Debate with Aron Ra

Otangelo · 51 Re: Debate with Aron Ra Fri Dec 25, 2020 12:19 pm

Otangelo

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Aron: Yes, we can. I get at least a few emails every week from former believers thanking me for leading them out the delusion you're still in. This has been going on for at least a decade or so. Many of them were just as certain as you are, until they began to see around wool over their eyes.
Reply: Nice dodge. You are good at it. They will not thank you anymore, once they realize they were blind, following a blind.

Aron: The citations you show now are talking about developmental biology, being pre-programed by heredity, literally by evolution in some cases, but not by a god.
Reply: Your alternative is chance to pre-program the minimal genome to have life a first get-go. You believe in the magical powers of chance, don't you?

Aron Common descent is not a hypothesis. It is confirmed.
Reply: Well, then why do science papers disagree with you? Prokaryotic evolution and the tree of life are two different things
The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761302/

And i am wondering if you know something about the 9 points i mention demonstrating why common ancestry is bunk, that i don't know?
https://reasonandscience.catsboard.com/t2239-evolution-common-descent-the-tree-of-life-a-failed-hypothesis

Aron: We have observed the change from unicellular to multicellular organisms in the lab,
Reply: Did cell-cell adhesion proteins, and signaling evolve in parallel ? If so, based on what evolutionary pressures ?

Aron: Now in the 21st century, they added a couple more mechanisms, epigenetics and endosymbiosis, and it is now the "modern evolutionary synthesis".
Reply: Yes, of course, easy deal. What evolved first: The histone code, readers, erasers, or writers?

Post-transcriptional modifications (PTMs) of histones affect gene transcription
https://reasonandscience.catsboard.com/t2727-post-transcriptional-modifications-ptms-of-histones-affect-gene-transcription

Aron: In this case, you were once again expected to produce some truth to your position, which you simply refused to do.
Reply: That would actually have to be your job. Once you prove that natural mechanisms suffice to explain all phenomena in the natural world, you can categorically accuse creationists to be liars. Then we are on the same level as flat earthers. I have not yet seen that day come. And until then, you are doing what you accuse us of doing. Making unsupported claims.

Aron: You citation agreed with this, listing one and only one scientific method, and then explained how that one method is applicable to both current or historical applications. But it's not a different "kind" of science.
Reply: Koonin disagrees with you. And so do i. They are different disciplines because they answer different questions. 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.

Aron: If you're going to use abduction, which you said you were, then you would need to know something about the supernatural. And you don't.
Reply: We know what signs of intelligent actions are. We can distinguish it from what unguided random mechanisms can't.

How to recognize the signature of (past) intelligent actions
https://reasonandscience.catsboard.com/t2805-how-to-recognize-the-signature-of-past-intelligent-action

Aron: If we detected that an intelligent designer was involved, we would use science, not theology.
Reply: We use science to understand how the world works. That gives us hints and direction if intelligene was more likely involved or not to create it. The identity is a quest of philosophy and theology, since God is not demonstrating himself to us.

Aron:You didn't even properly define what a god is.
Reply: A personal agent, endowed with power, and intelligence, existing above the natural world, without a beginning, and without an end.

Aron: You can't simply eliminate hundreds of gods worshiped by millions of people for thousands of years
Reply: The identity of God is a follow up, after the first ladder in a cumulative has been answered: If there rather IS a God(s) rather than not.

A cumulative case for the God of the Bible
https://reasonandscience.catsboard.com/t1753-a-cumulative-case-for-the-god-of-the-bible

Aron: It doesn't make any difference how the universe began or if it did.
Reply: If your aim is to defend naturalism as a consistent worldview, the origin of the universe, and why there is something rather than nothing, is a central issue.

Aron: More quote-mining. It is deliberately dishonest and misleading, but as I said, it is ubiquitous among creationists.
Reply: Nice doge. Do you expect me to provide an answer that comes from experimental evidence that has grown out of my own crap in the backyards ?

Nonrandom mutations : How life changes itself: the Read-Write (RW) genome
https://reasonandscience.catsboard.com/t1476-non-random-mutations-how-life-changes-itself-the-read-write-rw-genome

Werner Arber Nobel Prize in 1978, Physiology or Medicine (sharing the honor with Daniel Nathans and Hamilton O. Smith) for the discovery of restriction enzymes and their application to molecular genetics.
The deeper we penetrate in the studies of genetic exchange the more we discover a multitude of mechanisms" involved in human genetics that falsify the mutation plus natural selection core of macroevolution.
Arber, W, D. Nathans, and H. O. Smith. 1992. 1978 Physiology or Medicine, Nobel Lectures: Physiology or Medicine 1971-1980, 469-492.

-Mutation - the vast majority are negative.
Toward a realistic model of mutations affecting fitness. Keightley & Lynch, 2003, Evolution, 57:683 {685, 2003) https://onlinelibrary.wiley.com/.../j.0014-3820.2003... "...THE VAST MAJORITY OF MUTATIONS ARE DELETERIOUS. THIS IS ONE OF THE MOST WELL-ESTABLISHED PRINCIPLES OF EVOLUTIONARY GENETICS, SUPPORTED BY BOTH MOLECULAR AND QUANTITATIVE-GENETIC DATA."
"...a great deal of evidence from several sources strongly suggests that the overall effects of mutations are to REDUCE FITNESS."

"All of these experiments detected DOWNWARD trends in MA (mutation accumulation) line population mean fitness relative to control populations as generations accrued. As far as we know, there is NO CASE of even a single MA line maintained by bottle-necking that showed significantly higher fitness than its contemporary control populations."
"Ethyl methanesulfonate (EMS) mutagenesis experiments, in which controls are given identical treatment to mutagenized lines, other than a dose of mutagen, have also shown consistently strongly NEGATIVE EFFECTS on fitness traits in Drosophila."

"Similarly, transposable element insertional mutagenesis leads to REDUCED fitness in Drosophila."
"Although the above studies have focused on the fitness effects of mutations in the context of laboratory environments, substantial indirect evidence derived from molecular studies supports the contention that MOST MUTATIONS IN NATURAL POPULATIONS ARE DELETERIOUS."

"If mutations are neutral on average, C, the proportion of ‘missing’ amino-acid substitutions, would have an expected value of 0.0. However, IN ALL TAXA EXAMINED SO FAR, average values of C are in excess of 0.7, implying that the MAJORITY of amino-acid altering mutations are deleterious."

"The 214 generation experiment of Vassilieva et al. (2000) clarifies the slowly emerging pattern — as the period of MA (mutation accumulation) extended, PROGRESSIVELY LOWER FITNESS CLASSES ACCUMULATED, whereas the frequencies of the highest fitness classes observed in the controls PROGRESSIVELY DIMINISHED. Contrary to the suggestions of Shaw et al. (2002), there is NO EVIDENCE for improved fitness IN ANY periodically bottlenecked C. elegans line." (all emphasis added)

-Selection - has absolutely no ability to generate anything in order to add complexity... it's nothing more than what is already available.
-Sexual intercourse - actually constrains major change...

From the article below...
Heng and fellow researcher Root Gorelick, Ph.D., associate professor at Carleton University in Canada, propose that although diversity may result from a combination of genes, the primary function of sex is NOT about promoting diversity. Rather, it’s about keeping the genome context — an organism’s complete collection of genes arranged by chromosome composition and topology — as UNCHANGED as possible, thereby maintaining a species’ identity. This surprising analysis has been published as a cover article in a recent issue of the journal Evolution.

“If sex was merely for increasing genetic diversity, it would NOT have evolved in the first place,” said Heng. This is because asexual reproduction — in which only one parent is needed to procreate — leads to HIGHER rates of genetic diversity than sex.
In fact, two billion years ago in Earth’s biosphere, life relied exclusively on asexual reproduction, and every organism was capable of bearing young without costly competition to mate. With asexual species’ faster and more efficient mode of reproduction, the origin and maintenance of sex — not exactly the fittest means of reproduction — puzzles scientists, who for decades have been asking, Why has sex evolved and survived?
According to Heng, the hidden advantage sex has over asexual reproduction is that it CONSTRAINS MACROEVOLUTION — evolution at the genome level — to allow a species’ identity to survive. In other words, it PREVENTS “Species A” from morphing into “Species B.” Meanwhile, it also allows for microevolution — evolution at the gene level — to allow members of the species to adapt to the environment.
https://www.sciencedaily.com/rel.../2011/07/110707161037.htm

Aron: Now you know better. Evolution is a theory of biodiversity wherein one cannot grow out of one's ancestry.
Reply: Each branching point in the tree of life would therefore not be possible. You refute your own phylogeny claim, LOL.

Aron: See? I told you didn't know what macroevoluiton is. So that you do know, do you understand and accept that these are the actual definitions of those terms?
Reply: Did you just ignore the follow up at the link, just to make a point and attempt to portray me as ignorant? yes, i agree with your decription. But you are not telling me anything new that i have to be educated with. I continue:

https://reasonandscience.catsboard.com/t1390-macroevolution-fact-or-fantasy

What is a macroevolutionary novelty?
The change/transition, where one "kind" can evolve into another beyond the species level (i.e. primary speciation), like an organism, randomly changing/transition into a whole entire different organism with new fully functioning biological features, the emergence of new complex functions, a new genus or higher rank in taxonomy. The origin of new body plans, forms, and architecture. The origins of novel branches of the tree of life at levels above that of primary speciation. The origin and diversification of higher taxa. Of new phyla. From the supposed Last Universal Common Ancestor to unicellular eukaryotic cells. From unicellular to multicellular life. There Are Six Important Patterns of Macroevolution: Mass Extinctions. Adaptive Radiation. Convergent Evolution.

Aron: In addition to the documented development of new enzymes and chromosomes, novel synthesis abilities, denovo genes, and retroviral resistance, notable examples include the evolution of a new multicellular species arising from unicellular algae under direct observation in the lab.
Reply: Volvox is not helping you.

Unicellular and multicellular Organisms are best explained through design
https://reasonandscience.catsboard.com/t2010-unicellular-and-multicellular-organisms-are-best-explained-through-design

The situation in Pleodorina and Volvox is different. In these organisms, some of the cells of the colony (most in Volvox) are not able to live independently. If a nonreproductive cell is isolated from a Volvox colony, it will fail to reproduce itself by mitosis and eventually will die. What has happened? In some way, as yet unclear, Volvox has crossed the line separating simple colonial organisms from truly multicellular ones. Unlike Gonium, Volvox cannot be considered simply a colony of individual cells. It is a single organism whose cells have lost their ability to live independently. If a sufficient number of them become damaged, the entire sphere of cells will die.

Otangelo · 52 Re: Debate with Aron Ra Fri Dec 25, 2020 1:02 pm

Otangelo

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Aron: Wait, you still think macroevolution requires a change in body plans? I thought we went over this, and you assured me that you never said anything so stupid.
Reply: I replied already: The crux and issue in question is not macroevolution in a general sense, but macroevolution/primary speciation.

Primary, and secondary speciation
https://reasonandscience.catsboard.com/t2360-evolution-speciation-primary-and-secondary-speciation

Primary speciation
has been used to encompass the most basic and commonly recognized ways of initiating new species, the divergence of diploid populations to the level of species. Having a clear and well-supported phylogeny for the group of taxa being studied is particularly important in developing hypotheses about primary speciation. Unless sister taxa are compared, erroneous conclusions about the processes involved will be obtained. Within this major mode are more specific categories including allopatric speciation, the divergence of populations to the species level through isolation by geographic separation, parapatric speciation, divergence of popUlations to the species level even though populations maintain contiguous but nonoverlapping geographic distributions, and sympatric speciation, divergence of populations to the species level even though the populations occupy the same geographic region. Given the complex biotic and behavioral interactions that have been associated with sympatric speciation and the high probability that simple isolating mechanisms characterize pteridophytes, it seems unlikely that they speciate sympatrically at the diploid level.

Secondary Speciation
When it can be demonstrated that the speciation under investigation involved genomic-level changes, such as hybridization or polyploidy, a separate mode is proposed. The magnitude of genetic modification in secondary speciation often can be characterized, and it appears to be qualitatively different from that caused by the more incremental changes that are typical of primary speciation. Further, secondary speciation usually involves interactions between distinct and separate lineages that remain intact (autopolyploidy is the exception). These interactions result in the production of a new lineage that is reproductively isolated from its progenitors, shares significant portions of its genome with them, and is usually intermediate in morphology between them. Thus, instead of a single lineage evolving into two new lineages (as in primary speciation), two lineages interact to yield a third lineage, and all three lineages persist. Characterization of a variety of patterns provides circumstantial evidence of different kinds of secondary speciation. When different ploidy levels are detected among individuals that are morphologically uniform, autopolyploidy is suspected. Some summaries of speciation have used autopolyploidy as an example of "sympatric" speciation. However, autopolyploidy involves genome duplication, a mechanism that is quite different from those leading to the origin of diploid lineages. As reviewed by Gastony [34], speciation by chromosome doubling within pteridophyte species has been largely overlooked as a significant mechanism. In some groups, however, especially when accompanied by apomixis, autopolyploidy may occur frequently.

Aron: >> Nice dodge. That is MY ARGUMENT. Search the entire web, and show me if you can find a place where i supposedly copied the information from.
And your problem is: Your world view ends right here. Against facts, there are no arguments. Abiogenesis is impossible by all means. If you are so keen about honesty, its time to admit that your worldview is bunk.
My problem with your "worldview" is that it's all lies and needs to be corrected.
Reply: Then for sake, do it. Try to explain how EVEN ONE protein could have emerged prebiotically. I predict, you can't. Forget, the entire proteome for LUCA.

Proteins and Protein synthesis
https://reasonandscience.catsboard.com/t2706-main-topics-on-proteins-and-protein-synthesis

Proteins are structures of complex semantophoretic macromolecules that carry genetic information.

How Did Protein Synthesis Evolve?
The molecular processes underlying protein synthesis in present-day cells seem inextricably complex. Although we understand most of them, they do not make conceptual sense in the way that DNA transcription, DNA repair, and DNA replication do. It is especially difficult to imagine how protein synthesis evolved because it is now performed by a complex interlocking system of protein and RNA molecules; obviously the proteins could not have existed until an early version of the translation apparatus was already in place. As attractive as the RNA world idea is for envisioning early life, it does not explain how the modern-day system of protein synthesis arose.
Molecular biology of the cell, 6th ed. pg. 365

If you keep dodging this most crucial point, upon which your worldview either stands or falls, I will call you out, and call you a liar, as you call me ( unjustified)...

Aron: Creationists are the ones who pretend that everything was poofed out of nothing by god-magic.
Reply: 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.

But maybe you should get familiar with quantum mechanics.

Decoding reality - Information is fundamental
https://reasonandscience.catsboard.com/t3035-decoding-reality-information-is-fundamental
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"As a man who has devoted his whole life to the most clear-headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force that brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter."
“Das Wesen der Materie” (The Nature of Matter), speech at Florence, Italy, 1944 (from Archiv zur Geschichte der Max-Planck-Gesellschaft, Abt. Va, Rep. 11 Planck, Nr. 1797)

Aron: Thanks to Urey-Miller and a number of other, similar experiments, we now know that water, ammonia, methane and hydrogen generate amino acids when heated and charged with electricity.
Reply: So let me be clear. Success would be, if an experiment would provide evidence how the 20 amino acids could have originated prebiotically on early earth. That has NOT been done.
In one of your videos, you even falsely claimed that the 20 amino acids used in life were produced in a follow-up Urey Miller experiment in 2008. The volcano in a bottle, I guess. They produced some DIFFERENT amino acids, but not all those used in life.

The Miller Urey experiment
https://reasonandscience.catsboard.com/t2170-abiogenesis-the-miller-urey-experiment

If you can't make a brick, you can't make a house. Naturalistic scenarios are all based on ad-hoc anecdotal pseudo-scientific claims. In the Urey - Miller experiment, none of the following amino-acids were produced, all life essential: Cysteine Histidine Lysine Asparagine Pyrrolysine Proline Glutamine Arginine Threonine Selenocysteine Tryptophan Tyrosine

Never, in any simulated OOL experiment, the amino acid Tryptophan was synthesized. Why? The biosynthesis pathway to make tryptophan is the most biochemically expensive and most complicated process of all life essential amino acid pathways, and tightly regulated. Glucose feeds the Glycolysis pathway, which utilizes nine enzymatic steps and enzymes to produce phosphoenolpyruvate (PEP) and erythrose- 4-phosphate, which enter the Shikimake pathway, which uses another seven enzymes, to make chorismate, which enters the Tryptophan biosynthesis pathway, and after another five steps and enzymes, finally produces Tryptophan. So, in total, 21 enzymes.

But not any kind of enzyme. Some are highly sophisticated, veritable multienzyme nanomachines, like a paper called the bacterial tryptophan synthase, which channels the substrates through a long interconnecting tunnel with a clear logic: the substrate is not lost from the enzyme complex and diluted in the surrounding milieu. This phenomenon of direct transfer of enzyme-bound metabolic intermediates, or tunneling, increases the efficiency of the overall pathway by preventing loss and dilution of the intermediate. Smart, hah ??!!

You can have a closer look at the entire pathway to make tryptophan here:
https://reasonandscience.catsboard.com/t1740-origin-of-the-canonical-twenty-amino-acids-required-for-life#5939

Aron: Similarly, heating water to 70ºC in the presence of iron hydroxide (simulating geothermal vents in the anaerobic conditions of the prebiotic earth) also produced amino acids and alpha hydroxy acids in the lab.
https://www.wired.com/2008/10/forgotten-exper/
Reply: The hydrothermal-vent hypothesis , and why it fails
https://reasonandscience.catsboard.com/t1394-the-hydrothermal-vent-hypothesis-and-why-it-fails?highlight=hydrothermal

Dr. Stanley L. Miller, University of California San Diego 14
What about submarine vents as a source of prebiotic compounds?
I have a very simple response to that . Submarine vents don't make organic compounds, they decompose them. Indeed, these vents are one of the limiting factors on what organic compounds you are going to have in the primitive oceans. At the present time, the entire ocean goes through those vents in 10 million years. So all of the organic compounds get zapped every ten million years. That places a constraint on how much organic material you can get. Furthermore, it gives you a time scale for the origin of life. If all the polymers and other goodies that you make get destroyed, it means life has to start early and rapidly. If you look at the process in detail, it seems that long periods of time are detrimental, rather than helpful.

https://reasonandscience.catsboard.com/t2887-chemical-evolution-of-amino-acids-and-proteins-impossible

The problem of getting nitrogen to make amino acids and DNA on early earth 2:41
The problem of getting all amino acids used in llife by origin of life experiments 4:20
The problem of selecting 20 amino acids prebiotically out of hundreds supposedly existing on early earth. 6:08
The problem of concentrating the amino acids used in life at one assembly site. 7:15
The problem of understanding why life uses 20 amino acids, and not more or less. 9:00
The problem of homochirality 12:23
The problem of amino acid synthesis regulation 13:43
The problem of peptide bonding of amino acids to form proteins 14:12
The problem of linking the right amino acid side sequence together 17:15
The problem of getting the right forces to stabilize proteins - essential for their correct folding 19:32
The problem of hierarchical structures of proteins 19:50

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.

Otangelo · 53 Re: Debate with Aron Ra Fri Dec 25, 2020 1:34 pm

Otangelo

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Aron: Name a single natural law that was not devised by people. Who do you thing came up with Newton's laws of motion? Or Boyle's gas law? Lord Kelvin is credited with the Laws of Thermodynamics.
Reply: Yes, Laws are discovered and described. But before that happens, they had to be there....

Laws of Physics, where did they come from?
https://reasonandscience.catsboard.com/t1336-laws-of-physics-where-did-they-come-from

Our universe is indeed orderly, and in precisely the way necessary for it to serve as a suitable habitat for life. The wonderful internal ordering of the cosmos is matched only by its extraordinary economy. Each one of the fundamental laws of nature is essential to life itself. A universe lacking any of the laws would almost certainly be a universe without life.
https://web.archive.org/web/20110805203154/http://www.leaderu.com/real/ri9403/evidence.html

Paul Davies: The universe obeys mathematical laws; they are like a hidden subtext in nature. Science reveals that there is a coherent scheme of things, but scientists do not necessarily interpret that as evidence for meaning or purpose in the universe.

The only rational explanation is however that God created this coherent scheme of things since there is no other alternative explanation. That's why atheists rather than admit that, prefer to argue of " not knowing " of its cause.

Aron: So again we agree, the universe is not fine-tuned for life, certainly not for human life.
Reply: No. We disagree, of course.

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

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

Fine-tuning of the Laws of physics
Fine-tuning of the Big Bang
Fine-tuning of the cosmological constant
Fine-tuning of the initial conditions of the universe
Fine-tuning of the fundamental forces of the universe
Fine-tuning of the subatomic particles
Fine-tuning of the Milky Way Galaxy
Fine-tuning of the Solar System
Fine-tuning of the sun
Fine-tuning of the earth
Fine-tuning of the moon
Fine-tuning of the electromagnetic spectrum
Fine-tuning in biochemistry

Aron: I'm not a fan of the argument from improbability fallacy, nor of the fallacy that complexity should indicate a divine designer. No, an efficient simplicity would be the hallmark of intelligent design, not the unnecessarily excessive complexity we get with biochemistry. The only way that makes sense is if it is a haphazard pattern of emergence, which I know creationists never understand.
Reply: I could not CARE LESS if you are a fan of the argument or not. Actually, it is quite obvious why you are not a fan of it. That's because you are biased, and are unwilling to permit God to put the foot into your door. This is probably one of the greatest SMACKDOWN and KNOCK-OUT arguments against naturalism because we KNOW by experience that intelligence CAN make complex machines for specific purposes, while unguided random forces can't.
The lack of acknowledging this, puts you in the camp with Matt, and you both deserve the medal for ostrich behavior !!

Occams Razor
https://reasonandscience.catsboard.com/t2409-occams-razor?highlight=occams
Well, echoing Einstein, the answer is very easy: nothing is really simple if it does not work. Occam’s Razor is certainly not intended to promote false – thus, simplistic — theories in the name of their supposed “simplicity.” We should prefer a working explanation to one that does not, without arguing about “simplicity”. Such claims are really pointless, more philosophy than science. The only important scientific point is: what gives us an empirically well-supported, “best explanation”?

https://reasonandscience.catsboard.com/t2895-syllogistic-arguments-of-gods-existence-based-on-positive-evidence#8181

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

Otangelo · 54 Re: Debate with Aron Ra Sat Dec 26, 2020 10:46 am

God of the exact: Daniel’s Seventy Week Prophecy

Otangelo · 55 Re: Debate with Aron Ra Sat Dec 26, 2020 11:14 am

Otangelo

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Aron: I didn't dodge your point. I twice explained why I am scientifically and philosophically justified in saying there is no god and why you are not justified for saying there is one.
Reply: Do you have knowledge of all reality, including what is beyond the physical universe ? If you have not, you do not have absolute knowledge, and NO justification to say in absolute terms that there is no God. Again: You commit the fallacy which you accuse Creationists of.

Aron: Don't lie about me. You know as well as I do that you cannot produce scientific evidence in a discussion of science. Instead, you admitted (unwittingly) that your "evidence" was no more than the question-begging fallacy of circular reasoning routing back to the assumed conclusion, and that even that required a "leap of faith". You believe the claims in the Bible because the Bible says so, and you think the claim IS the evidence.

Reply: I can make a case for God ENTIRELY and ONLY using science and philosophy. It even points to the Biblical God.
Who do you think coined the term scientist ? It was William Whewell, an Anglican priest and theologian, who also came up with the words physicist, cathode, anode, and many other commonly used scientific terms. Essentially, the very language used by scientists today was invented by a believer.

When Charles Darwin wrote The Origin of Species in 1859—the work that first proposed the theory of evolution—he was definitely a believer in God. It’s true that as he grew older, he began to doubt the existence of a personal Creator who cared about his creatures, but Darwin always struggled with his lack of faith. He was at times a Christian and at times an agnostic. But he never thought that his scientific theory was incompatible with the idea of God. Rather, he thought that while God did not have a direct hand in creating the different species of the world, he did indeed create the natural laws that governed the cosmos—including the laws of evolutionary development.

And what of the science of genetics—the means through which evolution supposedly takes place? According to proponents of evolutionary theory, it is only through genetic mutation and the process of natural selection that life on this planet is able to undergo gradual development. Who, then, was the father of this field of study? The answer is Gregor Mendel—an Augustinian friar and abbot of a Catholic monastery! This monk, botanist, and professor of philosophy was the man whose famous experiments on peas led to the formulation of the rules of heredity and to the proposal of the existence of invisible “genes”—which provide a basis for the science of modern genetics.

Well, then what about the big bang theory—the leading explanation of how our universe began? In fact, the man who proposed both the theory of the expansion of the universe as
well as the big bang theory of the origin of the universe—effectively changing the whole course of modern cosmology—was Father Georges Lemaître, a Belgian astronomer and Roman Catholic priest! A priest came up with the big bang theory! This cleric, who taught physics at the Catholic University of Leuven, delivered a famous lecture on his theories in 1933 that was attended by Albert Einstein in California. When Einstein heard Father Lemaître delineate his theory, he said: “This is the most beautiful and satisfactory explanation of creation to which I have ever listened. Now how could this be?

How could the father of genetics be a monk and the father of the big bang theory be a priest? Didn’t these men know what all modern atheists seem to take for granted—that the very theories they espoused contradict the idea of God and nullify the possibility of his existence? Didn’t they know that their belief in God was therefore absurd? Were they really that blind?
Or is there, perhaps, another explanation? Could it be that these great men of science were not blind at all, but rather that modern atheists fail to understand the most simple principle of rational thought— namely, that explaining the scientific process of how the universe came to be does not in any way explain why it came to be. It does not explain the fundamental mystery of existence itself. This mystery can never be explained by science.

None of these giants in the field of science was an atheist. All believed in a Supreme Being who created and designed the universe

Aron: evidence of my position must be in the form of absolute proof.
Reply: I said IF you make ABSOLUTE claims, you have the burden of proof to back up your absolute claims. Otherwise, what i demand, is that materialists make a case providing reasons why the "only matter" hypothesis makes more sense than theism. You have miserably failed to substantiate that proposition so far. As all atheists that i know.

Aron: If you were capable of actual discussion, I could show you everything you really need to see. Because we really do have almost all the evidence you said did not exist.
Reply: Do it for your audience. Not for me. Lets see what you got. As said: 10^722000 is your number. Don't dodge.... unless you want to be unmasked as biased which i guess you don't like, right? How did proteins form prebiotically? You have not answered that. Start explaining for what reasons molecules prebiotically selected 20 amino acids out of hundreds supposedly existing on early earth... i am waiting....

Aron: Now, here are a list of such facts in evidence for evolution:.......
Reply: Now, here are a list of such facts in evidence for creation..........

Where Do Complex Organisms Come From?
https://reasonandscience.catsboard.com/t2316-evolution-where-do-complex-organisms-come-from

The BIG (umbrella) contributor to explain organismal complexity and biodiversity which falsifies and replaces unguided evolutionary mechanisms is preprogrammed prescribed instructional complex information encoded through ( at least ) 31 variations of genetic codes, and 31 epigenetic codes. Complex communication networks use signaling that act on a structural level in an integrated interlocked fashion, which are pre-programmed do direct growth and development, respond to nutrition demands, environmental cues, control reproduction, homeostasis, metabolism, defense systems, and cell death.

1. Genetic and epigenetic information directs the making of complex multicellular organisms, biodiversity, form, and architecture
2. This information is preprogrammed and prescribed to get a purposeful outcome. Each protein, metabolic pathway, organelle or system, each biomechanical structure and motion works based on principles that provide a specific function.
3 Pre-programming and prescribing a specific outcome is always the result of intention with foresight, able to instantiate a distant specific goal.
4. Foresight comes always from an intelligent agent. Therefore, biodiversity is the result of intelligent design, rather than unguided evolution.

The following mechanisms are involved in organismal development and growth:

1. The Gene regulation network orchestrates gene expression
2. Various signaling pathways generate Cell types and patterns
3. At least 23 Epigenetic Codes are multidimensional and perform various tasks essential to cell structure and development
4. Cell-Cell communication in various forms, especially important for animal development
5. Chromatin dance in the nucleus through extensile motors affect transcription and gene regulation
6. Post-transcriptional modifications (PTMs) of histones affect gene transcription
7. The DNA methylation code is like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on.
8. Homeobox and Hox gene expression is necessary for correct regional or local differentiation within a body plan
9. Noncoding DNA ( Junk DNA ) is transcribed into functional non-coding RNA molecules and switches protein-coding genes on or off.
10.  Transposons and Retrotransposons regulate genes
11. Centrosomes play a central role in the development
12. The precise arrangement of Cytoskeletal arrays provides critical structural information.
13. Membrane targets provide crucial information—spatial coordinates—for embryological development.
14. Ion Channels and Electromagnetic Fields influence the form of a developing organism
15. The Sugar Code forms information-rich structures that influence the arrangement of different cell types during embryological development.
16. Egg-polarity genes encode macromolecules deposited in the egg to organize the axes
17. Hormones  are special chemical messengers for development
18. Secreted morphogens growth factors direct cell fate decisions during embryonic development.
19. An adhesion code ensures robust pattern formation during tissue morphogenesis

How does biological multicellular complexity and a spatially organized body plan emerge?
https://reasonandscience.catsboard.com/t2990-how-does-biological-multicellular-complexity-and-a-spatially-organized-body-plan-emerge

Aron: When I say that I can prove evolution, I am using proof in the sense that a lawyer would, that proof is an overwhelming preponderance of evidence beyond reasonable doubt. It doesn't have to go beyond UNreasonable doubt.
Reply:  https://reasonandscience.catsboard.com/t2806-main-topics-about-evolution

What is fact in regards of evolution :
1. Change over time; history of nature; any sequence of events in nature
2. Changes in the frequencies of alleles in the gene pool of a population
3. Limited common descent: the idea that particular groups of organisms have descended from
a common ancestor.
4. The mechanisms responsible for the change required to produce limited descent with modification; chiefly pre-programmed selection acting on random variations or mutations
5. Natural selection acting up to two random mutations as shown in malaria ( See Behe's Edge of evolution )

What is not fact:
6. Universal common descent: the idea that all organisms have descended from a single common ancestor.
7. Blind watchmaker thesis: the idea that all organisms have descended from common ancestors through unguided, unintelligent, purposeless, material processes such as natural
selection acting on random variations or mutations; the idea that the Darwinian mechanism of natural selection acting on random variation, and other similarly naturalistic mechanisms, completely suffice to explain the origin of novel biological forms and the appearance of design in complex organisms.

What are the REAL mechanisms of biodiversity, replacing macroevolution?
https://www.youtube.com/watch?v=_IGrzrk6iBEre=youtu.be

Where Do Complex Organisms Come From?
https://reasonandscience.catsboard.com/t2316-where-do-complex-organisms-come-from

Why Darwins theory of evolution does not explain biodiversity
https://reasonandscience.catsboard.com/t2623-why-darwins-theory-of-evolution-does-not-explain-biodiversity

The tree of life, common descent, common ancestry, a failed hypothesis
https://reasonandscience.catsboard.com/t2239-the-tree-of-life-common-descent-common-ancestry-a-failed-hypothesis

Aron: You're also committing the fallacy of shifting the burden of proof when you say that atheists can't prove materialism, that the material world is all there is. You're forgetting that we're not saying that.
Reply: Atheists also have a burden of proof. All of us, in attempting to explain the world around us, move from a plethora of questions to a single responsibility:

There Are Only Two Kinds of Answers In the end, the answers to these questions can be divided into two simple categories: Answers from the perspective of philosophical naturalism (a view I held as an atheist), or answers that accept the existence of supernatural forces (a view I now hold as a theist). Atheists maintain that life’s most important questions can be answered from a purely naturalistic perspective (without the intervention of a supernatural, Divine Being). Theists argue that the evidence often leaves naturalism ‘wanting’ for answers while the intervention of an intelligent, transcendent Creator appears to be the best inference. In times like these, the theist finds it evidentially reasonable to infer a supernatural cause.

Aron: You have to SHOW that you're how and how we can know that.
Reply: If you cannot LOGICALLY exclude God as a possible explanation of origins, you cannot claim that the God hypothesis is impossible.

Aron: I know Krauss, and no he doesn't.
Reply: I know that he doesnt, but in that particular conversation with Dawkins he went that far. That deserved that parody. Also claiming that virtual particles can create the universe is silly to the extreme. His entire claims are silly .

Aron: being as material energy is eternal
Reply: Wow. Reeeeeallly ?? Ever heard about the 2nd law of thermodynamics ? How do you go from a high entropy state to a low one?

Aron: where did God come from? If we decide that this is an unanswerable question, why not save a step and conclude that the origin of the Universe is an unanswerable question? Or, if we say that God always existed, why not save a step, and conclude that the Universe always existed?
Reply: The universe had a beginning
https://reasonandscience.catsboard.com/t1297-beginning-the-universe-had-a-beginning
According to Hawking, Einstein, Rees, Vilenkin, Penzius, Jastrow, Krauss and 100’s of other physicists, finite nature (time/space/matter) had a beginning.

Who or what created God?

40:12 - Who created God?

Common atheist fallacies: exposed !!
https://www.youtube.com/watch?v=wK99BsNc2Ko&t=3054s

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

Aron: The Second Law points to: (1) a beginning Not necessarily for multiple reasons.
Reply: Nice dodge. Again. And you say you are not biased ? LOL

Otangelo · 56 Re: Debate with Aron Ra Sat Dec 26, 2020 11:44 am

Otangelo

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Aron: Does it matter? I mean, I'm sure I can find it. I've found other studies like that. But do I really need to waste my time answering your question when you'll only ignore the answer again?
Reply: See, when it comes to the specifics, you immediately dodge, rather than giving an honest answer. I can answer my question for you. They had all to emerge together, erasers, readers, and writers, and the histone code. None of them have function by themselves. That observation ALONE kills your worldview. But you cannot admit it, because you are emotionally committed to believe what you want to be true. Your claim that you are not biased is not demonstrated with your attitude, and how you deal with the difficult questions.

Aron: It is NOT my job to disprove your unsupported assertions. It is your job to show that they are justified.
Reply: Yes, it is your job. If you want to have a case for materialism, it must rest on its own feet. The new atheists tactic is a lousy one. We have a case, and you dismiss it, but do not provide a better one.... thats lame and cheap.

Aron:Once again, what you're calling materialism is the lack of any reason to believe in the supernatural world that you're claiming exists.
Reply: How i love to smear this on your face: 125 reasons to believe in God
https://reasonandscience.catsboard.com/t1276-125-reasons-to-believe-in-god

The obviousness of Creation is hidden from those who reject God. There is no evidence that we can exist without a creator.
Since there is being, being has always been. Beginning requires a beginner. Contingent beings depend on a necessary cause. Creation requires a creator. Design requires a designer.Laws require a lawmaker. Mathematics requires a mathematician. Fine-tuning requires a fine-tuner, Codes require a coder. Information requires an Informer. Translation requires a translator. Life has only been observed to come from life. Logic comes from logic, Consciousness comes from consciousness, Factories require a factory-maker, Objective moral values come from a moral giver. The "God of the gaps" argument is invalid. And so, that there is no evidence for God(s).

Aron: We don't care what you believe, except when people who believe as you do are in charge of everything at every level of State and Federal government, and you are imposing your falsehoods onto sequestered students and enforcing your religious bigotry against our Constitutional rights.
Reply: yes, i know that canard as well.... your script is not new to me. And i have an answer for that.

Why do positive, active, strong militant atheists or weak atheists/agnostics promote their views with such fervour and time spending?

https://reasonandscience.catsboard.com/t2379-why-do-postive-active-strong-militant-atheists-promote-naturalism-with-such-fervor-and-time-spending

Atheism is an idea that doesn’t matter. It leads to no good, it helps no one and it tends to either universal anarchy and chaos or totalitarian despotism, and the ultimate fate and consequence is to die and be judged upon their own sins and mistakes and paying for their sins and rejection of God in Hell forever and ever.

Jeffrey Dahmer:
If a person doesn’t think there is a God to be accountable to, then—then what's the point of trying to modify your behavior to keep it within acceptable ranges?,” "That's how I thought anyway. I always believed the theory of evolution as truth, that we all just came from the slime. When we, when we died, you know, that was it, there is nothing.”

Atheists protest against something they say that there is no evidence for. They have an itch they can’t scratch and it’s driving them crazy. They think the only salve to their itch is to convince others of what they themselves are not certain of. They are desperate to destroy others thinking that is the path to their salvation. Why should a theist know about your willingly chosen incredulity ¨& ignorance? Do you also wear t-shirts where you inform everyone that you don't believe in Pink Unicorns and Aliens? Is your internet-atheology-misotheology-activism & militancy not an entirely senseless foolish, and meaningless endeavor?

Aron: You're saying that a brother and sister can't be different from each other unless they're completely different from their parents?
Reply: Thats not what i am saying. What i say, IMHO, is this:

Irreducible Complexity: The existence of irreducible interdependent structures in biology is an undeniable fact

https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact#2133

A piston has no use by its own. But only, when working inside a gasoline engine. A flagellar filament structural protein has no use by its own unless inserted and conjoined with all other proteins to form the flagella filament proteins In the same sense, as an engineer would not project, invent, create and make a blueprint of a piston with no use by its own, but only conjoined, and together with all other parts while projecting a whole engine, envisioning its end function and use, its evident that unguided random natural events without foresight would not come up with assemblage of tiny molecular machines, enzymatic structures with unique contours, which bear no function by their own, but only when inserted in cellular structures with higher ends, being essential for cells to self-replicate, and perpetuate life.

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

Aron: I really didn't need to reply to anything in this whole post as none of was really relevant or substantive.
Reply: So here you are again dodging and exposing your bias. i can go a bit in detail here, and unmask why your narrative is BUNK.

The Origin of Multicellularity 5
From an evolutionary perspective, support for the transition from unicellular (single cell) to multicellular organisms requires the emergence of several novel biochemical systems. Such systems include:

- pathways that transform cells from generalized to specialized forms during growth and development;
- mechanisms for the migration of cells relative to each other during growth and development;
- structures that support cell-cell adhesions;
- and mechanisms for cell-cell communication.
- All of these systems have to be in place and operate in an integrated fashion to support multicellularity.

If you cannot deal honesty with this issue, you are demonstrating once again that your entire position is not based on evidence, but wishful thinking.

Aron: I told you, we have to start with amino acids first.
Reply: Yes, you have a LOT to explain in order to have a case. Starting by explaining how the 20 amino acids were selected prebiotically.

Aron: So let me be clear. Success would be, if an experiment would provide evidence how the 20 amino acids could have originated prebiotically on early earth. That has NOT been done.
That has been done, as I just showed you.
Reply: No, you didn't. Did tryptophan exist prebiotically ? If so, how did the transition from a prebiotic synthesis to a enzymatic/metabolic synthesis occur ?

Aron: Different experiments using different base chemicals each produced amino acids. That was the goal, to prove that could happen.
Reply: That is a far fetch from what is required. Once you find answers to the question that i ask here, we talk:

Open questions in prebiotic chemistry to explain the origin of the four basic building blocks of life
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759

I remind you, these are not simply open question, because they have not been investigated. Quite the contrary. They are open question despite the fact that over half a century science has tried, but only unraveled how big the problem actually is. It is a CONCEPTUAL problem. Molecules do not urge to themselves being sorted out into functional ones that life can use.

Aron: I correctly said that it was later discovered that the original study produced 22 amino acids, much more than previously thought. I made no false claim like you have.
Reply: Ok, i correct myself. It was not you. It was the Secular Humanist Society that heralded that ALL 20 of the amino acids found in proteins – plus a few others, were produced. That is not true. So since it was not those used in life, these experiments did not provide the evidence which you claim they have.....

Aron: I remind you that Stanley Miller died in 2007, still thinking his volcano in a bottle experiment was a "dud". Now we know better. Here is a study from just last year that shows, just as I already said, that heating water to 70ºC in the presence of iron hydroxide (simulating geothermal vents in the anaerobic conditions of the prebiotic earth) also produced amino acids and alpha hydroxy acids in the lab.
Reply: Did they produce all used in life? Did they figure out how early life sorted out those 20 used in life from those that are not used in life? Did they figure out how to solve the homochirality problem, and how to polymerize them ? If not, they have work to do. And i predict, these are not solvable problems, because molecules have no urge to become functional subunits for molecular machines....

Aron:Life should be able to be based on either left or right-handed amino acids, but we know that it doesn't work if they're mixed. So, given the evolutionary laws of monophyly and biodiversity, whatever life started with, it has to stick with. I hardly see why you think this is a problem?
Reply: Your bias shines through. You argue this is not a huge problem ? This KILLS your worldview, and since you are unwilling to acknowledge this OBVIOUS fact, i have good reasons to call
you out as dishonest which you really are.

Aron: You seem pretty desperate not to admit the simple truth that I already put to you. So let me ask that same question again, do you accept and admit that water, ammonia, methane and hydrogen generate amino acids when heated and charged with electricity? That the same thing happens when you change the mix to include Carbon-dioxide, nitrogen, hydrogen-sulfide and sulfur-dioxide? And that heating water to 70ºC in the presence of iron hydroxide also produced amino acids and alpha hydroxy acids in the lab?
Reply: Your deflection tactics do not work with me, Aron. Thats why you are inexcusable. I remember you did wear a T-Shirt once: Unforgivable. Yes, if you are unwilling to acknowledge that amino acid synthesis is an unsolvable problem, any other evidence you will dismiss as well. You and Matt Dillahunty go really together. You both are irrational and liars. You do NOT permit the evidence to lead wherever it is. Otherwis, RIGHT HERE, you would have given a stop, and said to yourself: Wait a minute. Nature cannot do this, unless a guiding hand was involved. Fortunately, i know you for many years already. And i am not writing this for you, but those that are following this topic. You Sir, need to repent and convert. God loves you. The one that you hate.

Aron: In order for a thing to exist, it must have properties. Natural laws are when we figure out some of those properties and phrase them in a succinct sentence or a mathematic equation. They are not called laws because of any cosmic legislator.
Reply: Wow. Really ? You must be kidding, right ?

https://en.wikipedia.org/wiki/Scientific_law

The argument of the nature of established laws
1. Physical or scientific law is a scientific generalization based on empirical observations of physical behavior. Law is defined in the following ways:
a. Absolute. Nothing in the universe appears to affect them. (Davies, 1992:82)
b. Stable. They are unchanged since they were first discovered (although they may have been shown to be approximations of more accurate laws).
c. Omnipotent. Everything in the universe apparently must comply with them (according to observations). (Davies, 1992:83)
2. Some of the examples of scientific or nature’s laws are:
a. The law of relativity by Einstein.
b. The four laws of thermodynamics.
c. The laws of conservation of energy.
d. The uncertainty principle etc.
e. Biological laws
i. Life is based on cells.
ii. All life has genes.
iii. All life occurs through biochemistry.
iv. Mendelian inheritance.
f. Conservation Laws.
i. Noether's theorem.
ii. Conservation of mass.
iii. Conservation of energy, momentum and angular momentum.
iv. Conservation of charge .
3. Einstein said that the laws already exist, man just discovers them.
4. Only an omnipotent, absolute eternal person can give absolute, stable and omnipotent laws for the whole universe.
5. That person all men call God.
6. Hence God exists.

Aron: What you're calling "fine-tuned for life" obviously isn't what you say it is nor why you say it is. Not that any of that has anything to do with evolution, which was the topic, if you could just focus.
Reply: This is full denialism. Amazing up to what length you go to deny the obvious.

John Gribbin and Martin Rees :
https://reasonandscience.catsboard.com/t2810-multi-tuning
If we modify the value of one of the fundamental constants, something invariably goes wrong, leading to a universe that is inhospitable to life as we know it. When we adjust a second constant in an attempt to fix the problem(s), the result, generally, is to create three new problems for everyone that we “solve.” The conditions in our universe really do seem to be uniquely suitable for life forms like ourselves, and perhaps even for any form of organic chemistry.

Changes in the relative strengths of gravity and electromagnetism affect not only cosmological processes but also galaxies, stars, and planets. The strong and weak nuclear forces determine the composition of the universe and, thus, the properties of galaxies, stars, and planets. As a result, we ultimately can’t divorce the chemistry of life from planetary geophysics or stellar astrophysics. Although we have only scratched the surface, it should be clear that
there are many examples of “cosmic-scale” fine-tuning in chemistry, particle physics, astrophysics, and cosmology. Most published discussions of such fine-tuning are limited to the requirements for life, but cosmic finetuning
extends well beyond mere habitability.

Aron: I don't want to be fooled into believing anything that is not evidently true.
Reply: Yes, sir, you are lying to yourself, and are not only an atheist, but a misotheist. You hate God. The problem with most people like you is that you have a distorted unreal idea about the character of God. Were it different, you would not want to know about anything else in this world, than to know God, and seek him, like a thirsty seeks for a spring to drink clear water. You don't know my God, thats why you deny him. Your problem, Aron, is not a scientific problem, but spiritual, of will and emotion. Your worldview is being exposed right here and right now, and you show your denialism nicely.

Aron: Once again, I have already corrected you on this; we are not looking for an individual first cell to be the common ancestor of all life. A first species, perhaps.
Reply: In that case, multiply that number , 10^722000 for any number of first cells or species you like. The odds will get just greater and greater. Another problem is that viruses and cells had to emerge together, since they are interdependent. Thats another BIG unsolved problem. Also there is a wide variety of virus replication machinery that does not exist in life, which you also to account for. How did it emerge ??!!

Aron: I note Otangelo has dodged nearly every question put to him.
Reply: Thats a big FAT lie. You, Sir, have dodged the most relevant issues, and simply denied its problems. Your worldview is bunk, and you are selfdelusional. As long as you live here on this godgiven mastersuite of the universe, you are fine. Its Gods gift to you. Once you depart, i wish you come to your sane mind, and realize that the God that you unjustly deny exists, loves you, and is waiting to save you. But that depends on your surrender, and give up your rebellion. God is good. And just.

Otangelo · 57 Re: Debate with Aron Ra Sun Dec 27, 2020 5:22 am

Otangelo

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Aron: Once again, as many others have already pointed out. DNA is not a code in the sense you're talking about. Meanings are not assigned for example.
Reply: That's blatantly wrong, and if you don't know that by now, you have either a) either a sloppy, or no understanding of biochemistry and biology, or b) once again, you attempt to dodge the raised issues which point to God, and are shamelessly lying. I won't point out, what i think it is....

The codon bases have a non-random correlation with the kind of amino acids which they code for. The first of the three letters relate to the kind of amino acid the codon stands for, giving the language a consistent meaning.

The order of the three input bases is arbitrary and interchangeable (i.e. the model does not include uneven distribution of assignment uncertainty due to a third base ‘wobble’). There is no codon ambiguity; each codon maps uniquely to one amino acid. To create signal-meaning pairs, for each selected amino acid to be transferred we had to determine its codon assignment according to the donor’s code.
https://www.nature.com/articles/s41598-018-21973-y

The Genetic Code (B): Basic Features and Codon Assignments
The assignment of codons to different amino acids was essentially completed by applying the trinucleotide binding technique discovered by Nirenberg and Leder to all the 64 possible synthetic ribotrinucleotides.
https://www.worldscientific.com/doi/abs/10.1142/9789812813626_0008

A survey of codon assignments for 20 amino acids.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC219908/

In translation, 64 genetic codons are ascribed to 20 amino acids

In the standard genetic code table, of the 64 triplets or codons, 61 codons correspond to the 20 amino acids
https://www.dovepress.com/synonymous-codons-influencing-gene-expression-in-organisms-peer-reviewed-fulltext-article-RRBC

The Universal Genetic Code and Non-Canonical Variants
Genetic code refers to the assignment of the codons to the amino acids, thus being the cornerstone template underling the translation process.
https://www.sciencedirect.com/topics/neuroscience/genetic-code

A new integrated symmetrical table for genetic codes
For the formation of proteins in living organism cells, it is found that each amino acid can be specified by either a minimum of one codon or up to a maximum of six possible codons. In other words, different codons specify the different number of amino acids. A table for genetic codes is a representation of translation for illustrating the different amino acids with their respectively specifying codons, that is, a set of rules by which information encoded in genetic material (RNA sequences) is translated into proteins (amino acid sequences) by living cells. There are a total of 64 possible codons, but there are only 20 amino acids specified by them.
https://arxiv.org/ftp/arxiv/papers/1703/1703.03787.pdf

A specification often refers to a set of documented requirements to be satisfied by a material, design, product, or service. A specification is often a type of technical standard.
https://en.wikipedia.org/wiki/Specification_(technical_standard)

A code is a set of rules that serve as generally accepted guidelines recommended for the industry to follow.
https://blog.nvent.com/erico-what-is-the-difference-between-a-code-standard-regulation-and-specification-in-the-electrical-industry/

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

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

1. In biology the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
2. The assignment of a word to represent something, like the word chair to an object to sit down, is always of mental origin.
3. On top of that, the translation of a word in one language, to another language, is also always of mental origin. For example the assignment of the word chair, in English, to xizi, in Chinese, can only be made by intelligence upon common agreement of meaning.
4. Since we know only of intelligence to be able to do so, this assignment is best explained by the deliberate, arbitrary action of a non-human intelligent agency.

1. In cells, information is encoded through the genetic code which is a set of rules, stored in DNA sequences of nucleotide triplets called codons. They are used to translate genetic information into amino acid polypeptide sequences, which make proteins ( the molecular machines, the working horses of the cell ). The assignment of codons (triplet nucleotides) to amino acids must be pre-established by a mind. And so, the information which is sent through the system, as well as the communication channels that permit encoding, sending, and decoding, which in life is done by over 25 extremely complex molecular machine systems, which do as well error check and repair to maintain genetic stability, and minimizing replication, transcription and translation errors, and permit organisms to pass accurately genetic information to their offspring, and survive. This system had to be set-up prior life began because life depends on it.
1. A code is a system of rules where a symbol, letters, words, or even sounds, gestures, or images, are assigned to something else. Translating information through a key, code, or cipher, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan.
2. Assignment which means designating, ascribing, corresponding, or correlating meaning of characters through a code system, where symbols of one language are assigned to symbols of another language that mean the same, requires a common agreement of meaning in order to establish communication, trough encoding, sending, and decoding. Semantics, Synthax, and pragmatics are always set up by intelligence.The origin of such complex communication systems is best explained by an intelligent designer.

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

Aron: You haven't shown that your intelligent designer is even possible, much less probable.
Reply: You understand the science, because i wrote the text for LAYPERSONS, and you know more than the average Joe, and answer like this? You, SIR, are a wilful ignorant, and not a honest truth seeker. Thats why you are inexcusable according to Romans Chapter1.19-23. And: Luke 12:48: For unto whomsoever much is given, of him shall much be required; You Sir, live in a priviledged age and time, where we have access to all this amazing information and evidence which points to God, and you willingly ignore it. Your claim that you are a truth seeker, is, franky speaking, A JOKE !! You demonstrate to be a Miso-theist. A God hater, for no good reasons, and it shows!! REPENT, before its too late, Aron. This is my good advice to you. God is graceful, forgiving, good, and does not throw out anybody that comes to him with a true heart of repentence. There will be a time where this is not possible anymore.

Aron: Even if your god had done it, you haven't shown how that happened, nor could you. But saying that a goddidit is not an explanation of anything, and it is unnecessary since we already have natural explanations that actually work and are backed by actual empirical evidence that we don't have believe in by faith.
Reply: You are lying shamelessly like the devil, because you know the science, which tells us otherwise.

Origin and evolution of the genetic code: the universal enigma
In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/

Koonin, the logic of chance, page 237
The origin of translation: The key ideas and models
During the 40 years since the discovery of the translation mechanism and deciphering of the genetic code, numerous theoretical (inevitably, speculative, sometimes far-fetched, often highly ingenious) models of the origin and evolution of various components of the translation apparatus and different aspects of the translation process have been proposed. It is unrealistic to provide here a thorough critical review of these models. Instead, I consider a few central ideas that are germane to the thinking about the origin of translation and then discuss in somewhat greater detail the only two coherent scenarios I am aware of. The main general point about the evolution of translation is that selection for protein synthesis could not have been the underlying cause behind the origin of the translation system. To evolve this complex system via the Darwinian route, numerous steps are required, but proteins appear only at the last steps; until that point, an evolving organism “does not know” how good proteins could be.

Furthermore, i did not address only the issue of the origin of the genetic code, but also the origin of the genetic information, and the information transmission and processing machinery, which is another major enigma of origins. You conveniently ignored to address it.

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

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

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

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

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

Aron: There was another study showed that synthetic molecules fold up into abiotic proteins". So life is not necessarily the only source of proteins.
Reply: Poppycock!! Synthetic molecules are the product of engineered processes in the lab, and have NOTHING to do with abiogenesis.

Aron: The synthesis of proteinous amino acids and amino acid polymers called “proteinoids” from inorganic molecules and thermal energy, and created the world‘s first potential protocell out of proteinoids and water.
Reply: Rather than sidestepping and posting irrelevant claims, you need actually to answer MY questions:

How could ammonia (NH3), the precursor for amino acid synthesis, have accumulated on prebiotic earth, if the lifetime of ammonia would be short because of its photochemical dissociation?
How could prebiotic events have delivered organosulfur compounds required in a few amino acids used in life, if in nature sulfur exists only in its most oxidized form (sulfate or SO4), and only some unique groups of procaryotes mediate the reduction of SO4 to its most reduced state (sulfide or H2S)?
How did unguided stochastic coincidence select the right amongst over 500 that occur naturally on earth?
How was the concomitant synthesis of undesired or irrelevant by-products avoided?
How were bifunctional monomers, that is, molecules with two functional groups so they combine with two others selected, and unifunctional monomers (with only one functional group) sorted out?
How did prebiotic events produce the twenty amino acids used in life? Eight proteinogenic amino acids were never abiotically synthesized under prebiotic conditions.
How did a prebiotic synthesis of biological amino acids avoid the concomitant synthesis of undesired or irrelevant by-products?
How could achiral precursors of amino acids have produced and concentrated only left-handed amino acids? ( The homochirality problem )
How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?
How would natural causes have selected twenty, and not more or less amino acids to make proteins?
How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?
How did nature "know" that the set of amino acids selected appears to be near ideal and optimal?
How did Amino acid synthesis regulation emerge? Biosynthetic pathways are often highly regulated such that building blocks are synthesized only when supplies are low.
How did the transition from prebiotic synthesis to cell synthesis of amino acids occur? A minimum of 112 enzymes is required to synthesize the 20 (+2) amino acids used in proteins.

Aron: But you don't care about what science has discovered.
Reply: But you care about what science has NOT discovered ? Because that can unravel unsolvable and unbridgeable problems, which only design can solve.

William Dembsky:
http://www.discovery.org/a/1256
The problem is that nature has too many options and without design couldn’t sort through all those options. The problem is that natural mechanisms are too unspecific to determine any particular outcome. Natural processes could theoretically form a protein, but also compatible with the formation of a plethora of other molecular assemblages, most of which have no biological significance. Nature allows them full freedom of arrangement. Yet it’s precisely that freedom that makes nature unable to account for specified outcomes of small probability.Nature, in this case, rather than being intent on doing only one thing, is open to doing any number of things. Yet when one of those things is a highly improbable specified event, design becomes the more compelling, better inference.

Aron: You're only interested in listing what you think science hasn't explained yet, and you deny that science has explained what it did.
Reply: Another false accusation against me. I acknowledge what science has explained. But you ignore what has not been explained, probably because if you investigate and see that the problem finds no solution, you have inevitably to acknowledge design as the better explanation. Which you don't want.

Aron: Because your belief system is a god of the gaps,
Reply: Sure. That canard could not be missing in your response....
1. if there is no money in the wallet
2. It's an argument of knowledge to say: There is no money in the wallet after you check.
3. The same happens in biochemistry. Science is doing abiogenesis research, checked, investigated, made falsifiable predictions and attempts to solve the mystery of life could have emerged naturally, but rather than solving the riddle is unraveling how unlikely the emergence of life is by unguided events and merely chemical reactions. DNA stores specified complex information, which is a blueprint, instructing the precise sequence of amino acids to make proteins. Such information has never been observed to emerge by chance, and therefore, we have evidence that something is extremely unlikely (e.g., that chance could inform the correct instructions to make proteins). Indeed, scientists will often debate whether an experiment's result should be considered evidence of absence. Something has proven not to be the result of X ( as chance, for example )
4. Intelligence can have the foresight and know-how to make things with a purpose, act towards achieving specific distant goals, and knows how to create codified language, and use that language to create blueprints, used to make complex machines, production lines, and interconnected factories. It can finely tune and arrange things to work in a precise fashion. it can shape and form parts that perform tasks by interacting like lock and key. None of all this has been observed to be achieved by any alternative non-intelligent mechanism. if anyone wants to propose an alternative to replace intelligence, it should meet the burden of proof, and falsify the claim of intelligent design based on empirical testing and falsification.
5. Hence, the argument of Intelligent Design as the best explanation of origins is based on experiments and observation, gained knowledge and experience. Not from ignorance.

Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. ( Contrast this with Popperian falsification, where propositions are corroborated to the degree that they successfully withstand attempts to falsify them ) When the available option forms a dichotomy, just to option, A, or not A, they form a mutually exclusive and exhaustive class, eliminating all the competitors entails that the proposition is true. As Sherlock Holmes's famous dictum says: when you have eliminated the impossible, whatever remains, however improbable, must be the truth. In this case, eliminative inductions, in fact, become deductions.

Aron: which is another fallacy.
Reply: Which you are not guilty of at all, right ? Ever heard of the " materialism of the gaps" ? We don't know how life started, but one day, science will find out, and it will be a naturalistic explanations.... LOL.

WE KNOW THAT THE GOD OF THE GAPS ARGUMENT IS INVALID. GOD IS AN INFERENCE OF THE BEST EXPLANATION BASED ON EVIDENCE, NOT IGNORANCE.

The argument that God is a gap filler is really boring, a beaten horse ad nauseam. Its invoked in almost every theist-atheist debate when atheists are unable to successfully refute a theist claim. No, God is NOT a gap filler. God is a logical inference based on the evidence observed in the natural world. If a theist would say, ''We don't know what caused 'x', therefore, God.'', it would be indeed a 'God of the gaps' fallacy. What we say, IMHO is: ''Based on current knowledge, an intelligent creative agency is a better explanation than materialistic naturalism." If one is not arguing from ignorance, but rather reasoning from the available evidence to the best explanation, is it not rather ludicrous to accuse them of launching a 'god of the gaps argument'? Randomness is a hugely overplayed idea in modern science, a desperate attempt to fill a shrinking corner for materialist reductionism, just as the ‘God of the Gaps' is derided by said materialists as the alleged last resort of Intelligent Design proponents.

Aron: Someone who knows you already warned me that "He will straight up ignore most of the regular evidence given for common descent just throw out the entire concept of common descent altogether for full blown YEC fundamentalism." And that is exactly what you've done.
Reply: I am certain you will also ignore the evidence against common decent, right?

Aron: You have avoided the topic of evolution and common descent
Reply: Not at all. Another false accusation. You even contradict yourself, since i gave already a reply in regards of common ancestry, which you duly ignored to address.

Aron: the very thing you said you wanted to talk about, and have instead shown your disrespect not just lying about me and to me with all manner of false accusations, fallacies and walls of text that you don't understand, and that even often argue against you. So from here on, I am keep you focused on the actual topic, since you can't do that yourself. I will help you.
Reply: I know your script fairly well. And i am sure, you throw these accusations in every debate against your opponents, don't you ? Psychological projection is a defence mechanism in which the human ego defends itself against unconscious impulses or qualities (both positive and negative) by denying their existence in themselves while attributing them to others. For example, a person who is habitually rude may constantly accuse other people of being rude. It incorporates blame shifting.

What happens when you have a whole bunch of uncomfortable, embarrassing and annoying emotions that you don’t want to unconsciously deal with? According to famous psychologist Sigmund Freud these emotions are projected on to other people, so that other people become carriers of our own perceived flaws. Fortunately (or unfortunately) for us, this form of emotional displacement makes it much easier to live with ourselves … because everyone else is responsible for our misery – not us!

Otangelo · 58 Re: Debate with Aron Ra Sun Dec 27, 2020 7:41 am

Otangelo

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AronI don't misrepresent things like you do. Earlier in this thread, you said that "a code is a system of rules where a symbol, letters, words, etc. are assigned to something else", that "all codes require arbitrary values being assigned and determined by agency to represent something else, and that "To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry." In an earlier email to me, you said, "Codes require a code-maker. Codified information comes always from a mind." So you are the one misrepresenting this. DNA is not a code in the sense you're talking about.
Reply: Yes, and all of this does not indicate that i claimed that DNA is a code. Another lie.

Aron We know how it can happen now. It may have happened differently then, or the same way. Doesn't make any difference really. It's like when you wake up in jail and can't remember what day it is or anything about last night. You don't know how you got there, but there you are. Are you really going to pretend that God teleported you into that cell? Or do you already know that there is a vastly more reasonable explanation, even if you don't know what it is yet?
Reply: And you are telling me that you do not use the "materialism of the gap" canard ? This is a prime example. We don't know, but it must have been a natural selection. These are the moments where you are showing your true colors. Any reasonable person would say: Yes, there is no reason why molecules should group themselves into a highly functional selected group of molecules, which by accident also are the most
adequate amongst a million of other possibilities. Design seems the better explanation.

Why are 20 amino acids used to make proteins? Why not more or less ? And why especially the ones that are used amongst hundreds available?
https://reasonandscience.catsboard.com/t3084-why-are-20-amino-acids-used-to-make-proteins-why-not-more-or-less-and-why-especially-the-ones-that-are-used-amongst-hundreds-available#8289

Paper Reports that Amino Acids Used by Life Are Finely Tuned to Explore “Chemistry Space” 3
June 5, 2015
A recent paper in Nature‘s journal Scientific Reports, “Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids,” has found that the twenty amino acids used by life are finely tuned to explore “chemistry space” and allow for maximal chemical reactions. Considering that this is a technical paper, they give an uncommonly lucid and concise explanation of what they did:

Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids 4
24 March 2015
We drew 10^8 random sets of 20 amino acids from our library of 1913 structures and compared their coverage of three chemical properties: size, charge, and hydrophobicity, to the standard amino acid alphabet. We measured how often the random sets demonstrated better coverage of chemistry space in one or more, two or more, or all three properties. In doing so, we found that better sets were extremely rare. In fact, when examining all three properties simultaneously, we detected only six sets with better coverage out of the 10^8 possibilities tested.

Luskin of Evolutionnews continues: That’s quite striking: out of 100 million different sets of twenty amino acids that they measured, only six are better able to explore “chemistry space” than the twenty amino acids that life uses. That suggests that life’s set of amino acids is finely tuned to one part in 16 million.

Nature continues: This is consistent with the hypothesis that natural selection influenced the composition of the encoded amino acid alphabet, contributing one more clue to the much deeper and wider debate regarding the roles of chance versus predictability in the evolution of life.

Debate with Aron Ra - Page 3 WHgxPWR

The number of random sets (out of 10^8, or 100,000,000) with better coverage than the encoded amino acids in one, two, or three properties.
Note that the circles are not drawn to scale; an appropriately scaled circle representing the number of random sets with better coverage in all three properties than the encoded set would only cover an area approximately 1/ 100th of that of the period at the end of this sentence.

Well, or maybe there was neither evolution, nor natural selection, and if chance is not a good explanatory candidate, we might consider another option, commonly ignored by secular science: Selection by an intelligent agency with foresight and higher intelligence.

Aron: If you were one of Darwin's neighbors when he was alive, you might whine that there are no transitional species, and that no one had ever shown how offspring inherit units of information from their parents, and you might crow that both of those are evidence for you magic imaginary friend. But since then we've found numerous transitional species, including two that Darwin specifically predicted, and now we know how genes and mutations work.
Reply: Fossils - Evidence AGAINST evolution
https://reasonandscience.catsboard.com/t1701-fossils-evidence-against-evolution

Schwartz, Jeffrey H. [Professor of Anthropology, University of Pittsburgh, USA], "Sudden Origins: Fossils, Genes, and the Emergence of Species," John Wiley & Sons: New York NY, 1999, p.3.
"A large number of well-trained scientists outside of evolutionary biology and paleontology have unfortunately gotten the idea that the fossil record is far more Darwinian than it is. This probably comes from the oversimplification inevitable in secondary sources: low-level textbooks semipopular articles, and so on. Also, there is probably some wishful thinking involved. In the years after Darwin, his advocates hoped to find predictable progressions. In general. these have not been found-yet the optimism has died hard and some pure fantasy has crept into textbooks."

Show me the transitional forms of oxygenic photosynthesis..... or of the tully monster..... or of the trilobite eye..... or of the 70 phyla of the Cambrian....

Aron: you think that whatever science can't explain counts as evidence for your god. That's not logical, but then neither are you. So you have to push back even further to whatever you think we don't yet know, just to deny what we do know, to pretend that we don't really know anything, even though we really do, and you don't.
Reply: Syllogistic - Arguments of Gods existence based on positive evidence
https://reasonandscience.catsboard.com/t2895-syllogistic-arguments-of-gods-existence-based-on-positive-evidence

Intelligent design theory is like a sword with two edges

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

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

Chance to find a message written on a cloud in the sky: "Jesus loves you" randomly, is as DNA creating its own software, and upon it, writing a complex algorithm to make a protein by accident.
https://www.youtube.com/watch?v=FT-RsCo1Flg

Aron: We can map geologic horizons to determine what strata we're working in. Where we were the most, there was an igneous deposit that had been radiometrically dated, (Uranium-lead, if I remember correctly) and another similar feature stratigraphically below where we were. So we knew that the fossils in this particular spot were from 262 to 263 million years old, the late Permian period.
Reply: Invite me the next time, and i will be more than happy to join and expose my views. Modern scientific dating is about as reasonable, reliable, and right as MSNBC commentators! Radiometric dating is always dependent on uniformitarian geologic interpretations–always. The age of the various strata, determined many years ago, are always used to “help” date a fossil. They use circular reasoning when they use rocks to date fossils and fossils to date rocks!

https://www.cs.unc.edu/~plaisted/ce/dating.html

Otangelo · 59 Re: Debate with Aron Ra Sun Dec 27, 2020 9:01 am

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Aron: The enormous body of evidence from all relevant fields shows that evolution definitely works, we know it works, and we can confirm and trace how it worked in the past, whereas your alternative is no more than fallacious reasoning in worship of a book of fairy tales.
Reply: Ok. Which of the following mechanisms are NOT involved in organismal development and growth ?

1. The Gene regulation network orchestrates gene expression
2. Various signaling pathways generate Cell types and patterns
3. At least 23 Epigenetic Codes are multidimensional and perform various tasks essential to cell structure and development
4. Cell-Cell communication in various forms, especially important for animal development
5. Chromatin dance in the nucleus through extensile motors affect transcription and gene regulation
6. Post-transcriptional modifications (PTMs) of histones affect gene transcription
7. The DNA methylation code is like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on.
8. Homeobox and Hox gene expression is necessary for correct regional or local differentiation within a body plan
9. Noncoding DNA ( Junk DNA ) is transcribed into functional non-coding RNA molecules and switches protein-coding genes on or off.
10.  Transposons and Retrotransposons regulate genes
11. Centrosomes play a central role in the development
12. The precise arrangement of Cytoskeletal arrays provides critical structural information.
13. Membrane targets provide crucial information—spatial coordinates—for embryological development.
14. Ion Channels and Electromagnetic Fields influence the form of a developing organism
15. The Sugar Code forms information-rich structures that influence the arrangement of different cell types during embryological development.
16. Egg-polarity genes encode macromolecules deposited in the egg to organize the axes
17. Hormones  are special chemical messengers for development
18. Secreted morphogens growth factors direct cell fate decisions during embryonic development.
19. An adhesion code ensures robust pattern formation during tissue morphogenesis

Aron: I told you, an inefficient simplicity would be one hallmark of a designer, if you had first showed that it was possible and probable for your designer to exist and you have explained the mechanism by which it does things. Then, whatever model you have has to account for all the evidence that the current model does, and do it better. You haven't presented anything but falsehoods, frauds and fallacies yet, because that's all you have.
Reply: What are you even talking about. The inadequacy of your answer you are completely OFF the job of doing a serious inquiry of origins. Making that correct distinction would be one of the FIRST things you would want to do, in order to compare naturalism to design. And you answer shows, you didn't. Keep exposing your bias, Aron. Its pathetic and telling.

How to recognize the signature of (past) intelligent actions
https://reasonandscience.catsboard.com/t2805-how-to-recognize-the-signature-of-past-intelligent-action

How to recognize the signature of (past) intelligent actions

Intelligence leaves behind a characteristic signature. The action or signature of an intelligent designer can be detected when we see :

1. Implementing things based on regular behavior, order, mathematical rules, laws, principles, physical constants, and logic gates

2. Something purposefully and intentionally developed and made to accomplish a specific goal(s). That includes specifically the generation and making of building blocks, energy, and information.

3. Repeating a variety of complex actions with precision based on methods that obey instructions, governed by rules.

4. An instructional complex blueprint (bauplan) or protocol to make objects ( machines, factories, houses, cars, etc.) which are irreducible complex, integrated, and an interdependent system or artifact composed of several interlocked, well-matched hierarchically arranged systems of parts contributing to a higher end of a complex system that would be useful only in the completion of that much larger system. The individual subsystems and parts are neither self-sufficient, and their origin cannot be explained individually, since, by themselves, they would be useless. The cause must be intelligent and with foresight, because the unity transcends every part, and thus must have been conceived as an idea, because, by definition, only an idea can hold together elements without destroying or fusing their distinctness. An idea cannot exist without a creator, so there must be an intelligent mind.

5. Artifacts which use might be employed in different systems ( a wheel is used in cars and airplanes )

6. Things that are precisely adjusted and finely-tuned to perform specific functions and purposes

7. Arrangement of materials and elements into details, colors, forms to produce an object or work of art able to transmit the sense of beauty, elegance, that pleases the aesthetic senses, especially the sight.

8. Establishing a language, code, communication, and information transmission system, that is 1. A language, 2. the information (message) produced upon that language, the 3 .information storage mechanism ( a hard disk, paper, etc.), 4. an information transmission system, that is: encoding - sending and decoding) and eventually fifth, sixth, and seventh ( not essential): translation, conversion, and transduction

9. Any scheme where instructional information governs, orchestrates, guides, and controls the performance of actions of constructing, creating, building, and operating. That includes operations and actions as adapting, choreographing, communicating, controlling product quality, coordinating, cutting, duplicating, elaborating strategies, engineering, error checking and detecting, and minimizing, expressing, fabricating, fine-tuning, foolproof, governing, guiding, implementing, information processing, interpreting, interconnecting, intermediating, instructing, logistic organizing, managing, monitoring, optimizing, orchestrating, organizing, positioning, monitoring and managing of quality, regulating, recruiting, recognizing, recycling, repairing, retrieving, shuttling, separating, self-destructing, selecting, signaling, stabilizing, storing, translating, transcribing, transmitting, transporting, waste managing.

10. Designed objects exhibit “constrained optimization.” The optimal or best-designed laptop computer is the one that is the best balance and compromise of multiple competing factors.

Check the link: There i will also give examples of how we have detected signs and the signature of design in nature.

Aron: Earlier, you said that "applying methodological naturalism to historical sciences is arbitrary and unjustified". But it IS justified and it's not arbitrary. Because there have to be facts to back the testimony.
Reply: NOT TRUE. A POSSIBLE explanation has just not to be disqualified for logical reasons. As long as it is coherent, logical, and possible, it is unjustified to exclude it.

Richard C. Lewontin who is a well-known geneticist and an evolutionist from Harvard University claims that he is first and foremost a materialist and then a scientist. He confesses;
“It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, so we cannot allow a Divine Foot in the door.”(Lewontin 1997)

Materialism regards itself as scientific, and indeed is often called “scientific materialism,” even by its opponents, but it has no legitimate claim to be part of science. It is, rather, a school of philosophy, one defined by the belief that nothing exists except matter, or, as Democritus put it, “atoms and the void.” 2

http://iose-gen.blogspot.com.br/2010/06/introduction-and-summary.html#methnat
No one can know with absolute certainty that the design hypothesis is false.  It follows from the absence of absolute knowledge, that each person should be willing to accept at least the possibility that the design hypothesis is correct, however remote that possibility might seem to him. Once a person makes that concession, as every honest person must, the game is up. The question is no longer whether ID is science or non-science. The question is whether the search for the truth of the matter about the natural world should be structurally biased against a possibly true hypothesis.

Aron: human migration always tracing back to Africa hundreds of thousands of years ago
Reply: Human origins: Created, or evolved?
https://reasonandscience.catsboard.com/t2683-is-the-genesis-account-of-literal-6-days-just-a-myth#8168

THE HISTORY OF HUMANITY IS IN OUR GENOME. WHAT WE KNOW ABOUT mtDNA OF HUMANS FITS THE 6000-YEAR TIMESCALE, EXPLAINS THE THREE HAPLOGROUPS, AND THE RELATIVE DIFFERENCES BETWEEN PRE AND POST FLOOD HUMANITY. One Eve in the beginning, population shrinks to 8 people (Noah, Noahs wife, 3 sons, 3 wives of Noahs sons). 3 boys get MTDNA from mom and then it ends. Genesis 9 says from these 3 the entire world was repopulated. We get our MTDNA from their 3 wives. Population would then grow and shrink to 8 at the time of the flood and then grow again momentarily ending with the splitting of people groups at the Tower of Babel.

Debate with Aron Ra - Page 3 Noahs_10

Aron: The Shroud of Turin was proven to be a hoax. Remember that I told you, creationism depends entirely on frauds, falsehoods and fallacies. Falsehoods and fallacies are you've presented so far. Now you've shown fraud too.
Reply: Maybe you should update your information a littlebit. The 1988 radiocarbon dating has been brought into question.

Age of the shroud of turin
https://reasonandscience.catsboard.com/t1688-shroud-of-turin#7139

An instructive inter-laboratory comparison: The 1988 radiocarbon dating of the Shroud of Turin Bryan Walsh⁎ , Larry Schwalbe Accepted 24 September 2019
The Shroud is unique because on one surface it contains clearly visible front and back images of a man, apparently crucified. Quite apart from any religious significance, the Shroud became, and remains, the focus of scientific inquiry because it is not known how the images on it were formed.

Most recently Casabianca et al. (2019), based on information obtained after a legal filing with the British Museum, showed that some of the original Shroud date measurements reported by the three laboratories to the British Museum were modified from their original ‘raw’ laboratory values and transformed into their published form using an unstated methodology.

Our review and analysis of the Shroud radiocarbon data reveal a significant shortcoming in the original report by Damon et al. (1989). The shortcoming begins with the lack of adherence to the protocol that W-W define for combining the inter-laboratory data sets.

Rogers (2005) proposed a method for cross checking the dates of ancient textiles by measuring the loss of vanillin from residual lignin at the growth nodes of linen fibers. The tests he performed on the Shroud threads suggested to him a much greater age than the results Damon et al.

Fanti et al. (2013) developed a series of relationships between characteristics of fiber over time and a method of estimating the age of the fabric. He subsequently applied these techniques to a series of fibers extracted from the Shroud and derived an estimated calendar age of 90 AD +/− 200 yrs (Fanti et al., 2015).

https://sci-hub.st/https://www.sciencedirect.com/science/article/pii/S2352409X19301865#b0025

Studies on the radiocarbon sample from the shroud of turin
The major problem in estimating the age of the shroud is the fact that the rate law is exponential; i.e., the maximum diurnal temperature is much more important than is the lowest storage temperature. However, some reasonable storage temperatures can be considered to give a range of predicted ages. If the shroud had been stored at a constant 25 ◦C, it would have taken about 1319 years to lose a conservative 95% of its vanillin. At 23 ◦C, it would have taken about 1845 years. At 20 ◦C, it would take about 3095 years. If the shroud had been produced between a.d. 1260 and 1390, as indicated by the radiocarbon analyses, lignin should be easy to detect. A linen produced in a.d. 1260 would have retained about 37% of its vanillin in 1978. The Raes threads, the Holland cloth, and all other medieval linens gave the test for vanillin wherever lignin could be observed on growth nodes. The disappearance of all traces of vanillin from the lignin in the shroud indicates a much older age than the radiocarbon laboratories reported
http://www.shroud.it/ROGERS-3.PDF

IS THE SHROUD REAL? POSSIBLY.
Christopher Ramsey, the director of the Oxford Radiocarbon Laboratory, thinks more testing is needed. So do many other scientists and archeologists. This is because there are significant scientific and non-religious reasons to doubt the validity of the tests. Chemical analysis, all nicely peer-reviewed in scientific journals and subsequently confirmed by numerous chemists, shows that samples tested are chemically unlike the whole cloth. It was probably a mixture of older threads and newer threads woven into the cloth as part of a medieval repair. Recent robust statistical studies add weight to this theory. Philip Ball, the former physical science editor for Nature when the carbon dating results were published, recently wrote: “It’s fair to say that, despite the seemingly definitive tests in 1988, the status of the Shroud of Turin is murkier than ever.” If we wish to be scientific we must admit we do not know how old the cloth is. But if the newer thread is about half of what was tested – and some evidence suggests that – it is possible that the cloth is from the time of Christ.
https://shroudstory.com/2010/01/22/more-death-certificate-on-the-shroud-of-turin/

New test dates Shroud of Turin to era of Christ
March 13. 2013
New scientific tests on the Shroud of Turin, which went on display Saturday in a special TV appearance introduced by the Pope, dates the cloth to ancient times, challenging earlier experiments dating it only to the Middle Ages. The new test, by scientists at the University of Padua in northern Italy, used the same fibers from the 1988 tests but disputes the findings. The new examination dates the shroud to between 300 BC and 400 AD, which would put it in the era of Christ. It determined that the earlier results may have been skewed by contamination from fibers used to repair the cloth when it was damaged by fire in the Middle Ages, the British newspaper reported.
https://www.usatoday.com/story/news/world/2013/03/30/shroud-turin-display/2038295/

Shroud Of Turin Real? New Research Dates Relic To 1st Century, Time Of Jesus Christ
Mar 29, 2013
Fanti and a research team from the University of Padua conducted three tests on tiny fibers extracted from the shroud during earlier carbon-14 dating tests conducted in 1988 The first two tests used infrared light and Raman spectroscopy, respectively, while the third employed a test analyzing different mechanical parameters relating to voltage. The results date the cloth to between 300 B.C. and 400 A.D.. Fanti said that researchers also found trace elements of soil "compatible with the soil of Jerusalem." "For me the [Shroud] comes from God because there are hundreds of clues in favor to the authenticity," he wrote, adding that there also "no sure proofs." Much of the controversy about the Shroud centers around carbon-14 dating tests from 1988 that concluded the piece of linen was a medieval forgery. However, those results may have been contaminated by fibers used to repair the cloth during the Middle Ages.
http://www.huffingtonpost.com/2013/03/28/shroud-of-turin-real-jesus_n_2971850.html

Giulio Fanti, Saverio Gaeta, The mystery of the Shroud The surprising scientific discoveries on the enigma of the cloth of Jesus, page 49
A linen fabric from Masada, the radiocarbon date of this Masada sample, assessed at the confidence level of the 95%, was between 59 A.D. and 213 AD: since the Jewish fortress was conquered by the Roman army in 74 AD, fabric fabrication cannot be assumed after this date.

Just in reference to the finding of Masada, it is remarkable the fact that numerous parameters derived from the FT-IR and Raman analyzes were very close to those of the Shroud linen. Even if you can't stating a priori that the two linen fabrics have comparable dates, in any case, is significant that the chemical characteristics of the two fabrics are comparable to each other. The final datum of this spectroscopic analysis, with reference to the linear combination of the ratios considered, has provided for the Shroud sample a value of 300 BC ± 400 years at the 95% confidence level.

Aron: No, it hasn't. Even AnswersInGenesis admits that was a hoax,
Reply: So you suddently take AIG as solid source of information ? LOL

Why do you think are ASOR and turkish archaeologists preparing a scientific investigation to Mount Ararat ? Whos opinion has more value: The one of a professional archeologist, or yours ?

Randall W. Younker Ph.D. Professor of Archaeology and History of Antiquity Director, (Biblical and Ancient Near Eastern Archaeology)
I think this discovery could be very important. I had not paid much attention to it before--indeed, was skeptical. But since I have been looking into it more, studying the images and talking to a number of people involved--including two people I know and trust who have actually been to the site, I am convinced it is not a recent fraud or fake--it has been up there for some time--so it is a legitimate archaeological site. As such, it deserves a careful study--if possible.

Aron: Yours is the fallacy because you're the one pretending to know things you don't know.
Reply: This is becoming childish. I do not make absolute claims. YOU ARE......

Aron: I can make a case for God ENTIRELY and ONLY using science and philosophy. Then why haven't you done that yet? What are you still waiting for?
Reply: You are now on Matt Dillahunty niveau ( aka scratching the bottom of the barrel ) of how dumb you argue. You have demonstrated that you have not even done your homework to actually set a target, and elucidate what would be evidence for God. Yes, your answer was TOTALLY unqualified. And after i am providing evidence , post after post, you keep asking this.

So here goes my challenge Aron. I gave you list upon which we can recognize the action of intelligence. Do you acknowledge it ? yes ot no?

Otangelo · 60 Re: Debate with Aron Ra Mon Dec 28, 2020 6:00 am

Otangelo

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Aron: What the fuck did this have to do with the preceding statement? Or with evolution from common ancestry?
Reply: Everything. The fact that you even ask, makes me wonder....

In order to say that some function is understood, every relevant step in the process must be elucidated. The relevant steps in biological processes occur ultimately at the molecular level, so a satisfactory explanation of a biological phenomenon such as sight, or digestion, or immunity, must include a molecular explanation. It is no longer sufficient, now that the black box of vision has been opened, for an ‘evolutionary explanation’ of that power to invoke only the anatomical structures of whole eyes, as Darwin did in the 19th century and as most popularizers of evolution continue to do today. Anatomy is, quite simply, irrelevant. So is the fossil record. It does not matter whether or not the fossil record is consistent with evolutionary theory, any more than it mattered in physics that Newton’s theory was consistent with everyday experience. The fossil record has nothing to tell us about, say, whether or how the interactions of 11-cis-retinal with rhodopsin, transducin, and phosphodiesterase could have developed step-by-step. Neither do the patterns of biogeography matter, or of population genetics, or the explanations that evolutionary theory has given for rudimentary organs or species abundance.

For a complete understanding of biological processes that define the intricate development of body architecture with striking precision, the orchestration of organismal development, cell and tissue shape, organization, and body form, it is necessary to understand as many integrative elements of biological systems as possible. Complex pattern formation involves numerous highly intricate biomolecular mechanisms that lead to the superb formation of tissue structures. That includes providing information that gives mechanical cues directing intra and extracellular shape changes and movements on the level of individual cells, but also tissue substratum as a whole. Answering the questions about how cells, tissues, and organisms masterfully develop and form, precedes the question IF evolutionary claims are compelling answers, explaining IF the evolutionary changes permit a purely blind primary macroevolutionary transition zone, morphogenesis of an entire organism moving and morph from one species to another on a first-degree speciation level, where novel features arise, like wings, eyes, ears, legs, arms, and so forth. The fact and truth are, that science is still far and away from having a complete answer to that question. But what we do know, permits to make informed conclusions.

Biodiversity and complex organismal architecture is explained by trillions of bits. Incredible amounts of data far beyond our imagination. Instructions, complex codified specifications, INFORMATION. Algorithms masterfully encoded in various genetic and sophisticated epigenetic languages and communication channels and networks. Neurotransmitters, through nanotubes between cells, communication through vesicles and amazingly, even light photons. Genes, but as well and especially various striking epigenetic signaling and bioelectric codes through various signaling networks provide cues to molecules and macromolecule complexes, and ingenious scaffold networks interpret and react in a variety of ways upon decoding and data processing of those instructions. Since signaling pathways work in an extraordinarily precise, in a synergetic integrated manner with the transcriptional regulatory network and complex short and long-range cross-talk between cells, these crucial instructions, crucial for advanced life forms, could not be the result of a random gradual increase of information. These superb information networks only operate and work in an integrated fashion, and had to be "born", and fully set up right from the beginning. Conveying codes, a system of rules to convert information, such as letters and words, into another form, and translation ciphers of one language to another are always sourced back to intelligent set-up. What we see in biochemistry is incredibly complex instructional codified information being stored through the genetic code ( codons) in a masterful information-storage molecule (DNA), encoded ( DNA polymerase), sent (mRNA), and decoded ( Ribosome), as well as epigenetic codes and languages, and several signaling pathways. The morphogenesis of organismal structure and shape is classified into two groups: The various instructional codes and languages using molecules that provide complex instructional cues of action based on information through signaling and secondly by force-generating molecules that are precisely directed through those signals, which are responsible for fantastic cell morphogenesis. Blueprints, instructional information, and master plans, which permit the striking autonomous self-organization and control of complex machines ( molecular machines) and exquisite factory parks ( cells) upon these are both always tracked back to an intelligent source which made both for purposeful, specific goals.   That brings us unambiguously to intelligent design. To the origin by an intelligent designer.

Aron: You said there were mechanisms at work at the Macroevolutionary level that were not working at the micro level. I asked you to explain what they are, but you ignored my question.
Reply: It seems as if you are kidding, but we know you are not. The ignorance of your question cannot be overstated, and exposed once again how much you wish God not to enter the picture. But he does, and powerfully so, and the evidence is undeniable. Whatever I claim, is not a presupposition, but the inference and result of years of scientific investigation. Each of the mechanisms listed contribute to organismal form and architecture.

1. The Gene regulation network orchestrates gene expression

EVOLUTIONARY BIOSCIENCE AS REGULATORY SYSTEMS BIOLOGY
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135751/

2. Various signalling pathways generate Cell types and patterns

- Hedgehog (Hh)
Erica Yao, Pao Tien Chuang, Hedgehog signalling: From basic research to clinical applications
https://www.sciencedirect.com/science/article/pii/S0929664615000340

- Wingless related (Wnt)
Katrin E. Wiese, Roel Nusse, Renée van Amerongen, Wnt signalling: conquering complexity
http://dev.biologists.org/content/145/12/dev165902

- Transforming growth factor-β (TGF-β)
D A Clark, R Coker Transforming growth factor-beta (TGF-beta)
https://www.ncbi.nlm.nih.gov/pubmed/9611771

- Receptor tyrosine kinase (RTK)
Receptor Tyrosine Kinase (RTK) Signaling Transduction
https://www.sinobiological.com/receptor-tyrosine-kinase-rtk-signaling-transduction.html

- Notch
Emma R. Andersson, Rickard Sandberg, Urban Lendahl Notch signalling: simplicity in design, versatility in function
http://dev.biologists.org/content/138/17/3593

- Janus kinase (JAK)/signal transducer
David W. Dodington Harsh R. Desai Minna Woo JAK/STAT – Emerging Players in Metabolism
https://www.cell.com/trends/endocrinology-metabolism/pdf/S1043-2760(17)30150-9.pdf

- Activators of transcription (STAT) protein kinases
Robert A Ortmann,1 Tammy Cheng,1 Roberta Visconti,1 David M Frucht ,1 and John J O'Shea1 Janus kinases and signal transducers and activators of transcription: their roles in cytokine signaling, development and immunoregulation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC129988/

- Nuclear hormone pathways
Maria Sirakov, Amina Boussouar, Elsa Kress, Carla Frau, Imtiaz Nisar Lone, Julien Nadjar, Dimitar Angelov, Michelina Plateroti The thyroid hormone nuclear receptor TRα1 controls the Notch signaling pathway and cell fate in murine intestine
http://dev.biologists.org/content/142/16/2764

- Bone morphogenetic proteins (BMP)
Richard N Wang 1, Jordan Green 1, Zhongliang Wang Bone Morphogenetic Protein (BMP) signaling in development and human diseases
https://www.ncbi.nlm.nih.gov/pubmed/25401122

- Epidermal growth factor receptors (EGFR)
https://www.sciencedirect.com/topics/medicine-and-dentistry/epidermal-growth-factor-receptor

- Fibroblast growth factors (FGF)
Nobuyuki Itoh, David M. Ornitz Fibroblast growth factors: from molecular evolution to roles in development, metabolism and disease
https://academic.oup.com/jb/article/149/2/121/837258

- DNA methylation
https://www.ncbi.nlm.nih.gov/pubmed/23877618

- Histone modification and incorporation of histone variants
https://www.researchgate.net/publication/270654681_Histone_Variants_and_Epigenetics

- Chromatin remodelling in Eukaryotic Cells
https://www.news-medical.net/life-sciences/Chromatin-Remodeling-Mechanisms-and-Importance.aspx

- Non-coding RNA-mediated epigenetic regulation

3. Epigenetic Codes perform various tasks essential to cell structure and development

1. The Over 30 different genetic Codes
2.  The Adhesion code
3.  The Apoptosis Code
4.  The Bioelectric code
5.  The Biophoton code
6.  The Calcium Code
7.  The Coactivator/corepressor/epigenetic code
8.  The DNA methylation Code
9.  The Domain substrate specificity code of Nonribosomal peptide synthetases (NRPS)
10. The error correcting code
11. The Genomic regulatory Code
12. The Glycomic Code
13. The Histone Code
14. The HOX Code
15. The Metabolic Code
16. The Myelin Code
17. The Neuronal spike-rate Code
18. The Non-ribosomal code
19. The Nucleosome Code
20. The Phosphorylation code
21. The Post-translational modification code for transcription factors
22. The RNA code
23. The Splicing Codes
24. The Signal Transduction Codes
25. The Signal Integration Codes
26. The Sugar Code
27. The Synaptic Adhesive Code
28. The Transcription factor code
29. The Transcriptional cis-regulatory code
30. The Tubulin Code
31. The Ubiquitin Code

4. Cell-Cell communication in various forms, especially important for animal development
Genes involved in Cell-Cell communication and transcriptional control are especially important for animal development
Molecular Biology of the Cell, 5th Ed, 2008: page 1308

5. Chromatin dance in the nucleus through extensile motors affect transcription and gene regulation
Transcription and gene regulation Genome topology has emerged as a key player in all genome functions.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837811/

6. Post-transcriptional modifications (PTMs) of histones affect gene transcription
Post-translational modifications (PTMs) of histones provide a fine-tuned mechanism for regulating chromatin structure and dynamics.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4099259/

7. The DNA methylation code is like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on.
DNA methylation has several uses in the vertebrate cell. A very important role is to work in conjunction with other gene expression control mechanisms to establish a particularly efficient form of gene repression.
Molecular Biology of the Cell, 5th Ed, 2008: Cell, page 467

8. Homeobox and Hox genes determine the shape of the body
https://www.jstor.org/stable/pdf/24996862.pdf?seq=1#page_scan_tab_contents

9. Noncoding DNA ( Junk DNA ) is transcribed into functional non-coding RNA molecules and switches protein-coding genes on or off.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394429/

10. Transposons and Retrotransposons regulate genes
http://dev.biologists.org/content/143/22/4101

11. Centrosomes play a central role in development
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734160/

12. The precise arrangement of Cytoskeletal arrays provides critical structural information.
The three major cytoskeletal filaments are responsible for different aspects of the cell’s spatial organization and mechanical properties.
Molecular Biology of the Cell By Bruce Alberts 6th. ed. page 889

13. Membrane targets provide crucial information—spatial coordinates—for embryological development.
Preexisting membrane targets, already positioned on the inside surface of the egg cell, determine where these molecules will attach and how they will function. These membrane targets provide crucial information—spatial coordinates—for embryological development.

14. Ion Channels and Electromagnetic Fields influence the form of a developing organism
https://pure.tue.nl/ws/files/10243383/20151217_CO_Vanegas.pdf

15. The Sugar Code forms information-rich structures which influence the arrangement of different cell types during embryological development.
https://www.ncbi.nlm.nih.gov/pubmed/15174156

16. Egg-polarity genes encode macromolecules deposited in the egg to organize the axes
http://jonlieffmd.com/blog/alternative-rna-splicing-in-evolution

17. Hormones  are special chemical messengers for development
https://en.wikibooks.org/wiki/Human_Physiology/The_endocrine_system

Reply : I gave you a genetic chart showing the phylogeny of modern canids, and I asked you to explain whatever problem you had with that chart.
Reply: I have no problem with secondary speciation. We know it happens. It explains why there were just a limited number of species on the ark, and then they specified and diversified. Thats why we have many more species on earth today. It fits perfectly our creation model.

In order for a new limb to evolve, let's say arms, not only would have there to be new information of where to locate the new limb in the body to be functional, ( hox genes ) and develop in the right sequence and order but also, at the same time, each of the seven mentioned items below would have to develop together :

1. Muscular system - essential for the movement of the body, maintains posture and circulates blood throughout the body.
2. Skeletal system - is the internal framework of the body.
3. Nervous system - is the part that coordinates its actions by transmitting signals to and from different parts of its body.
4. Endocrine System- hormones are signaling molecules that target distant organs to regulate physiology and behavior.
5. Circulatory system - is an organ system that permits blood to circulate and transport nutrients (such as amino acids and electrolytes), oxygen, carbon dioxide, hormones, and blood cells to and from the cells in the body.
6. Integumentary system - comprises the skin and its appendages acting to protect the body from various kinds of damage, such as loss of water or damages from outside
7. Lymphatic System It is part of the vascular system and an important part of the immune system, comprising a large network of lymphatic vessels that carry a clear fluid called lymph directionally towards the heart.

The human body is a system performing its basic functions including a set of seven well-matched interdependent systems, besides requiring five major components, 1) communication; (2) waste disposal; (3) nutrition;
(4) repair; and (5) reproduction. mutually interacting, where each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system.

Aron: You failed to produce any evidence either for your alternative reality
Reply: Your wilful ignorance shines through again. Thats why you are inexcusable in God's eyes. You ignore the OVERWHELMING evidence that points to God for reasons that only you know.
As said, every time you repeat your unjustified and dishonest mantra, i will reply with this:

125 reasons to believe in God

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

The obviousness of Creation is hidden from those who reject God. There is no evidence that we can exist without a creator.
Since there is being, being has always been. Beginning requires a beginner. Contingent beings depend on a necessary cause. Creation requires a creator. Design requires a designer.Laws require a lawmaker. Mathematics requires a mathematician. Fine-tuning requires a fine-tuner, Codes require a coder. Information requires an Informer. Translation requires a translator. Life has only been observed to come from life. Logic comes from logic, Consciousness comes from consciousness, Factories require a factory-maker, Objective moral values come from a moral giver. The "God of the gaps" argument is invalid. And so, that there is no evidence for God(s).

Scientists, most of them not believing in God, had to acknowledge and admit the overwhelming evidence pointing to the overwhelming appearance of design in the natural world:
https://reasonandscience.catsboard.com/t1276p25-125-reasons-to-believe-in-god#8282

Aron: or against the established science of common descent.
Reply: Established by whom? When? How? Because in my book, this is neither established, nor proven, but rather a falsified claim for the reasons already exposed.

DNA Replication Across Taxa , page 193: 2016
Genome sequencing of cells from the three domains of life, bacteria, archaea, and eukaryotes, reveal that most of the core replisome components evolved twice, independently. Thus, the bacterial core replisome enzymes do not share a common ancestor with the analogous components in eukaryotes and archaea, while the archaea and eukaryotic core replisome machinery share a common ancestor

Koonin, the logic of chance, page 331:

The reconstructed gene repertoire of LUCA also has gaping holes. The two most shocking ones are

(i) the absence of the key components of the DNA replication machinery, namely the polymerases that are responsible for the initiation (primases) and elongation of DNA replication and for gap-filling after primer removal, and the principal DNA helicases (Leipe, et al., 1999), and
(ii) the absence of most enzymes of lipid biosynthesis. These essential proteins fail to make it into the reconstructed gene repertoire of LUCA because the respective processes in bacteria, on one hand, and archaea, on the other hand, are catalyzed by different, unrelated enzymes and, in the case of membrane phospholipids, yield chemically distinct membranes.

bacteria and archaea have membranes made of water-repellent fatty molecules. Simple fatty molecules tend to flip around, making the membrane leaky, so both bacteria and archaea tacked on a water-loving phosphate group to stabilise the molecules and make their membranes impermeable. They took very different routes, though. Bacterial membranes are made of fatty acids bound to the phosphate group while archaeal membranes are made of isoprenes bonded to phosphate in a different way. This suggests that their membranes evolved independently. This leads to something of a paradox: if LUCA already had an impermeable membrane for exploiting proton gradients, why would its descendants have independently evolved two different kinds of impermeable membrane? 17

Aron: In fact, you avoided the topic altogether.
Reply: Not true. I responded to it, as i am doing again, right now. The fact that you are not acknowledging it, is your fault. Not mine.

Aron: I told you twice that your argument requires that you answer the Phylogeny Challenge, which you really should.
Reply: We can do that. You failed miserably as Angelmou, when you claimed that an intermediate archea was found, being the bridge from prokaryotes to eukaryotes. When i showed you a paper from 2017, where the claim made in 2015 was refuted. In fact, the endosymbiotic theory is also bunk for several reasons already exposed here. Just to remind you,

Did eukaryotes evolve from prokaryotic cells?
https://reasonandscience.catsboard.com/t1568-did-eukaryotes-evolve-from-prokaryotic-cells

1. There are no true intermediates in the prokaryote-to-eukaryote transition. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. The origin of eukaryotes is certainly one of early evolution's most important topics. “Throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another... Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic [i.e., bacterial] to eukaryotic [i.e., plant and animal] cells, let alone throughout the whole array of higher multicellular organisms.” The organizational complexity of the eukaryotes is so much greater than that of the prokaryotes that it is difficult to visualize how a eukaryote could have arisen from any known prokaryote (Hickman et al., 1997, p. 39). In eukaryotes the mitochondria produce most of the cell’s ATP (anaerobic glycolysis also produces some) and in plants the chloroplasts can also service this function. The mitochondria produce ATP in their internal membrane system called the cristae. Since bacteria lack mitochondria, as well as an internal membrane system, they must produce ATP in their cell membrane which they do by two basic steps. The bacterial cell membrane contains a unique structure designed to produce ATP and no comparable structure has been found in any eukaryotic cell (Jensen, Wright, and Robinson, 1997).

2. We do not know of any prokaryote able to engulf another cell. Only eukaryotes can do it.

3.  The Darwinian Basis of the Prokaryote-to-Eukaryote Transition Collapses
https://reasonandscience.catsboard.com/t1568-did-eukaryotes-evolve-from-prokaryotic-cells#3782
Mitochondria has a different genetic code, and there is no viable route for the evolution of the genetic code. Mitochondria use a slight variation on the conventional genetic code (for example, the codon UGA is a stop codon in the conventional code, but encodes for Tryptophan in mitochondria). This implicates that the genes of the ingested prokaryotes would need to have been recoded on their way to the nucleus. The situation becomes even worse when one considers that, in eukaryotic cells, a mitochondrial protein is coded with an extra length of polypeptide which acts as a "tag" to ensure that the relevant protein is recognised as being mitochondrial and dispatched accordingly. The significant number of specific co-ordinated modifications which would be required to facilitate such a transition, therefore, arguably make it exhibitive of irreducible complexity.

The different genetic codes
https://reasonandscience.catsboard.com/t2277-the-different-genetic-codeses
The National Center for Biotechnology Information (NCBI), currently acknowledges nineteen different coding languages for DNA. And i list 31 different ones.
If the mitochondria in invertebrates use a different genetic code from the mitochondria in vertebrates, and both of those codes are different from the “universal” genetic code, what does that tell us? It means that the eukaryotic cells that eventually evolved into invertebrates must have formed when a cell that used the “universal” code engulfed a cell that used a different code. However, the eukaryotic cells that eventually evolved into vertebrates must have formed when a cell that used the “universal” code engulfed a cell that used yet another different code. As a result, invertebrates must have evolved from one line of eukaryotic cells, while vertebrates must have evolved from a completely separate line of eukaryotic cells. But this isn’t possible, since evolution depends on vertebrates evolving from invertebrates. Now, of course, this serious problem can be solved by assuming that while invertebrates evolved into vertebrates, their mitochondria also evolved to use a different genetic code. However, I am not really sure how that would be possible. After all, the invertebrates spent millions of years evolving, and through all those years, their mitochondrial DNA was set up based on one code. How could the code change without destroying the function of the mitochondria? At minimum, this adds another task to the long, long list of unfinished tasks necessary to explain how evolution could possibly work. Along with explaining how nuclear DNA can evolve to produce the new structures needed to change invertebrates into vertebrates, proponents of evolution must also explain how, at the same time, mitochondria can evolve to use a different genetic code!

4. Membranes of dauther cells are only inherited by membranes of mother cells through fission.

Intracellular Compartments and Protein Sorting
https://reasonandscience.catsboard.com/t3048-intracellular-compartments-and-protein-sorting
Unlike a bacterium, which generally consists of a single intracellular compartment surrounded by a plasma membrane, a eukaryotic cell is elaborately subdivided into functionally distinct, membrane-enclosed compartments. Each compartment, or organelle, contains its own characteristic set of enzymes and other specialized molecules, and complex distribution systems transport-specific products from one compartment to another. To understand the eukaryotic cell, it is essential to know how the cell creates and maintains these compartments, what occurs in each of them, and how molecules move between them. Proteins confer upon each compartment its characteristic structural and functional properties. They catalyze the reactions that occur there and selectively transport small molecules into and out of the compartment. For membrane-enclosed organelles in the cytoplasm, proteins also serve as organelle-specific surface markers that direct new deliveries of proteins and lipids to the appropriate organelle. An animal cell contains about 10 billion (10^10) protein molecules of perhaps 10,000 kinds, and the synthesis of almost all of them begins in the cytosol, the space of the cytoplasm outside the membrane-enclosed organelles. Each newly synthesized protein is then delivered specifically to the organelle that requires it. . By tracing the protein traffic from one compartment to another, one can begin to make sense of the otherwise bewildering maze of intracellular membranes

5. Mitochondrial membrane biogenesis: phospholipids and proteins go hand in hand 1
https://reasonandscience.catsboard.com/t2128-cell-membranes-origins-through-natural-mechanisms-or-design
Mitochondrial membrane biogenesis requires the import and synthesis of proteins as well as phospholipids.The biochemical approach of Kutik et al. (2008) uncovered an unexpected role of the mitochondrial translocator assembly and maintenance protein, Tam41, in the biosynthesis of cardiolipin (CL), the signature phospholipid of mitochondria. The genetic analyses of Osman et al. (2009) led to the discovery of a new class of mitochondrial proteins that coordinately regulate CL and phosphatidylethanolamine, another key mitochondrial phospholipid. These elegant studies highlight overlapping functions and interdependent roles of mitochondrial phospholipid biosynthesis and protein import and assembly

6. The mitochondrial inner membrane has a unique composition of proteins and phospholipids, whose interdependence is crucial for mitochondrial function.

7. Most Organelles Cannot Be Constructed De Novo: They Require Information in the Organelle Itself
https://reasonandscience.catsboard.com/t2122-most-organelles-cannot-be-constructed-de-novo-they-require-information-in-the-organelle-itself

When a cell reproduces by division, it has to duplicate its organelles, in addition to its chromosomes. In general, cells do this by incorporating new molecules into the existing organelles, thereby enlarging them; the enlarged organelles then divide and are distributed to the two daughter cells. Thus, each daughter cell inherits a complete set of specialized cell membranes from its mother. This inheritance is essential because a cell could not make such membranes from scratch. If the ER were completely removed from a cell, for example, how could the cell reconstruct it? As we discuss later, the membrane proteins that define the ER and perform many of its functions are themselves products of the ER. A new ER could not be made without an existing ER or, at least, a membrane that specifically contains the protein translocators required to import selected proteins into the ER from the cytosol (including the ER-specific translocators themselves). The same is true for mitochondria and plastids. Thus, it seems that the information required to construct an organelle does not reside exclusively in the DNA that specifies the organelle’s proteins. Information in the form of at least one distinct protein that preexists in the organelle membrane is also required, and this information is passed from parent cell to daughter cells in the form of the organelle itself. Presumably, such information is essential for the propagation of the cell’s compartmental organization, just as the information in DNA is essential for the propagation of the cell’s nucleotide and amino acid sequences. the ER buds off a constant stream of transport vesicles that incorporate only a subset of ER proteins and therefore have a composition different from the ER itself. Similarly, the plasma membrane constantly buds off various types of specialized endocytic vesicles. Thus, some organelles can form from other organelles and do not have to be inherited at cell division.

8. The Interdependency of Lipid Membranes and Membrane Proteins
https://reasonandscience.catsboard.com/t2397-the-interdependency-of-lipid-membranes-and-membrane-proteins
A cell cannot produce the cell membrane de novo from scratch. It inherits it. Daughter cell membranes come only from mother cell membranes.

9. On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story
https://reasonandscience.catsboard.com/t1303-challenges-to-endosymbiotic-theory

Human mitochondrial DNA has just 16 569 base pairs, coding for only 37 genes, which are all essential for mitochondrial function, but far too little for a cell to survive. Thirteen of these genes produce proteins essential for ATP synthesis by oxidative phosphorylation, the other 25 coding for tRNA and rRNA, necessary for mitochondrial protein synthesis. Mitochondrial ribosomes are like bacterial ribosomes. None are involved in Ca2+ signaling. Yet, E. coli has some 300 essential genes which cannot be knocked-out without killing the cell, yet there are some 1500 proteins found inside a mitochondrion, several of which are involved in transporting Ca2+ in and out or responding to a rise in intra-mitochondrial free Ca2+. Mitochondrial divide, make proteins, make ATP, and carry out several other biochemical pathways, such as fatty acid oxidation. So if mitochondria originated from an endosymbiont such as Rickettsia there are three problems:
1. How did the endocytosed bacterium survive and multiply if its internal environment was oxidizing? The cytosol of all cells is reducing, preventing the formation of S–S bonds and damaging oxidative reactions involving reactive oxygen species. But, remember the first eukaryotes formed before there was significant oxygen in the atmosphere. So oxidative phosphorylation in mitochondria must have evolved after photosynthesis, some 2000 million years ago.
2. Since cells need at least 1200 proteins to survive, replicate, and synthesize their own building blocks, what happened to the proteins essential for nucleotide and nucleic acid, and protein synthesis, and the reactions necessary for ATP synthesis, e.g. glycolysis?
3. How did the 1500 or so mitochondrial proteins in the main genome become targeted to the mitochondria, if they were lost by the initial endosymbiont?

10. Origin of eukaryotes
https://reasonandscience.catsboard.com/t3046-the-major-hypothesized-transitions-in-evolution

Eukaryotic cells function on different physical principles compared to prokaryotic cells, which is directly due to their (comparatively) enormous size. The diversity of the outcomes of phylogenetic analysis, with the origin of eukaryotes scattered around the archaeal diversity, has led to considerable frustration and suggested that a ‘phylogenomic impasse’ has been reached, owing to the inadequacy of the available phylogenetic methods for disambiguating deep relationships

- Actins
- Centrioles
- Cell walls in plant cells
- Centrosome
- Cytoskeleton
- Cyanelles
- Chloroplasts
- DNA replication ( different than in prokaryotes)
- Directing new deliveries of proteins and lipids to the appropriate organelle
- Endosomes
- Eukaryotic flagellum
- Ejectosomes
- Haptonema.
- Histones
- Introns and exons
- Lysosome
- Meiosis
- Mitosis
- Mitochondrion
- Motor proteins ( dynein, kinesin etc.)
- Nucleus
- Nucleolus
- Nucleosomes
- Pseudopods
- Plastids
- Ribosome ( different than in prokaryotes )
- Spliceosome
- Complex distribution systems transport-specific products from one compartment to another.
- Obligate sexuality
- Over 30 different genetic codes
- Organelles ( Rough and smooth endoplasmic reticulum, Golgi apparatus, nucleus, mitochondrion, endosomes, lysosome, and peroxisome )
- Sexual recombination
- Tubulin cytoskeletons,
- The nuclear pores,
- The proteasome
- Ubiquitin signalling systems
- Undulipodia
- Vacuoles
- Vesicle

In plant cells:
- Tonoplast
- Plasmodesmata

Division of labor between nuclear, cytoplasm organelles (flagellates, other protozoa (eukaryotes)).

Debate with Aron Ra - Page 3 Geneal10

A current hy pothesis of genealogical relationships among eukary otic organisms, based on molecular sequence comparisons of ten genes. Note the dotted line that connects diplomonads (which include Giardia lamblia) and parabasalids to the remainder of tree. This indicates the uncertainty surrounding the nature and composition of early branches on the tree.

Aron: Because you don't understand anything about science and you sure don't know how to logic. I don't think you're stupid, but I don't think you're sane either, and I know you're not being honest.
Reply: Because of comments like this, you are not elevating yourself into a serious interlocutor about scientific issues. Namecalling is the lowest form of discoure, the last refuge of those who cannot disprove an opposing point of view. The Internet is dominated by the crude, the uninformed, the immature, the smug, the untalented, the repetitious, the pathetic, the hostile, the deluded, the self-righteous, and the shrill. Usually, the tool of the loser of a debate will resort to insulting, [Arostotle] Basic rule of thumb: When someone with opposite views starts calling you names, it means he has nothing left to debate against your argument. It also means: The proponent of intelligent design / creationism just won the debate. Namecalling serves no useful purpose and is, therefore, illogical My advice: Do not make any explicit adhom, calling me names, like a troll, stupid, idiot, religious nutter etc. , or accusing me of not thinking, or not using my brain. - Do also not try to attack my education, ( asking to go back to school, taking a science class etc. ) or ask for my credentials. It adds nothing to your case, nor does it make naturalism become more compelling.

Aron:All you do is recite false allegations and hateful generalizations
Reply: So when i go into details, you complain that my posts are long and tedious. But at the same time, you accuse me of hateful generalizations. If we want to elucidate that mechanisms are in play to explain organismal complexity, there is no way around of going into the nitty gritty of molecular biology. It might be tedious, but thats what it is. Did you not claim that you wish to unravel the truth ? Now that i present it, you complain again. Amazing!!

Aron: clinging desperately to your bigoted misunderstanding, which you are unable to question or correct.
Reply: What misunderstanding are you talking about?

Aron: there is no such thing as "materialism of the gaps".
Reply: Not only have you provided a CLASSIC during this debate, but if that serves you as comfort, it is a very common modo operandi. As shown here by Paulogia in my interaction with him:
https://www.youtube.com/watch?v=S-K5-9bTcaE

Aron: That was a stupid thing for you to say!
Reply: Stupid is when we are thrown in almost EVERY debate with this stupid canard.
God of the gaps and incredulity, a justified refutation of ID arguments?
https://reasonandscience.catsboard.com/t1983-gaps-god-of-the-gaps-and-incredulitya-justified-refutation-of-id-arguments

Aron: Likewise, DNA is not a code that must be pre-programmed by an intelligent agent.
Reply: That is probably one of the most foolish assertions that you have made during all these posts. The shoe hurts, doesn't it? The truth hurts, when it is not welcome. Isn't it, Aron? You claimed that you wanted to know the truth, and that you were unbiased. Now you show your true colours. You reject the truth, because it does not fit your preconceived and wished worldview without God. You hate HIM. You are a misotheist for unjustified reasons. You don't know God's goodness and love, that's why reject him. I am even suspiscious that you have as your father the father of lies, the devil, since you are constantly accusing me of lying, when all i am doing, is telling you the truth, and i back up EVERYTHING that i say with true, sound premises, and logical inferences. And you reject it.

Otangelo · 61 Re: Debate with Aron Ra Thu Dec 31, 2020 9:55 pm

Otangelo

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The main topics that I brought up have been:
1. The origin of life by natural means (abiogenesis) is a failed hypothesis
2. The origin of amino acids. You miserably failed to explain how 20 amino acids used in life could have been selected.
3. Preprogrammed instructional information
4. Many secular scientists acknowledge that there IS evidence of design in nature
5. The Genetic Code
6. The transition from prokaryotes to eukaryotes is not substantiated by the scientific evidence
7. Common ancestry is not substantiated by the scientific evidence
8. To explain biodiversity, we have to look into biochemistry and source the real mechanisms that are in play to build complex organismal architecture, adapt to the environment, nutrition availability, and development.
8. Phylogenetic trees are irrelevant to substantiate evolution
10. Biodiversity is explained by Genetic and epigenetic information, and signaling networks, which are preprogrammed and prescribed to get a purposeful outcome.

Aron: Creation never happened and is a lie
Reply: First lie.
That is an unsupported claim, since you cannot back it up with empirical proofs. What you accused creationists of doing, is precisely what you are guilty of.
To be clear, there is absolutely nothing wrong with searching for a purely material origin for the existence of reality and the physical world. However, if a claim based on those ideas is merely assumed to be true, and if that assumption is then used to institutionalize the attack on a valid scientific alternative, then that practice is not only illogical, but is a clear abuse of scientific practice. In fact, it is the ultimate “science stopper”. As it stands right now, if materialism is not true, there is no way under current practices for science to correct itself. And in a perfect irony, it is this concept of self-correction that materialists routinely use to promote their dominance over the institution.

Aron: Your religious objection is a god-of-the-gaps that can't even function in the presence of any actual knowledge. If there was evidence that pointed to God, you would have shown it by now. Instead you lie
Reply: Second lie.
You keep making this false and unfounded accusation, despite the fact that Gods existence can be substantiated based on POSITIVE evidence:

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

The obviousness of Creation is hidden from those who reject God. There is no evidence that we can exist without a creator.
Since there is being, being has always been. Beginning requires a beginner. Contingent beings depend on a necessary cause. Creation requires a creator. Design requires a designer.Laws require a lawmaker. Mathematics requires a mathematician. Fine-tuning requires a fine-tuner, Codes require a coder. Information requires an Informer. Translation requires a translator. Life has only been observed to come from life. Logic comes from logic, Consciousness comes from consciousness, Factories require a factory-maker, Objective moral values come from a moral giver. The "God of the gaps" argument is invalid. And so, that there is no evidence for God(s).

Aron: There is no evidence for Gods existence.
Reply: Third lie.
Your repetitive claim that there is no evidence for God's existence has been shown to be a lie. I have provided an entire list of SECULAR scientists who DISAGREE with you, and acknowledge that that that natural world looks suspiciously like a "fix" - but despite this - are unbelievers ( for whatever reason). So you cannot even resort to the canard that quotes of religious people are worthless because they are biased - the quotes i provided are mostly from non-theists.

Scientists, most of them not believing in God, had to acknowledge and admit the overwhelming evidence pointing to the overwhelming appearance of design in the natural world:
https://reasonandscience.catsboard.com/t1276p25-125-reasons-to-believe-in-god#8282

Aron: There is not pre-programmed information stored in genes.
Reply: Fourth lie.
DNA stores INDEED pre-programmed, prescribed, instructional, specified complex information as shown in the entire list of quotes from scientific papers:
https://reasonandscience.catsboard.com/t1281-dna-stores-literally-coded-information#8318

Aron: It is a lie to say that "operational science and historical science are two different "kinds" of science.
Reply: Fifth lie.
The distinction is perfectly valid, and objective and factual, because the two faculties deal with DIFFERENT questions.
https://rationalwiki.org/wiki/Historical_and_operational_science
"Historical science" is a term used to describe sciences in which data is provided primarily from past events and for which there is usually no direct experimental data, such as cosmology, astronomy, astrophysics, geology, paleontology, and archaeology. "Historical science" covers the Big Bang, geologic timeline, abiogenesis, evolution, and nebular hypothesis

"Operational science" is a term for any science that "deals with testing and verifying ideas.

Historical science, experimental science, and the scientific method
Historical research is sometimes said to be inferior to experimental research. Using examples from diverse historical disciplines, this paper demonstrates that such claims are misguided.
https://pdfs.semanticscholar.org/81ca/78baf41581a70ddf0af3115ea8255aace4fb.pdf

Aron: Creationists use a lot of logical fallacies trying to argue against evolution; one of them is the straw-man, misrepresenting what evolution is. For example, the notion that evolution means one thing giving birth to or turning into another fundamentally different thing. But that too is a lie.
Reply: Sixth lie
No creationist or intelligent design institution makes such a claim. Neither the Discovery Institute, nor Reasons.org, nor AIG, nor ICR, nor any that i know of. It's a straw man, and misrepresentation.

Aron: Because, as I said, we know that Adam & Eve are just a fairy tale
Reply: Seventh lie
As many other claims, that has been another absolute claim, which you have been unable to prove.

Aron: I note Otangelo has dodged nearly every question put to him.
Reply: Eight lie
I have addressed basically every relevant topic brought up by you, and responded accordingly.

Aron: God's existence is impossible. YOU can't show that any such possibility exists, it would be a lie to say that it does.
Reply: Ninth lie.
Intelligence is a known reality and therefore it is entirely legitimate for science to consider it among the possible causal factors in a given phenomenon coming about. Intelligent agency is currently the only causally adequate explanation for the machinery by which the cell translates DNA code having its assembly instructions also coded in the DNA.

Aron: DNA is not a code in the sense you're talking about.
Reply: Tenth lie.
You misrepresented what i wrote. I never said that DNA IS a code. DNA stores instructional information THROUGH a genetic Code. And on top of that, it has also overlapping codes, which point to design.

Aron: So you refuse to answer my simple yes or no questions, which you know you should, on the excuse that the peer-reviewed studies that I have already shown, as well as all those I have yet to show, are, in your hallucinatory alternative reality, somehow "unscientific"? And your excuse for that obvious lie is your wholly false assumption that we have to know absolutely everything before we can know anything at all?
Reply: Eleventh lie.
I said that there is no dispute that dogs have wolves as common ancestors. This is entirely irrelevant, because microevolution is not disputed.

Last, not least, you CLAIMED to be an honest truth seeker. But in face of the overwhelming evidence pointing to God brought to you, you rather than acknowledging it, have simply ignored it. That confirms and shows your bias.
You have an agenda, which is to promote atheism, DESPITE the evidence against. And while accusing your opponents of lying constantly, it is you doing so all along. That's called projection.
But why should someone expect anything else from you, knowing your track record? I didn't.... After all, i did this exchange not because of you, but because of those that read these lines.

But, anyway. I do not see you as my enemy. I just think you are self delusional. A blind, leading the blind.

Have a BLESSED 2021. God lets rain to the good, and the bad. To believers, and unbelievers..... So he is blessing you too.....

Otangelo · 62 Re: Debate with Aron Ra Thu Jan 07, 2021 1:05 pm

Otangelo

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Angelmou
2 hours ago
Angelmou "2. The cell has a complex information processing system ( through RNA polymerase, transcription factors, a spliceosome, a ribosome, chaperone enzymes, specialized transport proteins, and ATP"
Not all have ATP for example. You repeat this lie several times. ATP is a variation of the F0/1 inward with the helicases. The ancestral forms don't have them.
Reply: Structural Biochemistry/The Evolution of Membranes
F- and A/V- type ATPases are membrane-embedded proteins and were feasibly present in the LUCA (last universal common ancestor) due to their omnipresence in modern cellular life. 11
https://en.wikibooks.org/wiki/Structural_Biochemistry/The_Evolution_of_Membranes

The physiology and habitat of the last universal common ancestor
Cells conserve energy via chemiosmotic coupling14 with rotor–stator-type ATP synthases or via substrate-level phosphorylation (SLP)15. LUCA’s genes encompass components of two enzymes of energy metabolism: phosphotransacetylase (PTA) and an ATP synthase subunit 13

The irreducibly complex ATP Synthase nanomachine, amazing evidence of design
https://reasonandscience.catsboard.com/t1439-the-irreducibly-complex-atp-synthase-nanomachine-amazing-evidence-of-design

Angelmou "3. The cell contains a genetic code that is at or very close to a global optimum for error minimization across plausible parameter space"
Actually this is false - a two side outreading process would be more effective.
Reply: The genetic code is one in a million
if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.
http://www.ncbi.nlm.nih.gov/pubmed/9732450

The genetic code is nearly optimal for allowing additional information within protein-coding sequences
DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832087/?report=classic

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

"5. The cell has a complex translation system through a universal cipher,"
Angelmou: Actually no, there are alternative ciphers realized in Archean.
Reply: And that falsifies common ancestry nicely.

The different genetic codes
https://reasonandscience.catsboard.com/t2277-the-different-genetic-codes

Dobzhansky believed that the common ancestry of all living things could be seen in the universality of the genetic code. This was the basis of his claim that “all organisms, no matter how diverse in other respects, conserve the basic features of the primordiallife.”9 But we now know that the genetic code is not universal. Thomas Fox reported in 1985 that “some ‘real’ exceptions have come to light” in bacteria and single-celled organisms, “and the notion of universality will have to be discarded.” 10 The number of exceptions has grown since then; a 1995 review noted that “a relatively high incidence of non-universal codes has been discovered … widely distributed in various groups of organisms.” 11 The non-universality of the genetic code suggests that living things may well have had multiple origins. – Jonathan Wells and Paul Nelson, Rhetoric and Public Affairs, November 1998 2

The discovery of thirtythree variant genetic codes indicates that the chemical properties of the relevant monomers allow more than a single set of codon–amino acid assignments. The conclusion is straightforward: the chemical properties of amino acids and nucleotides do not determine a single universal genetic code; since there is not just one code, “it” cannot be inevitable. The codon–amino acid relationships that define the code are established and mediated by the catalytic action of some twenty separate proteins, the so-called aminoacyl-tRNA synthetases (one for each tRNA anticodon and amino-acid pair). Each of these proteins recognizes a specific amino acid and the specific tRNA with its corresponding anticodon and helps attach the appropriate amino acid to that tRNA molecule. Thus, instead of the code reducing to a simple set of chemical affinities between a small number of monomers, biochemists have found a functionally interdependent system of highly specific biopolymers, including mRNA, twenty specific tRNAs, and twenty specific synthetase proteins, each of which is itself constructed via information encoded on the very DNA that it helps to decode. This is an integrated complex system. To claim that deterministic chemical affinities made the origin of this system inevitable lacks empirical foundation. Given a pool of the bases necessary to tRNA and mRNA, given all necessary sugars and phosphates and all twenty amino acids used in proteins, would the molecules comprising the current translation system, let alone any particular genetic code, have had to arise? Indeed, would even a single synthetase have had to arise from a pool of all the necessary amino acids? Again, clearly not.
Signature in the Cell, Steve Meyer, page 201

Angelmou: "which assigns 61 codons (4x4x4=64-3 stop and start=64) to 20 amino acids and permits the translation of the genetic code into functional proteins"
Actually 21, but 20 + 1 sentence mark in humans.
Reply: That does not diminish your problem:
The Genetic Code was most likely implemented by intelligence.
1. In communications and information processing, code is a system of rules to convert information—such as assigning the meaning of a letter, word, into another form, ( as another word, letter, etc. )
2. In translation, 64 genetic codons are assigned to 20 amino acids. It refers to the assignment of the codons to the amino acids, thus being the cornerstone template underling the translation process.
3. Assignment means designating, ascribing, corresponding, correlating.
4. The universal triple-nucleotide genetic code can be the result either of a) a random selection through evolution, or b) the result of intelligent implementation.
5. We know by experience, that performing value assignment and codification is always a process of intelligence with an intended result. Nonintelligence, aka matter, molecules, nucleotides, etc. have never demonstrated to be able to generate codes, and have neither intent nor distant goals with a foresight to produce specific outcomes.
6. Therefore, the genetic code is the result of an intelligent setup.

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

Angelmou:"6. This constitutes a logical structure of information processing: DNA>>RNA>>>Protein,"
PLUS changing by the fragility of the system.
Reply: If error check and repair mechanisms, both, for DNA replication, and expression were not in place all along, life would never have started. This is smashing evidence of design.

DNA and RNA error checking and repair, amazing evidence of design
https://reasonandscience.catsboard.com/t2043-dna-and-rna-error-checking-and-repair-amazing-evidence-of-design

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

Angelmou: "7. There is no reason for information processing machinery to exist without the software, and vice versa."
No one said otherwise.
Reply: Good. In that case, you should become a defender of Intelligent Design.

Angelmou: "8. Systems of interconnected software and hardware are irreducibly complex."
They must base on former forms.
Reply: What does that even mean?

Angelmou: "9. A irreducible complex system can not arise in a stepwise, evolutionary manner. "
It can. Because the IC system like the cell system bases on fatbubble acid systems like Thymine DNA is a variations of U-DNA.
Reply: What are you even talking about?

Angelmou:"10. Only minds are capable to conceptualise"
Minds aka brain architectures are subsets of those systems - without the cells you would not have a mind, because your brain is made out of cells. Minds are not prior to themselves.
Reply: Argument from consciousness
1. Existing fundamentals—space, time, mass, charge can’t explain consciousness, which itself is something fundamental, and essentially different than physical things.
2. Consciousness englobes the mind, "qualia", intellectual activity, imagination, introspection, cognition, memories, awareness, experiencing, intentions, free volition, thought, free creation, invention, generation of information. It classifies, recognizes and judges behavior, good and evil. It is aware of beauty, and feels sensations and emotions. Those are all fundamental discrete indivisible non-quantifiable qualities of immaterial substance, a different identity from hard physical objects, matter and space. Perception, understanding, and evaluation of things adds a quality beyond and absent from natural physical matter and states, and can, therefore, not be reduced to known physical principles.
3. Hard objects are never observed spontaneously to transform themselves into abstract ideas. The mind cannot be an emergent property of the brain. To ascribe to the electrons in our brain the property to generate consciousness, and not to ascribe the same property to the electrons moving in a bulb, is in contradiction with quantum physics, which establishes that all electrons are equal and indistinguishable, that is they have all exactly the same properties. The mind is to the brain what a pianist is to a piano. The former (the pianist) is not reducible to the latter (the piano).
4. Therefore, dualism is true, and since the universe had a beginning, the mind precedes and exists beyond the universe. That mind is God.

Otangelo · 63 Re: Debate with Aron Ra Sat Jan 09, 2021 6:07 am

Otangelo

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AngelaMOU:
"Irreducible complexity is the observation where you can't take even 1 part out of a running system without breaking that CURRENT system's function. 1 good example is the gliding system of the Wallace flying frog. When you take out just 1 of the webs between the toes the frog would crash. This makes the system irreducible - to the fragility of taking just 1 part away the frog CRASH.
HOWEVER this irreducible complex gliding system, where you can't take 1 part out of it evolved from the swimming toes (as adaptation) by darwinian priciples. It got selected and interlocked the specific gliding complexity as recycling/repurposement from the former swimming & climbing "paw" purpose of the percursor forms.
Reply: Just removing one would certainly not make him crash. And thats reall1y not an example frequently given by ID theorists.

AngelaMOU: Otangelo and Co want to ignore the very fragile complexity to be irreducible in such mentioned systems and they also want to ignore it to be evolved SIMULTANEOUSLY, simply because they conflate the term Irreducible Complexity with ="Creation is true by default" / "Evolutionary history is false".
Reply: The making of Chlorophyll, and what it tells us about intelligent design

https://reasonandscience.catsboard.com/t1546-chlorophyll-and-what-it-tells-us-about-intelligent-design

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

What good would there be, if the pathway would go only up to the 15th step? none
What good would there be, if the pathway would go all the way through the 17th step? Chlorophyll would be produced, BUT:
What good for survival would there be for chlorophyll on its own, if not fully embedded in the photosynthesis process? none.
What good would there be for photosynthesis without chlorophyll in place, capturing light, and transmitting it to the photosystem? none, since capturing
light is essential for the whole process.

Question: ‘Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved?’

(1) glutamyl-tRNA synthetase;
(2) glutamyl-tRNA reductase;
(3) glutamate 1-semialdehyde aminotransferase;
(4) porphobilinogen synthase;
(5) hydroxymethylbilane synthase;
(6) uroporphyrinogen III synthase;
(7) uroporphyrinogen III decarboxylase;
(8 ) coproporphyrinogen III oxidative decarboxylase;
(9) protoporphyrinogen IX oxidase;
(10) protoporphyrin IX Mg-chelatase;
(11) S-adenosyl-L-methionine:Mg-protoporphyrin IX methyltransferase;
(12)–(14) Mg-protoporphyrin IX monomethyl ester oxidative cyclase;
(15) divinyl (proto)chlorophyllide 4-vinyl reductase;
(16) light-dependent NADPH:protochlorophyllide oxidoreductase or light-independent protochlorophyllide
reductase;
(17) chlorophyll synthase.

The assembly of chlorophyll takes seventeen enzymes.
Natural selection could not operate to favor a system with anything less than all seventeen being present and functioning. What evolutionary process could possibly produce complex sophisticated enzymes that generate nothing useful until the whole process is complete? Some proponents of evolution argue that the assumed primeval organic soup had many of the simpler chemicals and that only as they were used up did it become necessary to generate the earlier enzymes in the pathway. InThe Mystery of Life’s Origin: Reassessing Current Theories, the authors set forth the good basic chemistry that demonstrates that there could never have been an organic soup, and present some of the evidence out there in the world indicating that there never was. Denton and Overman also cite a number of experts who suggest that there is no evidence for such a primitive soup but rather considerable evidence against it.

Chlorophyll itself,  and many of the intermediates along its pathway of synthesis can form triplet states, which would destroy surrounding lipids by a free radical cascade apart from the context of the enzymes that manufacture them and the apoproteins into which they are inserted at the conclusion of their synthesis. According to Asada ‘triplet excited pigments are physiologically equivalent to the active oxygens’, and according to Sandmann and Scheer, chlorophyll triplets ‘are already highly toxic by themselves … .’The entire process of chlorophyll synthesis from δ-aminolevulinic acid to protoporphyrin IX is apparently tightly coupled to avoid leakage of intermediates. Almost all of the enzymes of chlorophyll biosynthesis are involved in handling phototoxic material. For many of these enzymes, if they are not there when their substrate is manufactured, the cell will be destroyed by their substrate on the loose in the wrong place at the wrong time. Apel has cited four of the enzymes of chlorophyll biosynthesis for which this has been proven to be the case. This is a significant problem for evolutionists, who need time for these enzymes to evolve successively. Each time a new enzyme evolved it would have produced a new phototoxin until the next enzyme evolved.

Triplet state chlorophyll, generated in the reaction centres when singlet (excited state) chlorophyll cannot get rid of its energy quickly enough, as may be the case when excess photon energy is coming in, lasts long enough to generate very damaging singlet oxygen (1O2), which attacks lipids, proteins, chlorophyll and DNA.Evolutionists maintain that ground-state oxygen (3O2, a triplet state biradical) was not around when photosynthesis evolved. There is, however, considerable evidence that there has never been a time in Earth’s history when there was not significant free oxygen in the atmosphere (see Dimroth and Kimberley, Thaxton, Bradley and Olsen, Overman and Pannenberg,34 Denton). The evolutionists’ own analyses suggest that the last common ancestor for the bacteria and archaea already had sophisticated enzyme systems for using O2 and for disarming its reactive by-products. Since these organisms had already evolved by 3.5 Ga, on the evolutionists’ timescale,37 this also suggests something rather ominous for the absence of oxygen theory.

In the system that presently exists, a sophisticated complex of enzymes and pigments quenches the excess energy and scavenges the dangerous oxygen species generated by excess light. CuZn superoxide dismutase (in most higher plants) converts superoxide (O2-), the primary product of photoreduction of dioxygen in PSI, to H2O2 in the highest-known diffusion-controlled rate among enzymatic reactions. It appears that about one molecule of superoxide dismutase attaches to the surface of the membrane in the vicinity of the PSI complex, along with ascorbate peroxidase (APX). Ascorbate reduces the H2O2 generated, in a reaction catalyzed by APX. The product of this reaction, the monodehydroascorbate radical, is reduced again to ascorbate by photoreduced ferredoxin (Fd) in PSI.The enzymes and other reducing species of this system could not evolve gradually and then microcompartmentalize over time because nothing works unless everything is in place. This means that the first appearance of oxygen would have been lethal to the cell, whether the source of oxygen was biological or non-biological. Enzymes such as superoxide dismutase would not have been able to evolve at all. APX, for example, has only about 31–33% homology with cytochrome c peroxidase, from which it is thought to have evolved.Cells without these enzymes exposed to ground-state oxygen would simply have been destroyed before hundreds of base pair changes generated the enzymes from something else.

Natural selection is not evolution’s friend. In answer to the question, ‘Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved?’

The question, ‘Why and how would evolution go about trying to produce a protein for binding pigment molecules before pigment molecules existed?’ is another major challenge for proponents of evolution.

If chlorophyll evolved before the antenna proteins that bind it, it would in all likelihood destroy the cell, so the proteins had to evolve first. But natural selection could not favor a ‘newly evolved’ protein which could bind chlorophyll and other pigment molecules before those crucial pigments had themselves come into existence! Each binding site must be engineered to bind chlorophyll an or chlorophyll b only or carotene only. The carotene molecules must be present in just the right places for quenching triplet states in the chlorophylls. Even if the pigment molecules were already around, producing just the right protein would be an extremely difficult task. It would not only have to bind pigment molecules only, but it would need to bind just the right pigments in just the right places in just the right orientation so that energy could be transferred perfectly between them, with a little lower energy at each step. Anything else would do nothing or would transfer energy at random, and the complex would accomplish nothing at best and burn up the cell at worst.

And there is another problem for evolution. The insertion of the pigment molecules changes the conformation of the apoprotein from about 20% to about 60% α-helical content. So evolution would have to produce a protein with a wrong shape that would assume just the right shape by the insertion of pigment molecules in just the right positions and orientations when those pigment molecules had not yet evolved.

The energy transfer timeframe between pigment molecules in the antenna complex is between 10-15 and 10-9seconds. The system that God engineered captures 95–99% of the photon energy for photochemistry, even though there are four other ways the energy can be lost during the slightly less than a billionth of a second the system has for capturing it. Humans certainly cannot begin to design systems with such efficiency, but the evolutionists are determined that chance, what Cairns-Smith calls ‘old fumble fingers’, can.

Our understanding of the assembly of apoproteins with their pigments is very poor, but we do know that the chloroplast encoded chlorophyll a binding proteins of PSI and PSII core complexes are inserted cotranslationally into the thylakoid. Protein intermediates of the D1 protein have been observed due to ribosome pausing. It may be that this ribosome pausing permits cotranslational binding of chlorophyll a to the protein. This kind of controlled insertion, with synthesis of otherwise phototoxic material, is precisely what we would expect from intelligent planning and forethought, but how might ‘old fumble fingers’ hit on such a scheme?

Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eight last steps are used by specific enzymes uniquely in this pathway.

Even if we find in the sequence space the right steps to make the enzymes required to permit the synthesis of the products of these intermediate steps, so what ? the intermediate products would have no function, and no survival advantage of the organism would be provided. Natural selection could not operate to favor a system with anything less than all seventeen enzymes being present, functioning and processing all intermediate products to get the final product. What evolutionary process could possibly produce complex sophisticated enzymes that generate nothing useful until the whole process is complete? And even if everything were in place correctly, and chlorophyll were synthesized correctly, so what ? Unless chlorophyll AND all other proteins and protein complexes were fully in place, fully evolved and functional, correctly interlocked and working in an interdependent manner, photosynthesis would not happen. But even if photosynthesis would happen, so what? Why would the organism choose such an extremely complex mechanism, if it was surviving just fine previously? Furthermore, you do not just need the right enzymes. For the assembly of a biological system of multiple parts, following steps must be explained: the origin of the genome information to produce all subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super intelligent and powerful designer, rather than mindless natural processes by chance, or/and evolution since we observe all the time minds capabilities producing machines and factories, producing machines and end products.

everything *has* to be in place at once or else an organism has no survival advantage. The thing is, there’s no driver for any of the pieces to evolve individually because single parts confer no advantage in and of themselves. The necessity for the parts of the system to be in place all at once is simply evidence of creation. Photosynthesis missing one piece (like chlorophylls) is like a car missing just one piece of the drive train (such as a differential); it’s not that it doesn’t function as well – it doesn’t function at all!

So that the term "irreducible complexity" is just another word for "my religious belief shall be true" (By dogma).
ICs are a prediction by evolution published since the 1910s years... long before Behe, his mentor Dembski or Otangelo etc. were around.

Muller wrote: "... thus a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former. It must result, in consequence, that a dropping out of, or even a slight change in any one of these parts is very likely to disturb fatally the whole machinery; for this reason we should expect very many, if not most, mutations to result in lethal factors ..." Muller 1918 pp. 463-464.
"V. The role of interlocking and diffusion of gene functions in hindering true reversal of evolution "... an embryological or physiological process or structure newly arisen by gene mutation, after becoming once established (with or without the aid of selection), later takes more and more part in the whole complex interplay of vital processes. For still further mutations that arise are now allowed to stay if only they work in harmony with all genes that are already present, and, of these further mutations, some will naturally depend, for their proper working, on the new process or structure under consideration. Being thus finally woven, as it were, into the most intimate fabric of the organism, the once novel character can no longer be withdrawn with impunity, and may have become vitally necessary." Muller 1939 pp. 271-272.
Where Otangelo also conflated H.J.Muller with K.R. Miller from the Kitzmiller v dover trial against the DI church guys financed by
Fieldstaed & Company / the evangelical christian missionary Stewardship Foundation & Maclellan Foundation etc.

AngelaMOU: "Look at the Sheltand pony & how complicated it is! The head, the hooves, tail and legs and torso...and not to mention the inner organs like the liver, stomach, muscle tissues and bones... All this is impossible to just fall from the sky at pure happenstances! Just to assemble in my garden into a living breathing shetland pony to jump and (gish) gallop around! And you also can't take its head away! It would die!
Therefore the body parts must be glued together from separate pieces...all by a fiddle-fuddler...that is my (AND ONLY MY) God!"
Reply: How organisms becase as complex as we know they did, is actually far from answered yet by science, despite the 150 year old claim that " evolution did it".
But the evidence does not lead to the conclusion that unguided evolutionary pressures have that creative powers.

Where Do Complex Organisms Come From?
https://reasonandscience.catsboard.com/t2316-evolution-where-do-complex-organisms-come-from

How do biological multicellular complexity and a spatially organized body plan emerge?
https://reasonandscience.catsboard.com/t2990-how-does-biological-multicellular-complexity-and-a-spatially-organized-body-plan-emerge

1. Biological sciences have come to discover in the last decades that major morphological innovation, development and body form are based on at least 16 different, but integrative mechanisms, the interplay of genes with the gene regulatory network, Trans and Retrotransposons, so-called Junk DNA, gene splicing and recombination, and at least two dozen epigenetic informational code systems, some, like the glycan ( sugar) code, far more complex than the genetic code, on the membrane - exterior side of cells, Post-transcriptional modifications (PTMs) of histones, hormones, Ion Channels and Electromagnetic Fields that are not specified by nuclear DNA, Membrane targets and patterns, Cytoskeletal arrays, Centrosomes, and inheritance by cell memory which is not defined through DNA sequences alone.

2. These varied mechanisms orchestrate gene expression, generate Cell types and patterns, perform various tasks essential to cell structure and development, are responsible for important tasks of organismal development, affect gene transcription, switch protein-coding genes on or off, determine the shape of the body, regulate genes, provide critical structural information and spatial coordinates for embryological development, influence the form of a developing organism and the arrangement of different cell types during embryological development, organize the axes, and act as chemical messengers for development

3. Neo-Darwinism and the Modern Synthesis have proposed traditionally a gene-centric view, a scientific metabiological proposal going back to Darwin's " On the origin of species ", where first natural selection was proposed as the mechanism of biodiversity, and later, gene variation defining how bodies are built and organized. Not even recently proposed alternatives, like the third way, neutral theory, inclusive fitness theory, Saltationism, Saltatory ontogeny, mutationism, Genetic drift, or combined theories, do full justice by taking into account all organizational physiological hierarchy and complexity which empirical science has come to discover.

4. Only a holistic view, namely structuralism and systems biology, take into account all influences that form cell form and size, body development and growth, providing adequate descriptions of the scientific evidence.

The BIG ( umbrella ) contributor to explain organismal complexity and biodiversity which falsifies and replaces unguided evolutionary mechanisms is preprogrammed prescribed instructional complex information encoded through ( at least ) 31 variations of genetic codes, and 31 epigenetic codes. Complex communication networks use signaling that act on a structural level in an integrated interlocked fashion, which are pre-programmed do direct growth and development, respond to nutrition demands, environmental cues, control reproduction, homeostasis, metabolism, defense systems, and cell death.

1. Genetic and epigenetic information directs the making of complex multicellular organisms, biodiversity, form, and architecture
2. This information is preprogrammed and prescribed to get a purposeful outcome. Each protein, metabolic pathway, organelle or system, each biomechanical structure and motion works based on principles that provide a specific function.
3 Preprogramming and prescribing a specific outcome is always the result of intention with foresight, able to instantiate a distant specific goal.
4. Foresight comes always from an intelligent agent. Therefore, biodiversity is the result of intelligent design, rather than unguided evolution.

They are apt to communicate, crosstalk, signal, regulate, govern, control, recruit, interpret, recognize, orchestrate, elaborate strategies, guide and so forth. All codes, blueprints, and languages are inventions by intelligence. Therefore, the genetic and epigenetic codes and signaling networks and the instructions to build cells and complex biological organisms were most likely created by an intelligent agency.

AngelaMOU: The flat fact that ponies are bred over generations from horses, while horses and donkeys and several zebra species (in general) came from even older Equine ancestry is ignored.
Reply: Who denies micro-evolution and human domestication of wild animals like wolves becoming dogs etc?

AngelaMOU: Otangelo does this with proteins, cell organelles and cellular machinery...
where he points in long monologues the complexity out without actually adressing the repurposement towards newer or altered functionality...EVER
Reply: From where did these enzymes be repurposed?

(10) protoporphyrin IX Mg-chelatase;
(11) S-adenosyl-L-methionine:Mg-protoporphyrin IX methyltransferase;
(12)–(14) Mg-protoporphyrin IX monomethyl ester oxidative cyclase;
(15) divinyl (proto)chlorophyllide 4-vinyl reductase;
(16) light-dependent NADPH:protochlorophyllide oxidoreductase or light-independent protochlorophyllide
reductase;
(17) chlorophyll synthase.

AngelaMOU: So does Otangelo start again with rhodopsin.
https://royalsocietypublishing.org/doi/10.1098/rspb.2019.1182 & https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879442/ & https://www.nature.com/articles/s41598-020-73606-y
And if you point out the evolutionary pathway...he gets dementia a day later and starts...surprise surprise again with rhodopsin.
Reply: Evolution of Rhodopsins
Opsins are a group of proteins that underlie the molecular basis of various light sensing systems including phototaxis, circadian (daily) rhythms, eye sight, and a type of photosynthesis. Opsins are retinal proteins because they bind to a light-activated, non-protein chromophore called retinal. All opsin proteins are embedded in cell membranes, crossing the membrane seven times. 6

Functional residues, such as those within the catalytic sites of enzymes, are highly constrained and thus well conserved across organisms because mutations within these sites are normally deleterious. 3

That raises the question how these G Proteins emerged in the first place since they are highly specific and prone to mutations.

An often cited source of evolutionary novelty is the recruiting and co-option of extant building blocks, and incorporate them into new systems, by natural selection of new functions. Rhodopsin would have to undergo evolution by recruiting All-trans-retinal chromophores, which it would have to find ready fully formed and functional, and finely tuned and right-sized to fit the binding pocket, a molecule obtained by a complex multistep biosynthesis pathway starting with carotenoid chromophores from fruits, flowers, trees or vegetables. 4   It would require elaborated import mechanisms and the information how to insert it in the binding pocket, and attached at the right place, and the insertion of a protonated retinal Schiff base  ( The term Schiff base is normally applied to these compounds when they are being used as ligands  )

The crystal structure of rhodopsin reveals that the chromophore-binding pocket is well defined, suggesting that the binding pocket has high specificity for the Schiff base and the b ionone ring. 14

The binding of the chromophore to the opsin is essential to trigger the conformational change and must be precise and functional from the beginning. Following is required :

1. a Schiff base linkage
2. a Lys296 residue where chromophore retinal covalently binds
3. the side chain of the residue
4. an essential amino acid residue called "counter ion". The counterion, a negatively charged amino acid residue that stabilizes a positive charge on the retinylidene chromophore, is essential for rhodopsin to receive visible light. 17
5. There is a pivotal role of the covalent bond between the retinal chromophore and the lysine residue at position 296 in the activation pathway of rhodopsin

Unless all of these specific points were not just right from the beginning, rhodopsin would not be functional. Each of these processes demands already coordinated and finetuned interplay and precise orchestration between opsin and retinal.

Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105

Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if subsystems or parts are put together in the right order, they also need to interface correctly.

The question is: How did opsins and their configuration of seven precisely folded alpha helix transmembranes emerge?

Rao et. al.  have proposed that "...the packing of seven helices together may represent a uniquely stable arrangement that has been achieved through a process of convergent evolution." 10

Here we go. We " have proposed ".... convergent evolution. But but.... where is the evidence ??

In the paper: The Origins of Novel Protein Interactions during Animal Opsin Evolution, the authors make the remarkable admittance:

Genetic changes are known to modify phenotype during evolution by altering the interactions between a protein and its ecological or biochemical environment, by modulating existing protein-protein interaction. However, the specific genetic changes that give rise to the evolutionary origins of novel protein-protein interactions HAVE RARELY BEEN DOCUMENTED IN DETAIL.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001054

[size=16]Origin of correct protein folding, a major problem in evolutionary biology[/size]

The precision upon which opsins must fold into their seven transmembrane configuration is staggering:

Biophysicists at JILA have measured protein folding in more detail than ever before, revealing behavior that is surprisingly more complex than previously known. . . .2  the JILA team identified 14 intermediate states—seven times as many as previously observed—in just one part of bacteriorhodopsin, a protein in microbes that converts light to chemical energy and is widely studied in research. “The increased complexity was stunning,” said project leader Tom Perkins, a National Institute of Standards and Technology (NIST)  “Better instruments revealed all sorts of hidden dynamics that were obscured over the last 17 years when using conventional technology.” “If you miss most of the intermediate states, then you don’t really understand the system,” he said. Knowledge of protein folding is important because proteins must assume the correct 3-D structure to function properly. Misfolding may inactivate a protein or make it toxic. Several neurodegenerative and other diseases are attributed to incorrect folding of certain proteins.
https://www.nist.gov/news-events/news/2017/03/jila-team-discovers-many-new-twists-protein-folding

AngelaMOU: I explained him that he wanted to switch to cell origin/abiogenesis topics, because he did not want to face that the whole human complexity is 1 adaptation from ape ancestral complexity (humans are still apes and remain in that clade anyway).
And a human cell is not ex nihilo "fallen from the sky"/ assembled from separate organelles and molecules taken out of a drawer.
Reply: Chimps, our brothers ?
https://reasonandscience.catsboard.com/t2272-chimps-our-brothers

AngelaMOU: The different TYPES of ATP was about the inward mutation of the F0/F1 & helicase function switches.
Aka:
https://www.life.illinois.edu/crofts/bioph354/Evol_F1.html
https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2890%2980014-A
www.sciencedirect.com
The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio
Members of the FoF1, AoA1 and VoV1 family of ATP synthases and ATPases have undergone at least two reversals in primary function. The first was from a…
www.sciencedirect.com www.sciencedirect.com
etc.
Reply:  The irreducibly complex ATP Synthase nanomachine, amazing evidence of design
https://reasonandscience.catsboard.com/t1439-the-irreducibly-complex-atp-synthase-nanomachine-amazing-evidence-of-design

The physiology and habitat of the last universal common ancestor
Cells conserve energy via chemiosmotic coupling14 with rotor–stator-type ATP synthases or via substrate-level phosphorylation (SLP)15. LUCA’s genes encompass components of two enzymes of energy metabolism: phosphotransacetylase (PTA) and an ATP synthase subunit 13

Since evolution by natural selection requires reproduction, and since reproduction requires life, which requires ATPase, the enzyme is, therefore, a prerequisite for evolution. But with evolution out of order until ATPase ‘appears’, evolution is not even in the running as a model to explain the origin of the molecular motor.

At least five of the below-mentioned parts are ESSENTIAL and IRREDUCIBLE. Take away one, and ATP synthase ceases to function. Neither could any of the sub-parts simply be co-opted from anywhere else. That would be the same as to say, in order to make a motor function, and a cylinder is missing, go search and find any cylinder nearby, co-opt it, and solved is the problem. The thing is that cylinders come in all size, specification, materials etc. And there is no goal-oriented search of parts that fit through evolution Evolution has no foresight. Furthermore, there must be the information on how and when and where to mount the parts, at the exact place, in the right sequence. That's a far fetch for a mindless tinkerer to be able to achieve.

1.The nucleotide binding stator subunits (“cylinders”) :  The electrostatic interaction of these rotor and stator charges is essential for torque generation
2.The central stalk (“crankshaft”) : The torsional elasticity of the central stalk and the bending and stretching elasticity of the peripheral stalk create an elastic coupling between Fo and F1. It is essential.
3, The A/V rotor subunit (“adapter”) ; It is not used in all ATP synthase motors, and can, therefore, be reduced.
4. The Rotor ring (“turbine”) ; A ring of 8–15 identical c-subunits is essential for ion-translocation by the rotary electromotor of the ubiquitous FOF1-
ATPase.
5. The Jon channel-forming subunit ; Subunit a harbours the ion channel that provides access to the binding site on the c11 ring in the middle of the membrane from the periplasmic surface. The channel is essential for the operation of the enzyme because mutants in which the channel is blocked are completely inactive in both the ATP synthesis and/or coupled ATP hydrolysis mode
6. The peripheral stalk (“pushrod”) ; The peripheral stalk of F-ATPases is an essential component of these enzymes. It extends from the membrane distal point of the F1 catalytic domain along the surface of the F1 domain with subunit a in the membrane domain.
7 - 11 do not exist in all atp synthase motors, and can, therefore, be reduced.

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC27776/
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3846802/
4. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043045
5. http://onlinelibrary.wiley.com/doi/10.1046/j.1432-1033.2002.03264.x/pdf
6. https://www.ncbi.nlm.nih.gov/pubmed/16697972

AngelaMOU: Otangelo wrote:
"The cell contains a genetic code that is at or very close to a global optimum for error minimization across plausible parameter space"

I mentioned that a two-way reading system instead of the weird leading and legging strand with DNA replication like with the Okazaki fragment etc. is not an optimum there, but unnecessesarily convoluted.
Reply: What has DNA replication to do with the optimality of the genetic code?

DNA replication, and its mind boggling nano technology that defies naturalistic explanations
https://reasonandscience.catsboard.com/t1849-dna-replication-of-prokaryotes

The Argument of the Original Replicator
In prokaryotic cells, DNA replication involves more than thirty specialized proteins to perform tasks necessary for building and accurately copying the genetic molecule.
Each of these proteins is essential and required for the proper replicating process. Not a single one of these proteins can be missing, otherwise, the whole process breaks down, and is unable to perform its task correctly. DNA repair mechanisms must also be in place, fully functional, and working properly, otherwise, the mutation rate will be too high, and the cell dies. 18
The individual parts and proteins require by themselves complex assembly proteins to be built.
The individual parts, assembly proteins, and proteins individually would have no function on their own. They have only function interconnected in the working whole.
The individual parts must be readily available on the construction site of the RNA replication complex, being correctly interlocked, interlinked, and have the right interface compatibility to be able to interact correctly together. All this requires information and meta-information ( information that directs the expression of the genomic information for construction of the individual proteins, and correct timing of expression, and as well the information of the correct assembly sequence. )
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.
DNA replication requires coded, complex, specified information and meta-information, and the DNA replication process is irreducibly complex.
Therefore, DNA replication is best explained through design.

Origin and Evolution of DNA and DNA Replication Machineries
The transition from the RNA to the DNA world was a major event in the history of life. The invention of DNA required the appearance of enzymatic activities for both synthesis of DNA precursors, retro-transcription of RNA templates and replication of single and double-stranded DNA molecules. Several of these enzymatic activities have been invented independently more than once, indicating that the transition from RNA to DNA genomes was more complex than previously thought. The distribution of the different protein families corresponding to these activities in the three domains of life (Archaea, Eukarya, and Bacteria) is puzzling. In many cases, Archaea and Eukarya contain the same version of these proteins, whereas Bacteria contain another version. However, in other cases, such as thymidylate synthases or type II DNA topoisomerases, the phylogenetic distributions of these proteins do not follow this simple pattern. Several hypotheses have been proposed to explain these observations, including independent invention of DNA and DNA replication proteins, ancient gene transfer and gene loss, and/or nonorthologous replacement.
https://www.ncbi.nlm.nih.gov/books/NBK6360/?fbclid=IwAR34sXRkv5xbOPBZEmSZhbB04SCYaY7cYsTOibuCSfH9aYC3NGohfWSEHCE

AngelaMOU: 4 is not adressing the point that the system not to be perfect or mutations would not happen (at all).
He also skipped something there.
He referred formerly to the Minimal genome project in which Otangelo thought the reduction of a current complex cell to shrink it to basic functions without it being lethal is identical with LUCA.
The reduced form is not the precursor form.

This is like you reduce a bird to stay alive even without feathers and arms (putting the arm away) and then claim it is absolutely the theropod dino ancestor - not getting why this is not a reconstructed precursor.
Reply:  Did the information or the DNA come first? Did the nucleotides or the DNA or the RNA or the AMINO ACIDS or the PROTEIN come first? The architecture of the cell, including the cell wall, nucleus, sub-cellular compartments and a myriad of molecular machines, did not originate from DNA, but was created separately and alongside DNA. Neither can exist without the other. Thus, a large, yet immeasurable, part of biological information resides in living organisms outside DNA.
What came first, the molecular machine called ATP synthase or the protein and RNA manufacturing machines that rely on ATP to produce the ATP synthase machine?
It takes DNA to make proteins. But it takes proteins to make DNA. What came first ?
It takes ATP energy to make enzymes. But it takes enzymes to make ATP. What came first ?

Otangelo · 64 Re: Debate with Aron Ra Sat Jan 09, 2021 8:01 am

Otangelo

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Angelamou: you wanted to suggest it is molecules swirling around - just one step - LUCA.
Reply: What I suggest is, that this is the ONLY way it can happen: But God creating life in one step.

The cell is irreducibly complex
https://reasonandscience.catsboard.com/t1299-abiogenesis-the-cell-is-irreducibly-complex

But we both know, that this is not possible for many many reasons - which we have discussed in several occasions - but abiogenesis is actually one of my preferred topics, we can go there any time again - i am more than happy to do this.

Angelamou: why you demand omniscience from other human beings/scientists and you did not really wated to get to it
Reply: No, not at all. And no. I am not just filling gaps of knowledge with God. I point out why we see principles in nature to make complex things, which require FORESIGHT - which non-intelligent mechanisms do not have - and that is an UNSOLVABLE problem for naturalists as you are, but refuse to acknowledge it.

Despite 200 years of denialism, the watchmaker argument, and hoyle's 747 - tornado analogy has NEVER been solved, but with scientific advance, has only aggravated. And when these conceptual problems are being pointed out, you and many others simply ignore these undeniable facts, which simply and frankly, KILL your worldview without God.

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

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