My articles

How to recognize the signature of (past) intelligent actions

https://reasonandscience.catsboard.com/t2805-how-to-recognize-intelligently-made-artefacts

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.

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
https://reasonandscience.catsboard.com/t2544-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
https://sciencetrends.com/dna-called-blueprint-life-heres/

Biological Cells are equal to a complex of millions of interlinked factories
https://reasonandscience.catsboard.com/t2245-biological-cells-are-like-an-industry-complex-full-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: 
https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins#6664


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

https://reasonandscience.catsboard.com/t2508-abiogenesis-calculations-of-life-beginning-through-unguided-natural-random-events#6665

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
https://reasonandscience.catsboard.com/t1279-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,”
https://www.scientificamerican.com/article/how-structure-arose-in-the-primordial-soup/

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
https://reasonandscience.catsboard.com/t1276-125-reasons-to-believe-in-god



1. https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins#6664

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
https://reasonandscience.catsboard.com/t1277-fine-tuning-of-the-universe

Calculations of life beginning through unguided, natural, random events.
https://reasonandscience.catsboard.com/t2508-calculations-of-life-beginning-through-unguided-natural-random-events

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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390871/

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.

Intra-protein signalling channels that are essential in translation from messenger RNA to proteins.......just......wow !!

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 !!

https://phys.org/news/2009-04-networks-genetic-code.html

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."

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199515/

In the nonliving world, without the input of directed energy, the big rule is the second law of thermodynamics which tells us how things change in the universe. Fact is, we go always downhill towards uniformity and equilibrium what the physicists call heat death but in the living world it seems we're going the other way instead of going down the systems are setup to maintain a constant energy gradient and homeostasis of such, by the uptake of energy in form of sunlight ( through photosynthesis ) , or the consumption of carbohydrates, which permits to be too far from equilibrium states and obtaining reaching purposeful dynamic activity very different to the heat death of the nonliving world. One other major distinction between living and non-living is that living things have an agenda, and whenever we detect or discover a protein, we immediately ask its purpose.

Nonliving things don't have an agenda rocks and planets and atoms and molecules have no agenda. But we all understand living things seem to have an agenda

How did chemistry become biology? The transformation is a remarkable one in that a molecular system, as for example a small strand of DNA, has a weight of 10 minus 21 grams. A Bacteria, however, is nine orders of magnitude larger a very complex system. Nine orders might sound like a small number but what it means in real terms is that the equivalent of something the size of a pinch of salt became the size of several hundred elephants !! So to go from a DNA strand to a living bacteria is an enormous transformation.

Gribbin & Rees, Cosmic coincidences, page 20
So our existence tells us that the Universe must have expanded, and be expanding, neither too fast nor too slow, but at just the "right" rate to allow elements to be cooked in stars. This may not seem a particularly impressive insight. After all, perhaps there is a large range of expansion rates that qualify as "right" for stars like the Sun to exist. But when we convert the discussion into the proper description of the Universe, Einstein's mathematical description of space and time, and work backwards to see how critical the expansion rate must have been at the time of the Big Bang, we find that the Universe is balanced far more crucially than the metaphorical knife edge. If we push back to the
earliest time at which our theories of physics can be thought to have any validity, the implication is that the relevant number, the so-called "density parameter," was set, in the beginning, with an accuracy of 1 part in 10^60 . Changing that parameter, either way, by a fraction given by a decimal point followed by 60 zeroes and a 1, would have made the Universe unsuitable for life as we know it.

Gods existence is overwhelmingly obvious!

Never in human history, it has been more irrational and unjustifiable to be an atheist and unbeliever, than today. The scientific evidence points without permitting any doubt to the requirement of a creator of the living. All biological systems depend on the transmission of instructional information, and for this information to flow, the initial setup of various systems of languages, information encoded by these languages, and communication channels, duly connected by sender and receiver for this information to flow, is required. In fact, at least five signalling networks are life essential and had to be present when life began. These are enormously complex, giving rise to the ability of organisms to have an impressive range of plasticity, to adapt quickly to different environments, food resources, and reaction to harm and disease by immunological resistance.

Imagine that you go to the airport, to take an aeroplane. You get your ticket and go to the gate. There you find a totem where you put your ticket, which is recognized through laser. After the recognition of the information on your ticket, the totem will signal bus no.2 to come to the gate where you are, the bus receives the signal, directs itself to the gate, and a display attached to the totem will immediately inform you: Go outside to bus no.2, that will bring you to your plane. Imagine how complex and information-rich such an event is. Infact, humans today are struggling to develop autonomous cars. But in the cell, all this happens fully automatically, and in a programmed fashion, without external information input requirement.

Now someone that saw the whole system the first time, would ask you: How was this system set up: By intelligent engineers, or a burst of random unguided events put the whole system together? Even the question is of course, foolish. And if someone would answer: I have no idea if intelligence was required, or , most probably luck & trial and errors, that would sound even more foolish.

But that is EXACTLY what an atheist or agnostic will answer. How irrational is that?

Consider:

Each protein, when it is synthesized and is coming out of the Ribosome factory, which assembles proteins, comes with a tag. That tag is an amino acid sequence, like a bar code. The signal recognition particle (SRP), is like the totem described above. The SRP reads the tag of the protein, and "calls" a transport vesicle, equivalent to bus no.2 in the analogy above. The protein is encapsulated into the vesicle, where the protein is protected, and the vesicle starts its journey.

It has all instructions to lead the protein where it is needed to perform its function, for example as the transmembrane channel, functioning as a gate. In human cells, there are 2,3 billion proteins (!!!), each located at the right place. So that vesicle shuttle needs to know where its protein cargo has its destination amongst billions of possible places. That is as if you had to find the right road and number in New York.

How was all this set up? By chance?

There are also tubulins inside of Cells, which are equivalent to highways. Kinesin proteins are other motor proteins that transport molecules to the right destinations in Cells. And how do Kinesisns know how to find their destination? Tubulins have the map encoded in their structure, and Kinesins read them. It's like a GPS which tells the driver the direction it has to go.

How is the origin of such highly sophisticated molecular GPS system best explained? By chance? I don't think so.....

You think evolution came up with it? Nope !! Evolution is not your worldview saver !!. Evolution was not even on the block when all this stuff had to be set up to kick-start life. All you could claim, if you deny an intelligent creator, is chance /luck/trial & error / a random information system generator. Does that make sense to you? Well.... if you love the no-God hypothesis enough, you will have the courage to say: Chance. Or: " We don't know yet, but science will find out".

Honestly: And you think that is a rational, honest answer ????
I don't think so. Its unjustified denial of the evidence at hand.

You can even agree with me. But that will still not lead you to God. Unless you desire to know God, his goodness and seek him, you will not find him. Maybe you carry all that baggage of arguments, where you think, they justify your unbelief. Maybe you accuse God of being unjust, permitting evil, rape, Condon slavery and all that.

Once you do a reset in your mind, and start from scratch, and actually try to experience God, he will reveal himself to you, and you will encounter a loving, just, graceful almighty creator which loves you independently of your rebellion, pretty different than the fantasious caricature portrayed by so many misotheists. Don't keep fooling yourself.......

https://reasonandscience.catsboard.com/t2096-the-astonishing-language-written-on-microtubules-amazing-evidence-of-design?highlight=tubulin

Amino acids are the theist's friend and the atheist's nightmare

In order to have a functional protein, you need to have amino acids.

In order to have the amino acids used in life, you have to select the right ones amongst over 500 that occur naturally on earth.

To get functional ones, you need to sort them out between left-handed and right-handed ones ( the homochirality problem). Only left-handed amino acids are used in cells.

There is no selection process known besides the one used in cells by sophisticated enzymes, which produce only left-handed amino acids.

Amino acids used for life have amino groups and carboxyl groups. To form a chain, it is necessary to have the reaction of 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.

The useful amino acids would have to be joined and brought together at the same assembly site in enough quantity.

There are four different ways to bond them together by the side chains. if bonded to the wrong side chain, no deal.

The formation of amide bonds without the assistance of enzymes poses a major challenge for theories of the origin of life.

Instructional/specified complex information is required to get the right amino acid sequence which is essential to get the functionality in a vast sequence space ( amongst trillions os possible sequences, rare are the ones that provide function )

Before amino acids would join into a sequence providing functional folding, it would disintegrate if hit by UV radiation.

But even IF that would not be the case, most proteins become only functional, if they are joined into holo-enzymes, where various amino acid chains come together like lock and key.

If that would occur, the tertiary or quaternary structure in most cases would bear no function without the insertion of a co-factor inside the pocket, like retinal in the opsin pocket, forming rhodopsin.

But even IF there would emerge a functional protein on the early earth, by itself, it would be like a piston outside the engine block of an automobile. Many proteins bear only function once they are integrated in an assembly line, producing sophisticated molecular products used in life.

But even IF we had an assembly line of enzymes producing a functional product, what good would there be for that product, if the cell would not know where that product is required in the Cell?

For example, chlorophyll requires the complex biosynthesis process of 17 enzymes, lined up in the right order, each producing the substrate used by the next enzyme.  But chlorophyll has no function unless inserted in the light-harvesting antenna complex used in photosynthesis to capture light and funnel it to the reaction center.  

But even if that complex, chlorophyll and the LHC would be fully set up, they have no function without all over 30 protein complexes forming photosynthesis, used to make hydrocarbons, essential for all advanced life forms.  

Now, let's suppose all this would assemble by a freaky random accident on early earth, there would still be no mechanisms of transition from a prebiotic assembly, to Cell factory synthesis.

Get the picture ?

The estimated number of sequences capable of adopting the h repressor fold is still an exceedingly small fraction, about one in 10^63 of the total number of possible 92-residue sequences.
http://onlinelibrary.wiley.com.sci-hub.cc/doi/10.1002/prot.340070403/full

The interdependent and irreducible structures required to make proteins
https://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins

Peptide bonding of amino acids to form proteins and its origins
https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins

Forces Stabilizing Proteins - essential for their correct folding
https://reasonandscience.catsboard.com/t2692-forces-stabilizing-proteins-essential-for-their-correct-folding

Proteins: how they provide striking evidence of design
https://reasonandscience.catsboard.com/t2062-proteins-how-they-provide-striking-evidence-of-design

Biosynthesis of Iron-sulfur clusters, basic building blocks for life  
https://reasonandscience.catsboard.com/t2285-iron-sulfur-clusters-basic-building-blocks-for-life

Titin the largest proteins known and titin-telethonin complex - the strongest protein bond found so far in nature
https://reasonandscience.catsboard.com/t2671-titin-the-largest-proteins-known-and-the-titin-telethonin-complex-the-strongest-protein-bond-found-so-far-in-nature

The gravity of atheist arguments surrounds always the claim: " No evidence of Gods existence ". With evidence, what is meant is: There are no good reasons to believe in a God. Subsequently asked: What would be good reasons to believe in God, often, the reply is: Oh, I have no idea. But if God exists, he knows what would convince me of his existence. As an all-knowing God, he could give me just the evidence that he knows would convince me.

So, in reality, someone going that line of reasoning, cannot claim that there is no evidence, or that there are no good reasons to believe in God. He just does not, for whatever reasons, recognize the evidence or reasons given.

When a theist begins to provide his evidence and reasons for believing in God, atheists commonly have in their toolbox and ready on their lips, a refutation of every and each argument. Often, these arguments are actively researched and accumulated over years and decades, and elaborated efforts are made in the attempt to provide a consistent atheological framework in order to keep God out of the doorsteps.

And, as I have seen time and time again, when unbelievers are cornered, and the only rational explanation is: and therefore God, - their cop-out is:

" I don't know", and attempt to reinforce that confessed ignorance by saying: And that is a totally honest position.

Today, the theist does actually not require much effort. Atheists openly admit right and straight from the beginning: " Our position in regards to origins is: We don't know, but it wasn't God."

So a mix of agnosticism with atheism.

Oh well. If strong atheism cannot be defended rationally, the honest answer is not: I don't know, but one day we might find out, but, If the No-God hypothesis cannot be defended rationally, the Null-hypothesis should be God, until proven the contrary.

Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. Provided the proposition, together with its competitors, form a mutually exclusive and exhaustive class, eliminating all the competitors entails that the proposition is true. Since either there is a God, or not, either one or the other is true. As Sherlock Holmes famous dictum says: when you have eliminated the impossible, whatever remains, however not fully comprehensible, but logically possible, must be the truth. Eliminative inductions, in fact, become deductions.

If strong atheism, or philosophical materialism has no convincing explanatory power, then saying: Most probably, God exists, is the only justifiable, logical, correct, rational conclusion.

It is reinforced by providing as well positive arguments, that is inferences that are not based on gaps of knowledge. Where a scientific or philosophical argument is built on positive evidence, based on what is recognized as the action solely of intelligence, of which chance is incapable of.

So there are reasons why materialism cannot be logically deducted, and reasons why theism can be, and together, they form a compelling, rational, convincing foundation to be a theist.

The physical laws and natural course of things lead to disintegration and racemization of molecules, and chemical compounds. Anyone knows the process. Leave a molecule alone or chemical compound alone for enough time and it disintegrates.

But the origin of life would have had to follow the opposite pathway in the other direction, of complexification from the chemical, abiotic, to biological direction of complexity.

One direction into disorder, the other into higher organisational order.

We know only of one mechanism by experience to be able to create order from disorder. Complexity, from chaos. Functional structures, from purposeless inanimated matter.

intelligence.

In ancient times, God revealed himself to folks, tribes and nations merely by natural , aka general revelation thourth the order of the natural world. That was probably going hand in hand with limited direct revelation. We know of tribes which received prophecies much before messengers of God came to bring the gospel, describing that messenger, so they were prepared. So the knowledge of the creator was always extant in one way or the other.

Other tribes formed their religions based on idolatry and demon worship. Animism in many cases was going hand in hand with the claim that nature was filled with demons & Gods, and it was tabu to explore it, otherwise, the revenge of these Gods was assured.

With the spread of Christianity, came the scientific revolution, removing these fears.

The human mind is by nature curious, attempting to explore and understand the world we live in and make sense of it. The remarkable advance of greek philosophers in early days gives testimony of how even back then, thousands of years ago, the brightest of human minds were even capable of fathom atoms and think about the invisible.

But worldviews go always hand in hand with doubts. The more one is sustained with evidence, the more solid and satisfying it becomes.

As a Christian, I did enormous progress, from a rather Bible-based worldview to one, sustained and confirmed by science and philosophy. A worldview is like a puzzle. The more peaces that are brought together, the more clear the picture becomes, and the more one feels certain about the veracity of its postulates and conclusions.

I am an intellectually satisfied Christian. Fifteen years ago, in a debate with an atheist, he was able to shake my faith, by claiming that the Egyptian pyramids were much older, not matching with the biblical timeline. This did shake my faith, but even then, I knew, searching for more accurate data, it would become clear that the Bible was right in the end.

Today, I wake up every day in the morning, and think about the greatness of my Lord, and give thank for his grace and love, and HIS plans for my life, what he did, is doing, and will do, and can count on HIS intervention to make my prayers become true. My faith is not shaky, but I KNOW my Lord lives, and acts in favour on my behalf because this is HIS promises in the Bible. That's wonderful. And I can experience HIS miracles becoming reality.

The atheist, however, must constantly live with cognitive dissonance, and can never find intellectual satisfaction, as Dawkins claimed ( because evolution is supposedly true ). Atheists are in most cases badly informed, make up their views on poor and superficial information based on a poor epistemology, and must constantly feed their doubts with new answers which however are never bright and clear, but always based on superficial explanations, which cannot go too deep. When they do and unravel the philosophical and scientific bankruptcy, an effective shield is used: The today so commonly used canard: " I don't know, and that is a perfectly valid and honest position". The self-delusion is strong in this one.

And its truly boring to hear it over and over. But hey. To each , their own....

Richard Dawkins, Outgrowing God, page 129:

If DNA is not a blueprint of a baby, what is it? It’s a set of instructions for how to build a baby, and that’s a very different matter. It’s more like a recipe for making a cake. Or like a computer program whose instructions are obeyed in order: first do this, then do that, then if so-and-so is true do … otherwise do …and so on for thousands of instructions. A computer program is like a very long recipe, complicated by branch points. A recipe is like a very short program, with only a dozen or so instructions.

Dear Richard ,

we are not anymore in 1986, where people were so uninformed and naive to believe in your fairies and storytelling, as told in the blind watchmaker, to take your assertions at face value.

We are in 2019, 33 years later, and a lot has changed since then. Not all ( there is still a heck of gullible, non-thinking dudes around ), but many have learned a lot about DNA, and what information entails. For example, those instructions are always the result of an intelligent mind, which instructs to have things done according to a specific purpose. The instructions in DNA, for example, are, indeed, as you wonderfully laid out, to make a baby.

As such, your book, rather than showing how to outgrow God, is demonstrating the power of the creator. He programs the instructions, the information in DNA to build babies.

The instructional program to make babies is indeed awesome, complex in such a way that science, after decades of intensive research, still struggles to fully understand this incredible instruction program.

A newborn baby is already consistent of trillions of cells, each placed in the right order in the body, forming an integrated organ which works wonderfully in a joint venture with all organs together, in a complementary way.

These instructions define in each cell division and replication what kind of cell each will become amongst 200 different cells, its size, where it will have to be placed in the organism, they will specify the cell-cell adhesion mechanisms, four types of cell junctions, and which ones will be used in each cell to adhere to the neighbor cells,

how to construct sophisticated communication channels, a web of information sharing, far more complex than the world wide web, channels, where also molecules are transported, from one cell to another, tagged to find their correct destination, instructions, when cells will have to self destroy, when they have fulfilled their purpose during development, the time period the cell keeps alive in the body.

There are also instructions on how to count each cell division and stop at the right time. If cell division goes 43, rather than 42 rounds, awful malformation and death is the result.

We know by experience, that such sophisticated instructions come always from intelligence. In the case of babies, from an intelligent mind which capabilities are far above ours.

Based on that experience and knowledge, and the evidence shown in biology, we are granted to make a rational inference, namely that the instructions to make babies come from God, the creator of the universe and life.

This is an inference based on evidence, not gaps and ignorance.

The ignorance can be found by the ones that deny this obvious fact, and think that natural selection, a mindless process, is capable of this. This can only be claimed by people which are blind, unwilling to acknowledge their creator, and based on bad will, suppress the obvious truth.

1. Dawkins: DNA is a set of instructions for how to build a baby
2. Instructions are ALWAYS given by an intelligent mind
3. Therefore, the set of instructions stored in DNA came from an intelligent mind.

I joined an Astrobiology group, and posted my video on abiogenesis. The administrator did permit the posting, and after i refuted each of the Admin's objections , he wrote as follows:

" Sorry but none of this makes sense from where I stand. As a philosopher, I must say that this is just a lose assortment of statements, none of which is backed by facts and none of which explains the origin of life. Anyway, I don't think we are getting anywhere with this discussion, so let's just wrap it up. For future reference I want to restate that this group is run by a network of researchers at Lxxx University with the intention of being a forum for discussion and announcements about astrobiology. If anyone does not like the ramifications set by science and logic and wants to discuss from, let's say, a religious perspective, you are welcome to do that somewhere else. This is not the place. "

My reply:
]
XXXX since you muted my post about abiogenesis, i am surprised you did not kick me out of the group. I give you that. Nice.

Academia should always be a place to openly share ideas, even if one does not agree with the other viewpoing, but that is more than regularly not the case ( as you just demonstrated )

You claim that the inference of design does belong to religion. This is the common cop out to mute the dialogue at its roots. I vehemently object and disagree.

Design by an intelligent powerful agency is besides of unguided lucky events a POSSIBLE inference to explain the origin of life and biodiversity, and as such, deserves as much to be scrutinized as any other option. There are basically just two anyway. While a designer has a powerful tool to bring forward life, namely intelligence, luck has none. Its just random chaotic events organizing themselves into the most complex organized structure known to mankind with the purpose to create and perpetuate life.

Once, no reference to the identity of that said intelligence is made, that might have acted past back in time bringing forward life, and all kind of life forms, there is no allusion to religion, organized religion, and the quest of the identity of the designer is left to philosophy and theology.

As such, the Design hypothesis is being disregarded, ignored, and excluded and suppressed without justification.

The result, we see all over in science papers dealing with origins. Pseudo-scientific claims about how supposedly natural events brought forward the most complex factory in the universe, and its blueprint together with it, and even more, self replication, the epitome of advancement of manufacturing technology.

Academia truly needs a rethink, and growing out of the rambling of Huxley and cohorts of the X-Club. They have laid a despicable philosophical foundation and by intimidation. by the method of shout, scream and ridicule, they achieved their goals, The God hypothesis was pushed back and stored in the closet, and brandmarked as pseudoscience, and thrown out of academia.

Shamefully, this is the prevalent status quo until today. Despite the fact, that science has unravelled a technology os unparalleled and unimagined sophistication, beaty and complexity in the molecular world, which would only be rationally explained by the creative force of a divine agency, that possible explanation suppodedly deserves no credit, no memtion, bust must be kept mute.

What the leading professors and leading academics which hold to that view keep doing, is suppressing free dialogue, hijacking the very foundation of science, persecuting any student which defies that state of affairs, threat to hijack to permit going forward in their careers, and all kind of bulling and discrimation. Sad but true.

When someone talks about adaptation and microevolution, the common idea is that we are dealing with a rather slow process, taking various generations for an animal to adapt to an environment and new traits to spread in the population. As it has been reported in the last decade by Shapiro et al, organisms have a read - write genome. jumping genes are one example. They edit the genome by themselves. Some mutations are non-random, but some loci are designed to mutate more generously in order to permit adaptations.

But on a deeper level, cells are designed to adapt constantly and with high speed to various environmental demands, grow and nutrition, and react to stress. Proteins are constantly produced or degraded, and amino acids for example are recycled, with incredible efficiency and speed. While some molecules are harvested and stored, like glycogen, to provide energy to the cell, most other building blocks, like nucleotides, sugars, nitrogen atoms, etc are only produced when needed, in the right amount. Smart feedback loops regulate the production in molecular production lines, and there is never over production, but metabolism and catabolism is a finely adjusted, controlled and orchestrated process. That permits the cell never to waste space by storing molecules which are not needed. This kind of adaptation to react to different environmental conditions, and nutrition demands needs to be fully set up and functioning right from the start of life.

Cells use sophisitcated communication systems, like various signalling patwhays to permit these kind of ultrafast adaptations to take place. So the range of elasticity and adaptation occurs on various levels and a far wider range than commonly acknowledged. Cells are veritable computers wich regulate, govern, control, recruit, interprete, recognise, orchestrate, choreograph, elaborate strategies, guide, instruct, fine-tune, monitor, organize the production output from individual molecules to entire chemical production lines, which are build up and disassemble in high speed and orchestrated manner, do thousands of such operations in parallel ( E. Coli, a simple bacteria, performs 1500 parallel metabolic processes in parallel ). Entire organelles like mitochondria are transported on molecular highways ( tubulins ) by molecular taxis ( kinesins) to various places where needed to produce ATP energy.

How did all this emerge ? By random, unguided events, or design?

Materialists totally overestimate what randomness can do. And totally underrate that its rational to infer that an intelligence, far superiour to ours, a powerful creator, best explains the permeation of information in the whole universe, the origin of language and symbols and codes to communicate by us, and equally existing in the animal world, by fish and whales, and biological Cells which host a multitude of languages, codes, information, and information transmission systems. Its origin is best explained by a creator capable of all this. The universe as a whole is sustained and operates on extremely precise mathematical formulas, a multitude of constants must be adjusted to the extreme, the genetic code specifies the setup of proteins, over 23 epigenetic languages define the make of complex organisms, logic gates based on boolean logic orchestrate gene expression. All of this is dependent on one quality: Intelligence.

Becoming a Christian means, giving up your little rebellious life, where you are your own King and ruler, and where You and your desires are the end station and destination of all your ventures, aims and enterprises, and acknowledging, that there is someone above you. Which is the true and only capable ruler of your life. He is not there to be your dictator, but your loving father and friend, which directs you in accordance to your own advance and development in the relationship with HIM. A little baby makes pooh all the time. The father cleans it, and life moves forward and goes on. In the trajectory, the child grows, becomes adult, and uncontrolled pooh is back behind. In that trajectory, the child ( you ) learns more and more about the father, and gains trust and confidence. That relationship deepens in accordance with the experiences made.

A child of God that makes no compromises and loves the heavenly father, grows. In that development and relationship, The Child learns more and more about the father, his nature and Character. That happens in various ways and directions. One is how the father directs his child's life. We observe Gods actions, conduction, advice of directions, answered prayers, and so forth.

Another is , we learn about Gods power and wisdom by observing his creation. What we see there, says about Gods intelligence and power. That gives us inspiration for admiration and worship.

By contemplating Christ and his miracles, death, suffering, and resurrection, we learn about Gods immeasurable strength of will, love, and sense of justice. This knowledge gives us a deep sense of admiration, and trust in a just, powerful, and loving God. By growing in Christ, our roots deepen, and we gain knowledge, that we can use gracefully to demonstrate to others what a immeasurably loving God we serve, and so, are of inestimable value for others, that receive the chance to know and surrender to the great Lord which we serve.

Our lives become graceful, because God involves us in the enterprise of redemption of a world and souls that are lost. We are meaningful to God, and to others. We are not on the margin of human history, but right in the center of the spot. We are the ones observed with attention by the heavenly creatures, bringing the gospel to the unsaved, and each soul that becomes a member of Gods family is reason for party by the angels. We are worthy, not because we are something by our own. But when Christ lives in us, great things happen. Christians are the true beholders of a great treasure in their lives. It is not gold, silver, manmade wealth, but one that is invisible, enriching the human soul and mind. It is to know our creator, savior, and Lord.

Where are you, in this story? If you do not belong to Gods family, your destination is accumulating debts by God through your sins, die, be judged in front of the great white throne, because there will be no sin unanswered ( either Christ paid for you on the cross, or you pay by yourself ) and exist forever and ever suffering for your choice of exactly that godless graceless self-sufficient existence. Think carefully, choose wisely, be smart. Christ is the only way to heaven. There is no other. He is the key. He gives eternal life to his children and friends. Why would you not like to become one of them ?

The make of Nitrogenase enzymes: By evolution, or design ?

In order to have ammonia essential for the make of DNA, amino- acids and lipids, nitrogen in the air has to be fixed. The uptake of ammonia by microorganisms depends on the interdependent nitrogen cycle. The nitrogen cycle is interdependent with the carbon cycle, and the other energy cycles. 


Energy cycles, how did they "take off" ?
https://reasonandscience.catsboard.com/t2660-energy-cycles-how-did-they-take-off

Nitrogen fixation is an amazingly complex process. 
https://reasonandscience.catsboard.com/t2590-origins-what-cause-explains-best-our-existence-and-why#5864

Only a few bacterias fix nitrogen. The most proeminent one are Cyanobacteria

Cyanobacterias, amazing evidence of design
https://reasonandscience.catsboard.com/t1551-cyanobacteria-amazing-evidence-of-design

Nitrogen fixation is catalyzed by the nitrogenase complex, a very intricate system with nitrogenase reductase and dinitrogenase as the main components. Nitrogenase is central to life on our planet. Nitrogen fixation has always been considered of fundamental importance, not only for its significance in global nutrition, but also because of the relevance of nitrogenase as a model system for examining processes such as multiple electron oxidation-reduction reactions, complex biological metal assembly, and even nucleotide-dependent signal transduction. The process is highly energetically costly and thus tightly regulated. Nitrogenase is an extremely complex enzyme system composed of two proteins designated the Fe protein and the MoFe protein. With assistance from an energy source (ATP) and a powerful and specific complementary reducing agent (ferredoxin), nitrogen molecules are bound and cleaved with surgical precision. In this way, a ‘molecular sledgehammer’ is applied to the N=N bond, and a single nitrogen molecule yields two molecules of ammonia. The ammonia then ascends the ‘food chain’, and is used as amino groups in protein synthesis for plants and animals. This is a very tiny mechanism but multiplied on a large scale it is of critical importance in allowing plant growth and food production on our planet to continue.

One thing is certain—that matter obeying existing laws of chemistry could not have created, on its own, such a masterpiece of chemical engineering.
Substantial energy input is needed to overcome this large activation energy and break the N=N triple bond. In this biological system, the energy is provided by ATP.

The nitrogenase complex requires three metal clusters as co-factors. They demonstrate the amazing catalytic ability of iron-sulfur clusters in biological systems. The biosynthesis of one of the three co-factors,  the MoFe, is extremely complex.

Biosynthesis of the Cofactors of Nitrogenase  
https://reasonandscience.catsboard.com/t2429-biosynthesis-of-the-cofactors-of-nitrogenase

It must be assembled in a multistep process. That begins with the recruiting of Sulfur, Iron, and molybdenum to the assembly site. Sulfur must be obtained in the right form. Six different enzymes are needed in the sulfur synthesis pathway. 

Biosynthesis of Iron-sulfur clusters, basic building blocks for life  
https://reasonandscience.catsboard.com/t2285-iron-sulfur-clusters-basic-building-blocks-for-life

Sulfur must be imported by specialized membrane protein channels, called sulfate transporters. 

Iron mobilization and uptake is a far more complex process. It requires the transformation of iron in the environment into siderophores, an iron form that organisms can uptake, and import into the cell. Three major sets of components are involved in iron uptake in Gram-negative bacteria. First non-ribosomal peptide synthetases. The second component required for proper iron uptake is the export system for siderophores are essential, because they produce the siderophores needed to chelate iron in the extracellular space. ABC transporters have the job of uptake of the product

Amazing molecular assembly lines and non-ribosomal amino-acid chain formation pathways come to light
https://reasonandscience.catsboard.com/t2445-new-amazing-molecular-assembly-lines-and-non-ribosomal-amino-acid-chain-formation-pathways-come-to-light

The short-range of the strong nuclear force is strong, extending no farther than atomic nuclei. But despite its short range, changing the strong nuclear force would have many wide-ranging consequences, most of them detrimental to life.  The periodic table of the elements would look different with a changed strong nuclear force. If it were weaker, there would be fewer stable chemical elements. The more complex organisms require about twenty-seven chemical elements. Instead of ninety-two naturally occurring elements, a universe with a strong force weaker by 50 percent would have contained only about twenty to thirty. That would eliminate Iron and molybdenum, which are life-essential elements, used in many co-factors required in life-essential proteins. 

Iron Uptake and Homeostasis in Cells 
https://reasonandscience.catsboard.com/t2443-iron-uptake-and-homeostasis-in-prokaryotic-microorganisms

Maintaining adequate intracellular levels of transition metals is fundamental to the survival of all organisms. While all transition metals are toxic at elevated intracellular concentrations, metals such as iron, zinc, copper, and manganese are essential to many cellular functions. In prokaryotes, the concerted action of a battery of membrane-embedded transport proteins controls a delicate balance between sufficient acquisition and overload.

Once, the basic materials have been imported, the assembly of of co-factors can begin. 

Biosynthesis of FeMo-co

https://reasonandscience.catsboard.com/t2429-biosynthesis-of-the-cofactors-of-nitrogenase#5924

Biosynthesis of FeMoco is a complicated process that requires several Nif gene products, specifically those of nifS, nifQ, nifB, nifE, nifN, nifV, nifH, nifD, and nifK . Assembly of nitrogenase FeMo-co is a considerable chemical feat because of its complexity and intricacy. 

Once the co-factors are synthesized, they can be incorporated in the assembly of the nitrogenase enzyme. That is not a simple feat either. Metallocluster carrier proteins escort FeMo-co biosynthetic intermediates in their transit between scaffolds. The insertion of FeMo-co into apo-NifDK generates a mature, functional holoenzyme

Following we summarize what we know of the biosynthetic processes that lead to the formation of active MoFe protein.

1. Molybdate enters the cell and is processed by NifQ, or possibly just cystine, to form a putative Mo-S containing species.
2. Iron (possibly from NifU) and sulfur (from NifS activity) are combined by NifB to form NifBco.
3. NifBco binds to NifN2E2 .
4. The next events are still obscure, but it is widely assumed that NifN2E2 acts as a scaffold for the combination of NifBco with the putative MoS species to form FeMoco.
5. In the final stage of activation, FeMoco is bound to the ‘‘apo- MoFe protein.’’ The ‘‘apo-MoFe proteins’’ must be bound to NifY or . NifY or dissociate after the activation of the MoFe protein by FeMoco. The role
of (NifY) may be to hold the ‘‘apo-MoFe protein’’ in an open conformation that will allow access of FeMoco to its binding site.

By evolution, or design ?

Jesus said: I am the truth, the way, and life.
Jesus is described in Revelation as the alpha and omega.

Alpha is one of the fundamental constants in physics. If it had not the precise value that it has, there would be no life in the universe.

One of these fundamental constants is the fine-structure constant, or alpha, which is the coupling constant for the electromagnetic force and equal to about 1/137.0359. If alpha were just 4% bigger or smaller than it is, stars wouldn't be able to make carbon and oxygen, which would have made it impossible for life as we know it to exist.

The reason 137 has obsessed so many thinkers to try and find the math behind it is clear. Einstein wrote, “In a reasonable theory there are no numbers whose values are only empirically determinable.”

“It is impossible for human minds to construct something as infinitely rich as mathematics, that so successfully describes our universe down to the finest detail. Given that it is impossible for anything else to describe our world so accurately, it is also impossible to conclude that the universe is not mathematical.

It’s often said that the whole of biology is explained by chemistry, the whole of chemistry by physics and the whole of physics by mathematics, the queen of the sciences. If all physics is contained within mathematics, it has the most radical consequences.

If, however, there’s only one physics, defined entirely by ontological mathematics (which is a single, interlocked edifice) then the fact that there is life in our universe is no accident at all.

But it points straightforward to the one, which has the name:

Alpha & Omega.

Revelation 22:13
I am the Alpha and the Omega, the First and the Last, the Beginning and the End.

https://www.secretsinplainsight.com/why-137/

Where did Glucose come from in a prebiotic world ?

https://reasonandscience.catsboard.com/t2061p200-my-articles#7220

Although the usual example of a primordial fermentation is that of glucose, it is unlikely that large quantities of this sugar were available in the primitive environment because of its instability.

The ultimate origin of  Glucose - sugars is a huge problem for those who believe in life from non-life without requiring a creator.  In order to provide credible explanations of how life emerged, a crucial question must be answered : Where did Glucose come from in a prebiotic  earth ? The source of glucose and other sugars used in metabolic processes would have to lie in an energy-collecting process. Without some means to create such sugar, limitations of food supply for metabolic processes would make the origin of life probably impossible.

Abiogenesis is understood enough to conclude, that the probabilities are too small, that life could have emerged naturally, without a guiding intelligence. A main unknown issue about the origin of life is to identify the first energy capture and carbon fixation mechanism used by the primitive organisms that populated the young biosphere. A prebiotic system should have also been able to implement the core reactions involved in central metabolism abiotically and nonenzymatically. One of them, the reverse TCA cycle is often proposed as the leading candidate to be the first carbon fixation mechanism. Sugars are versatile molecules, belonging to a general class of compounds known as carbohydrates, which serve a structural role as well as providing energy for the cell. Science today shifts its hope to find the solution of the riddle to hydrothermal vents because they are populated by chemoautotrophic bacterias, which use this alternative mechanism for Carbon fixation, namely the reverse Citric Acid Cycle, or tricarboxylic Cycle (TCA). The TCA is the central hub from which all basic building blocks for life are derived, by all three domains of life. So the origin of the TCA is a central OOL problem. The enzymes used in the cycle are:

1, malate dehydrogenase ( FDH )
2, fumarate hydratase (fumarase)
3, fumarate reductase
4, succinyl-CoA synthetase
5, 2-oxoglutarate:ferredoxin oxidoreductase
6, isocitrate dehydrogenase
7, aconitate hydratase (aconitase)
8, ATP citrate lyase
9, pyruvate:ferredoxin oxidoreductase   Fdred, reduced ferredoxin.

Lets give a closer look just at the first enzyme.

In anaerobic organisms, FDH is an NAD+-independent enzyme containing a complex list of metal centers sensitive to oxygen, including tungsten (W), molybdenum (Mo), non-haem iron and molybdopterin guanine dinucleotide (MGD) cofactors.

These trace minerals and metals must be detected and be available in the surrounding of the place where life supposedly began. In modern cells, these metals are imported by extremely complex membrane transport channel proteins. Remember, in some of the life-essential proteins, the metal co-factors require the three elements: Iron, sulfur, and molybdenum. So these three have to be imported into the cell. Each one of the minerals has their own specific import channel proteins. Let's start with Iron. Iron is not available in a useful form for the cell. So before the import can begin, Iron has to be chelated and transformed into useful form. That occurs by an amazingly complex nano-factory called non-ribosomal peptide synthetase, which works like in factory assembly lines, transforming iron into so-called siderophores.

These siderophores are then detected by membrane channel proteins, bound and imported, using energy that is supplied by adenosine triphosphate. In the case of molybdenum, there is an extremely high affinity, and just a few, less than half a dozen amino acid residues at the right place in the protein recognize and bind the trace metal. If these residues are not the correct ones amongst twenty used in life, no deal, the metal is not recognized.  

The same import process has to occur with iron, sulfur, and molybdenum. In the case of molybdenum, the metal has to be stored, once imported into the cell,  to be available whenever needed. A storage protein has a special cage to store the metal, and special molecular needles are literally ejecting or shooting the metal into the cage to be stored there and at disposal when needed.

Once other signaling networks detect the need of the cell to synthesize a protein using metal clusters, the whole machinery is put to work and a whole orchestration to produce a metal cluster containing protein begins.

The metal clusters require a very complex assembly process. In the procedure, helper proteins are required, called chaperones, which conduct the metals to the assembly site, and help in the scaffolding and assembly. This is a multistep process, requiring various enzymes, this is a literal assembly line doing the process using various finely tuned molecular machines. Once the metal cluster is ready, it must be inserted into the protein through other helper proteins which know how exactly the cluster has to be inserted, and how to be bound to the nearby polypeptide chains of the apoprotein complex.

Of course, this is a simplified explanation, but it gives a grasp of the complexity of the whole process. Thousands of metal clusters containing proteins are required to kick-start the life-essential processes. Transcription of DNA, translation, etc.

And now consider, that some proteins do not require just one metal cluster, but various, often aligned in a very specific order to permit electron transport chains performing their duty.

And now consider, that all this had to emerge without evolution. Either by lucky accidents or design.

What mechanism explains the feat better?

Check out more info on molybden enzymes at my library, reasonandscience. The topic, search: Proteins with molybdenum clusters, essential for life
at the section: Origin of life.

This is in my view a remarkable finding:

According to a peer-reviewed scientific paper published in Science magazine in 2016: Design and synthesis of a minimal bacterial genome, in their best approximation to a minimal cell, it has a 531000-base pairs genome that encodes 473 gene products, being substantially smaller than M. genitalium (580 kbp), which has the smallest genome of any naturally occurring cell that has been grown in pure culture, having a genome that contains the core set of genes that are required for cellular life. That means, all its genes are essential and irreducible. It encodes for 438 proteins

Glucose transporters are listed as essential proteins to keep the basic functions of life This is no suprise, since glucose is the most important source of energy for cellular respiration.

They are conserved ( non-evolved) across all domains of life.

So, these membrane proteins as being part of the original minimal proteome, to start life, could not have emerged through evolution, but had to be fully set up to start life, and cellular self replication.

The size of Sugar transporters of E.Coli is 491 amino acids. This is the relevant part:

Glutamine 161 of Glutl Glucose Transporter Is Critical for Transport Activity and Exofacial Ligand Binding

https://sci-hub.tw/https://www.jbc.org/content/269/32/20533?ijkey=ed7617405401ff7f5a8222213f48373ba8f0e5c2&keytype2=tf_ipsecsha

Two observations indicate that the Glutamine GlnI6l is a particularly crucial amino acid residue for the function of the Glutl transporter. First, the activity of the transporter is strikingly reduced by mutations at this residue.

A nonconservative substitution of leucine for the glutamine reduced transport activity by 50-fold, and a conservative substitution of asparagine for the glutamine reduced intrinsic activity by 10-fold. Second, the conservative substitution of asparagine for Gln161 reduced the apparent affinity of an exofacial ligand for the external binding site by 18-fold. Thus, the lack of a single side chain methylene group (the difference in structure between glutamine and asparagine) was sufficient to grossly perturb the function and ligand binding characteristics of Glutl. It thus seems unlikely that the severe disruption in transport activity observed for the Gln161 mutants was due to a major change in the tertiary structure of the molecule. Rather, these considerations suggest that the precise geometry of the glutamine side chain must be preserved for optimal transporter function. These data are consistent with GlP constituting an essential part of the exofacial substrate-binding site of the transporter

This is remarkable. The mutation/substitution of just ONE amino acid disrupts the glucose transport function in a considerable way. That demonstrates the high specificity required for the protein to bear function.

Of course, that rises the question: How did these proteins emerge on a prebiotic earth, where natural selection did not exist yet? These proteins had to emerge from scratch. And if there was no Glucose to import, they would bear no function.

This is extraordinary evidence, that irreducible complexity is a far more drammatic issue than commonly acknowledged. Just the misplacement of one single amino acid residue interrupts the import of glucose, and primportial cells would starve to death by literally having not the capacity to import food for energy and survival !!

This is a GREAT example of intelligent design.

Is it justified to blame God for creating pathogenic Coronaviruses ?
 
With the recent outbreak of the Coronavirus, some might ask: Why did God create pathogenic viruses? Does that substantiate the accusation ( so often heard, coming from the atheist camp) that God cannot be benevolent, but is evil?

Coronavirus lineages suggest that bat coronaviruses are older than those recognized in other animals and that the human severe acute respiratory syndrome from coronavirus was directly derived from viruses from wild animals in wet markets of southern China. Bats are likely the natural hosts for all presently known coronavirus lineages and that all coronaviruses recognized in other species were derived from viruses residing in bats. 11

Coronaviruses cause respiratory and intestinal infections in animals and humans1. They were not considered to be highly pathogenic to humans until the outbreak of severe acute respiratory syndrome (SARS) in 2002 and 2003 in Guangdong province, China 3

Remarkably, in Leviticus 11.13, we read:
13 “‘These are the birds you are to regard as unclean and not eat because they are unclean:....... and the bat.

The 21 viral types that wreak havoc with the human body represent an insignificant fraction of the 100 million viral types on earth. Most viruses are actually vital to our very existence. They keep ecosystems diverse and balanced.
Bacterial death is absolutely necessary for other living organisms.

Our mismanagement did put us at risk of some viruses. So we don’t know where Ebola comes from, but if we knew where it came from, would we be able to link it to mismanagement or just ignorance? We’ve encountered viruses in places where we went for pretty ecologically destructive reasons. Those viruses passing into humans and causing disease resulted from mismanagement coupled with not knowing.10

Globally the oceans contain 10^30 viruses. If you lined them all up they would extend for 10 million light-years or 100 times the distance across our galaxy. Collectively they would weigh as much as 75 million blue whales. Viruses are not living organisms. They are simply bits of genetic material (DNA or RNA) covered in protein, that behave like parasites. They attach to their target cell (the host), inject their genetic material, and replicate themselves using the host cells’ metabolic pathways.

Algae and plants are primary producers, the foundation of the world’s ecosystems. Using sunlight they turn raw elements like carbon dioxide, nitrogen, and phosphorus into organic matter. In turn, they are eaten by herbivores, which are in turn eaten by other animals, and so on. Energy and nutrients are passed on up the food chain until animals die. But what ensures that the primary producers get the raw elements they need to get started?

The answer hinges on the viruses’ relationship with bacteria. A virus doesn’t go hunting for its prey. It relies on randomly encountering a host — it’s a numbers game. When the host, such as a bacterial cell, grows rapidly, that number increases. The more of a bacterial species there is, the more likely it will come into contact with its viral nemesis — “killing the winner”. This means that no single bacterial species dominates an ecosystem for very long.

In freshwater, for example, you see very high rates of bacterial growth. You would think this high bacterial production would become part of the food chain and end up as fish food. But that is rarely the case.

We now realize that the bacteria actually disappear from these ecosystems. So where do the bacteria go?

The answer lies in the interaction of bacteria and viruses. When a virus bursts open a bacterial cell its “guts” are spewed back into the water along with all the new viruses. The cell contents then become food for the neighboring bacteria, thereby stimulating their growth. These bacteria increase in numbers and upon coming into contact with their viral nemesis they, too, become infected and lyse. This process of viral infection, lysis, and nutrient release occur over and over again. Bacteria are, in effect, cannibalizing each other with the help of their associated viruses. Very quickly, the elements that support the food web are put back into circulation with the help of viruses.

This interaction ensures inorganic nutrients are readily available to algae and plants on which ecosystems depend. It’s the combination of high bacterial growth and viral infection that keeps ecosystems functioning.  Freshwater viral/bacterial interactions appear to be a critical link in carbon cycle between the land and atmosphere. 9

The Logic of Chance: The Nature and Origin of Biological Evolution, Eugene V. Koonin:
Probably an even more fundamental departure from the three-domain schema is the discovery of the Virus World, with its unanticipated, astonishing expanse and the equally surprising evolutionary connectedness. Virus-like parasites inevitably emerge in any replicator systems, so THERE IS NO EXAGGERATION IN THE STATEMENT THAT THERE IS NO LIFE WITHOUT VIRUSES.

The role of viruses in ecology
Viruses are important microbial predators that influence global biogeochemical cycles 8  They are not primarily pathogens, which is a biased view based on the history of medicine. Most viruses do not cause diseases. Viruses cause diseases if a well-established equilibrium gets out of balance. Viruses help in building genomes. Viruses and bacteria belong to the human body and our environment as a well-balanced ecosystem. Only in unbalanced situations do viruses cause infectious diseases or cancer. 7  Although bacteria pass genetic information to each other using several processes such as pili transfer (see below), viral transfer is now known to be critically important. Viruses normally do not, and should not, cause disease. Only if something goes wrong, such as a mutation or accidental inappropriate movement of genes, do they cause problems. Evidence is accumulating to suggest that most or all harmful viruses and bacteria are mutated forms of non-pathogens. Pathogenic organisms result from gene shuffling, which inadvertently disrupts the normal species-host relationship. 6  

In this world of fast and easy travel, emerging viruses are increasingly becoming a major danger to world health. Coronaviruses are a notable example. Particularly virulent forms have emerged from their natural animal hosts and pose a threat to human communities. 2

Coronaviruses

Coronaviruses contain a genome composed of a long RNA strand—one of the largest of all RNA viruses. This genome acts just like a messenger RNA when it infects a cell, and directs the synthesis of two long polyproteins that include the machinery that the virus needs to replicate new viruses. These proteins include a replication/transcription complex that makes more RNA, several structural proteins that construct new virions, and two proteases. The proteases play essential roles in cutting the polyproteins into all of these functional pieces.

Proteases likely arose at the earliest stages as destructive enzymes necessary for protein catabolism and the generation of amino acids in primitive organisms. 2  Proteases act as sharp scissors and catalyze highly specific reactions of proteolytic processing, producing new protein products. They are relevant in the control of multiple biological processes in all living organisms. Proteases regulate the fate, localization, and activity of many proteins, modulate protein-protein interactions, create new bioactive molecules, contribute to the processing of cellular information, and generate, transduce, and amplify molecular signals.

As a direct result of these multiple actions, proteases influence DNA replication and transcription, cell proliferation and differentiation, tissue morphogenesis and remodeling, heat shock and unfolded protein responses, angiogenesis, neurogenesis, ovulation, fertilization, wound repair, stem cell mobilization, hemostasis, blood coagulation, inflammation, immunity, autophagy, senescence, necrosis, and apoptosis.

Consistent with these essential roles of proteases in cell behavior and survival and death of all organisms, alterations in proteolytic systems underlie multiple pathological conditions such as cancer, neurodegenerative disorders, and inflammatory and cardiovascular diseases.

Proteases also play key roles in plants and contribute to the processing, maturation, or destruction of specific sets of proteins in response to developmental cues or to variations in environmental conditions.

The main protease of coronavirus makes most of these cuts. The one shown (PDB entry 6lu7) is from the 2019-nCoV coronavirus that is currently posing dangers in Wuhan. It is a dimer of two identical subunits that together form two active sites.

1. https://www.hpcwire.com/off-the-wire/protein-data-bank-archive-adds-new-coronavirus-protease-structure/
2. https://pdb101.rcsb.org/motm/242
3. https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/30531947
4. https://www.rcsb.org/3d-view/6LU7/1
5. https://en.wikipedia.org/wiki/Coronavirus
6. https://creation.com/did-god-make-pathogenic-viruses
7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755228/
8. https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2009.02101.x
9. https://theconversation.com/viruses-dont-deserve-their-bad-rap-theyre-the-unsung-heroes-you-never-see-46887
10. https://www.christianitytoday.com/ct/2018/august-web-only/why-zika-and-other-viruses-dont-disprove-gods-goodness.html
11. https://jvi.asm.org/content/81/8/4012

Atheists have a lack of understanding about who God is. God is love, and God is truth. The truth is sometimes shocking, radical and crude. It is remarkable that God did not hide in his holy book, the Bible, the occurrences of the wipeout of the Canaanites, and all his judgments of sin, even knowing, that many would read about it, and use it as a pretext to accuse HIM. God, as being completely true, and light has nothing to hide. And is able to justify ALL his actions to the ones that criticize HIM.

Men are by nature arrogant, rebellish, and think they can live victoriously on this earth without surrendering to Christ. That blinds them towards the truth of God's character, which is essentially good, truthful, just, and loving. But man's understanding is also darkened by his will. He neglects a deeper understanding of the events described in the Old Testament and thinks he can be in a position to criticize God. Despite his limited understanding. That's arrogance pure.

Men also think they can explain their existence without a creator.
If I would put ink, snippets of paper, plastic, copper, raw metals on the table in a random, chaotic form, and hire a team of highly skilled engineers, scientists, and software engineers, and give them the task to do a research program, to find out how these snippets, ink, and random parts could somehow transform themselves into a blueprint, and that blueprint providing the precise instructions to make machines and a complex factory, and give them almost unlimited funds and time, you would certainly say, that's pure nonsense, a waste of money and time. It will never gonna happen. It is impossible.

But that is PRECISELY what abiogenesis research is about. Governments have funded such programs for decades, and incalculable amounts of public money have been wasted with NO result AT ALL.

Abiogenesis research is maybe the most irrational, futile, nonsensical scientific enterprise performed by science. That could / should have been already obvious 70 years ago, when DNA was discovered, and the Urey Miller experiment was performed.

The ONLY outcome ?

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.

Re-conceptualizing the origins of life 2017 Dec 28
The origin of life is widely regarded as one of the most important open problems in science. It is also notorious for being one of the most difficult. It is now almost 100 years since scientific efforts to solve the problem began in earnest, with the work of Oparin and Haldane. ‘Bottom-up’ approaches have not yet generated anything nearly as complex as a living cell. At most, we are lucky to generate short polypeptides or polynucleotides or simple vesicles—a far cry from the complexity of anything living.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5686397/?fbclid=IwAR0jkHj-5MnRw5MMgm6xijPFMWlPbbQ5XOlkC9ZmFsE645yl-5zjrQgs4HQ

From time to time I think about what makes atheism so attractive. Why do so many give great value to a worldview without God? Ok. The reasons are manyfold. Agreed. But one predominant reason, in my view, is the promise of the serpent to Adam and Eve. You will be like God. Now, that does not englobe only the knowledge of good and evil. But also autonomy. Pride. The wish to be capable and to win over the challenges that we encounter in life through our own capabilities and capacities. And to rule without anyone above us giving them to us.

And the history of humanity is all about how a perfect world where everything works like a machine without God, and where we are capable as we hope, is a big failure. We are slaves of our own inclinations and own nature. Many struggles to admit this, and try to justify every action of themselves. No matter what. Have you ever met people that think they are always right? I have. I think it is a common characteristic of atheists to not being humble and recognize their own limitations.

For me, it has been a big " dong " of freedom to recognize that I am not as I wish to be. Perfect, capable, strong, and always right. It has been freeing to know that I can come to the Lord with all my weaknesses and shortcomings and bad inclinations, confess my sins, and ask God to make me new. To permit HIS nature to dwell inside of me, and turn my heart of stone into a heart of flesh. To trust HIM, and to know that he is my strength. To stop pretending to be someone that I am not.

To live as a Christian means to be freed of the bonds os self-deception and cognitive dissonance. It means to be free to recognize God's power and wonderfulness, and that we all depend on the great I AM. I am free to worship the one that deserves worship: The perfect, holy, all-powerful Lord of all nations. The one which understanding and intelligence exceed by far ours. The one, that nonetheless, of being the one sitting on the throne ruling all the universe, and all life, became one of us. Humiliated himself to gain a victory that exceeds all perfectness.

God is far beyond just being perfect and holy. He has gained a victory over evil. Over sin. Over Satan. Overall fallen universe and regained something that was lost. That is exceedingly sublime and awesome. Yes, we have an awesome God, and we can never fully describe his awesomeness and greatness. We can only grasp it in a very limited manner with our limited human mind. But the little bit that we understand, permits us to knee in front of his throne, and praise HIM, and sing:

Psalm 95:1-11 ESV /
Oh come, let us sing to the Lord; let us make a joyful noise to the rock of our salvation! Let us come into his presence with thanksgiving; let us make a joyful noise to him with songs of praise! For the Lord is a great God, and a great King above all gods. In his hand are the depths of the earth; the heights of the mountains are his also. The sea is his, for he made it, and his hands formed the dry land. ...

Revelation 7:12 ESV
Saying, “Amen! Blessing and glory and wisdom and thanksgiving and honor and power and might be to our God forever and ever! Amen.”