. Similarly, we have not dealt with the biochemistry of the end product, the role that vitamin B12 plays in biological systems, the beguiling chemical transformations it is able to mediate. These aspects, harnessed with the many unanswered questions concerning its biosynthesis, can be addressed in future reviews on Nature’s most interesting and charismatic vitamin.

So how does science attempt to explain the origin of the extraordinary molecule? One paper claims:

The Origin and Evolution of Ribonucleotide Reduction
2015 Feb 27
In class II RNRs the electron-hole on AdoCbl-derived dAdo• is transferred to the 3' position of the substrate nucleotide via a cysteinyl radical intermediate. 5 Assuming an evolutionary process based on tinkering, i.e., modification of present components rather than inventions from scratch, our model of the protoRNR tries to deviate as little as possible from what is observed in modern biochemistry.

Amazing. An evolutionary process based on tinkering. Let that sink in, LOL.... How does such a proposal make sense? If the author wishes not to deviate much from the mechanisms observed in modern enzymes, he has to acknowledge for the origin of the most complex biosynthesis pathways to produce one of the most sophisticated cofactors known ( Vitamin B12 in RNR Class II enzymes ). That is not logical nor rational. An evident answer would be that intelligence with specific goals was involved, namely to create the most effective and advanced bioinformational molecule known to man: DNA.

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Intra-protein signalling channels that are essential in translation from messenger RNA to !!

Aminoacyl tRNA Synthetases are essential in the translation machinery from messenger RNA to charge tRNA, with the right amino acids. The paper linked describes, how INTRAPROTEIN communication channels signal from one allosteric binding site where codon recognition takes place, to the other where after recognition, the right amino acid is selected, to be attached afterwards to the tRNA, which transfers it in the next step to the assembly site in the Ribosome, where the condensation reaction takes place, the amino acids is attached and protein polypeptide elongation takes place.

Amazing is, that all this had to emerge prior when life began.....
Intra-protein signalling within two allosteric binding sites, that had to emerge prior life began. Just fan tas tic !!

From a pool of thousands of amino acids and tRNAs in the cell, each aminoacyl-tRNA synthetase must recognize and pair the correct amino acid and tRNA. After this pairing has occurred, the tRNA is transported to the ribosome where the messenger RNA obtained from the DNA sequence is translated into a protein.

How the signal is transmitted from the anticodon on the tRNA at one end of the protein-tRNA complex to the site of chemical reaction in the aminoacyl-tRNA synthetase at the other end has puzzled scientists for a long time. Now, using network analysis algorithms in combination with molecular dynamics simulations, the U. of I. researchers have been able to identify the network of interactions.

"The signaling pathways in the protein-tRNA complexes are analogous to air travel, where passengers departing from small airports pass through major hubs on their way to distant destinations," Luthey-Schulten said. "So too in biology, modules of amino acids and nucleotides communicate using paths that pass through a few important interconnecting links."

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