Ribosomes amazing nano machines: by evolution, or design ?

Ribosomes amazing nano machines

https://******************************/t1661-translation-through-ribosomes-amazing-nano-machines

Translation is one of the most complex biological processes, involving diverse protein factors and enzymes as well as messenger and transfer RNAs. The sequence of the PTC is possibly the most relevant stretch of nucleic acid to be studied if one aims to understand the origin of life. Nowadays, it is a consensus that the ribosome should be understood as a prebiotic machine that predated the origin of cells. The contingent appearance of this ribozyme capable of binding amino acids together was crucial to both the initial emergence and further development of the phenomenon of life7

The ribosome is a ‘‘living fossil‘‘, a particle so central to all cellular processes that it has essentially become frozen in time, preserving many ancestral features in its molecular structure. 8

The origin of the ribosomal protein synthesis network is considered to be the singular defining event in the origin of cells and the Tree of Life 4

* Each cell contains around 10 million ribosomes, i.e. 7000 ribosomes are produced in the nucleolus each minute.
* Each ribosome contains around 80 proteins, i.e. more than 0.5 million ribosomal proteins are synthesized in the cytoplasm per minute.
* The nuclear membrane contains approximately 5000 pores. Thus, more than 100 ribosomal proteins are imported from the cytoplasm to the nucleus per pore and minute. At the same time 3 ribosomal subunits are exported from the nucleus to the cytoplasm per pore and minute.

The evidence from the ribosome
a. “Spontaneous formation of the unlocked state of the ribosome is a multi-step process.”
b. The L1 stalks of the ribosome bend, rotate and uncouple – undergoing at least four distinct stalk positions while each tRNA ratchets through the assembly tunnel. At one stage, for instance, “the L1 stalk domain closes and the 30S subunit undergoes a counterclockwise, ratchet-like rotation” with respect to another domain of the factory. This is not simple. “Subunit ratcheting is a complex set of motions that entails the remodeling of numerous bridging contacts found at the subunit interface that are involved in substrate positioning.”
c.The enzyme machine that translates a cell’s DNA code into the proteins of life is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products… To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is “shocking” and reveals just how much of a stickler (insisting) the ribosome is about high-fidelity protein synthesis. (Rachel Green, a Howard Hughes Medical Institute investigator and professor of molecular biology and genetics: The Ribosome: Perfectionist Protein-maker Trashes Errors, 2009)
4. Interactions between molecules are not simply matters of matching electrons with protons. Instead, large structural molecules form machines with moving parts. These parts experience the same kinds of forces and motions that we experience at the macro level: stretching, bending, leverage, spring tension, ratcheting, rotation and translocation. The same units of force and energy are appropriate for both – except at vastly different levels.
5. Every day, Every day, essays about molecular machines are giving more and more biomolecular details, many without mentioning evolution and giving details about the process of how these machines evolved. Ribosomes, however, are life essential, and a prerequisite to make the proteins which replicate DNA, hence, it had to emerge prior evolution could start. So its emergence cannot be explained by evolution.
6. These complexities are best explained by the work of an intelligent agency.
7. Hence, most probably, God exists.

Comparative genomic reconstructions of the gene repertoire of LUCA(S) point to a complex translation system that includes at least 18 of the 20 aminoacyl-tRNA synthetases (aaRS), several translation factors, at least 40 ribosomal proteins, and several enzymes involved in rRNA and tRNA modification. It appears that the core of the translation system was already fully shaped in LUCA(S) (Anantharaman, et al., 2002).

I'd contribute if I could, but the honest truth is I don't know much about this topic. This is probably something @AronRa would be interested in so I've given him a quick ping there to see if he wants to take it up.

Also, welcome to the league

The Ribosome is one of the greatest wonders of molecular nanotechnology ever devised by our amazing unfathomable creator.

Koonin, the logic of chance, page 376
Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage is extremely difficult even within a speculative scheme let alone experimentally. Speaking of ribosomes, they are so well structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working. Design some machinery which behaves like this and I personally will build a temple to your name!

My comment: Fortunately, people that recognize the magnificence of the creator of the Ribosome, build him churches and temples all over the globe, and give HIM glory.

rationalist said:

My comment: Fortunately, people that recognize the magnificence of the creator of the Ribosome, build him churches and temples all over the globe, and give HIM glory.

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Well, as much as I dislike putting words in peoples mouths, what you mean here is the people who believe the Ribozome has a magnificent creator build temples and churches all over the world, since the existence of this creator you refer to is by no means established.

*SD* said:

Well, as much as I dislike putting words in peoples mouths, what you mean here is the people who believe the Ribozome has a magnificent creator build temples and churches all over the world, since the existence of this creator you refer to is by no means established.

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They recognize HIM by reasonable faith. Yes.

So... male gendered then? You aren't going to do well if you continue in this vein, but that's entirely your call.

Hi Rationalist.

I think I recognise you, but you are very welcome to keep your identity private and I will respect that.

This is an argument from incredulity and God of the gaps, as was Michael Behe’s irreducible complexity and so many other things over the centuries that we have come to understand and explain. Each one had a potential creator, as deemed by the biased or lazy folk who were content to stand in awe, but go no further, content in their pre-conviction. A similar effect to the ever changing return dates of Messiah’s, with each passing one, quickly forgotten and erased or excused.

You cannot merely appeal to something that seems too amazing to have occurred naturally and use that as evidence for a higher or supernatural power, let alone a God (and the one of your preference) and to include this in a scientific argument is wrong, irrelevant and shows the bias/intentions/motives. It is good to show the complexity of things for perspective, as it is also fair to show the work done to explain such complex features over vast lengths of time, and in a fair way.

Incredulity, awe or wonder are all well and good, as are ny gaps in our knowledge or understanding, but are not evidences, or an excuse to stop examining.

This subject matter here is quite technical and one for specialists, not lay people who are not in a position to get a good grasp and be able to respond and point to related research on it.

A lay discussion here would tend to generate more heat than light, and given some theological content in the body of your link, I am not convinced that there is an open mind or search for real truth or independent facts that may override a belief system. But stranger thinks have happened and science welcomes challenges with open arms, not fear of being caught out about something. Most Christians are evolutionists btw.

I am Otangelo. Nothing to hide. I posted this topic upon Aron Ra's suggestion.

No, I don't think the argument is based on gaps or lack of knowledge.

1. The set up of a language, and upon it, the programming of a completely autonomous communication network, which directs the operation of a complex factory, which during operation error checks and performs repairs, to make specific purposeful products, is always the product of an intelligent agency.

2. Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, they can halt the translation process on the fly, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.

3. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder, does science confess that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: an intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.

rationalist said:

I am Otangelo. Nothing to hide. I posted this topic upon Aron Ra's suggestion.

No, I don't think the argument is based on gaps or lack of knowledge.

1. The set up of a language, and upon it, the programming of a completely autonomous communication network, which directs the operation of a complex factory, which during operation error checks and performs repairs, to make specific purposeful products, is always the product of an intelligent agency.

2. Ribosomes are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They form complex circuits. They perform masterfully long-range signaling and perform information transfer between remote functional sites. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They choreograph, collaborate, modulate, regulate, monitor the translation status, sensor quality, synchronize, they can halt the translation process on the fly, and coordinate extremely complex movements, like rotations and elongations, even helped by external synchronization systems. to direct movements during translation. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.

3. The Ribosome had to be fully operational when life began. This means the origin of the Ribosome cannot be explained by Darwinian evolution. No wonder, does science confess that the history of these polypeptides remains an enigma. But for us, theists, the enigma has an explanation: an intelligent cognitive agency, a powerful creator, God, through his direct intervention, wonderful creative force, and activity, created this awe-inspiring life-essential factory inside of many orders of magnitude greater cell factories, fully operational right from the beginning.

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Yeah, so you've been banned from just about every call in show that deals with this topic already.

*SD* said:

Yeah, so you've been banned from just about every call in show that deals with this topic already.

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I have been banned to call in at the shows run by Matt the Hang up guy because he cannot handle my arguments. That does not refute my argument above about the Ribosome.

You didnt really make an argument, you made a bunch of assertions and non sequiturs, which is what you always do.

It's neither here nor there where he is banned where talking and/or discussing on League of Reason. We are discussing his standpoints not attacking the person.

I'm not attacking the person, I'm stating that I'm familiar with who he is, and the positions he's espousing here have already been dealt with repeatedly on other platforms and yet he continues to do the same thing. Background information is useful to others, his 'arguments' will stand or fall on their own merits and I'm not stopping him from making them, I'm just predicting how this thread will go. His opening gambit is nothing but non-sequiturs and bald assertions, and the fact that this has already been covered elsewhere (several times, at length) is, in my view, relevant.

There's also the fact he hasn't addressed my two previous posts above this one with anything more than a repetition of the claim he's provided zero evidence or solid argument for. I don't think he even knows what he's trying to argue for. Brachio gave him a detailed reply, and he responded by re-asserting the original claims with very little else by way of extra content, and this seems to be all he ever really does. There's no ad-hominem on my part, I've been perfectly polite and haven't moderated him in any way shape or form, nor do I intend to unless it becomes absolutely necessary, I just consider him a bad faith interlocutor, that's not ad-hom, it's just an opinion based on what I already know, and it's not representative of anyone here other than me.

Protein folding, surprising mechanisms point to an arranged set up

https://***************************...-through-ribosomes-amazing-nano-machines#8052

Proteins, in order to become functional, must fold into very specific 3D shapes, which happens right when they come out of the ribosome, where they are synthesized. Specific protein shape and conformation depends on the interactions between its amino acid side chains. For a protein to function it must fold into a resting state which is a complex three-dimensional structure. If a protein fails to fold into its functional structure then it is not only without function but it can become toxic to the cell. As proteins fold, they test a variety of conformations before reaching their final form, which is unique and compact. Folded proteins are stabilized by thousands of noncovalent bonds between amino acids. A relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows. 1

If we take one of the smallest free living bacteria, they have about 1300 proteins, with an average of about 400 amino acids. If their amino acid sequence and arrangement were to emerge prebiotically, without the instructional information from a genome, more attempts would be required than the number of atoms in the universe, to get the right set. Not considering all the inherent problems with this scenario, like the lack of mechanisms to select the right amino acid set used in life, and sorting out of the right-handed ones ( life uses only left-handed amino-acids ), the fact that some amino acids never have been found besides being synthesized in the Cell, this is a major problem. And so the fact, that the linking bonds of these polymers are peptide and ester bonds. In both cases, the polymerization reaction is thermodynamically uphill, with hydrolysis being favored. ( hydrolysis means that any chemical reaction in which a molecule of water ruptures one or more chemical bonds ) How then can polymers be synthesized? For prebiotic scenarios, there is no compelling answer. In the cell, the monomers have been chemically activated by an input of metabolic energy so that polymerization is spontaneous in the presence of ribosomes that catalyze polymerization. Catalyzing bond formation in the Ribosome comes out to be a very carefully engineered and precise process, where the surrounding ribonucleotides must be placed very precisely, at the right place. How do proteins fold from a linear sequence of amino acids into functional form, where they can operate as molecular machines ?

Science has unraveled surprising and astonishing details of what mechanisms might be in place, answering this question.

One of the most important mechanisms that play a vital role in the cell is the amino acid peptide bond formation during protein synthesis. It takes place in the so-called peptidyl transferase center, which is the reaction center in the Ribosome. Peptide bond formation is by no means a simple, or trivial task. The process is so intriguingly complex, that a science paper in 2015 had still to admit that: The process of peptide bond formation is of particular importance, being the heart of protein synthesis. 1 The detailed mechanism of peptidyl transfer, as well as the atoms and functional groups involved in this process are still in limbo.

The ribosome speeds up the reaction rate and catalyzes peptide bond formation 10 million times faster than compared to an uncatalyzed reaction. The ribosome subunit, where the catalysis takes place, is called 23S ribosomal RNA. It has a length of 2904 nucleotides(in E. coli).

A precise, minutely orchestrated arrangement of just two main players amongst these 2904 nucleotides is absolutely essential, the interaction of ribose 2'-OH at position A2451 , and the 2’ hydroxyl of the P site substrate A76 . They are pivotal in orienting substrates in the active site for optimal catalysis, and play a key role in polypeptide bond formation.

My comment: Consider this as an extraordinary engineering feat. Amongst 2905 nucleotides, just one is the main player interacting with another to promote this life essential reaction, and had to be positioned precisely in the right spot.

Evidently, the positioning of all substrates, transition states, and ribosomal residues contributing to the concerted redistribution of charges must be tightly controlled to achieve efficient transpeptidation compatible with the observed in vivo rates of amino acid polymerization of about 20 amino acids per second.

Molecular biology of the Cell, Alberts, 6th ed. pg. 369

Producing an overall speed of translation of 20 amino acids incorporated per second in bacteria. Mutant bacteria with a specific alteration in the small ribosomal subunit have longer delays and translate mRNA into protein with an accuracy considerably higher than this; however, protein synthesis is so slow in these mutants that the bacteria are barely able to survive.

Question: How could the right speed have been obtained with trial and error, if slow mutants do not survive? Had the speed not to be right from the beginning?

This 2'-OH renders almost full catalytic power. These data highlight the unique functional role of the A2451 2'-OH for peptide bond synthesis among all other functional groups at the ribosomal peptidyl transferase active site. Key in this reaction is the presence of a proton shuttling group. The observed 100-fold reduction in the reaction rate by mutation of P-site A76 20-OH group is indication of this group's activity during the peptidyl transfer reaction.

Remember this functional group, A2451. I will return to it at the end of this article.

Remarkably, as we will see in the following, protein folding is not only dependent on the amino acid sequence, or stabilizing forces.

A paper reports:
Protein folding in living cells requires a mechanism of action through direct manipulation of the peptide backbone during polypeptide bond formation. Considering the rotating motion of the tRNA 3’-end in the peptidyltransferase center of the ribosome, it is possible that this motion might introduce rotation to the nascent peptide and influence the peptide’s folding pathway. The 3’ terminus of the tRNA in the A-site of the ribosome peptidyl transferase center turns by nearly 180 degrees in every translation elongation cycle. Only a 45-degree swing is necessary to achieve the proper stereochemistry of the peptide bond formation; the function of the remaining portion of the turn is hypothesized to be needed to facilitate co-translational folding

Experimental results are in line with our hypothetical mechanism through which the ribosome directly altesr the conformations of proteins by applying mechanical force to the peptide backbone. In vivo the peptide backbone can be manipulated into conformations that cannot be reached without assistance because they are either thermodynamically unstable or kinetically inaccessible. The results of our simulations thus demonstrate the feasibility of a protein folding mechanism during peptide bond formation.

My comment: This demonstrates that protein folding ( which is essential to get functional proteins ) is a complex, finely orchestrated process that depends not only on the correct amino acid sequence, and the decrease in Gibbs free energy, but also an active energy-dependent process. The mechanism of action of the ribosome (protein folding machine ). That means, without the concerted action of the ribosome, the original minimal proteome would never have formed prebiotically in absence of the ribosome, directly involved in the folding process. The ability of any present-day protein to fold in isolation and without assistance not shared by most proteins. Thus, the notion of an active, energy-dependent protein folding mechanism in vivo reinforces the understanding of an intelligently bioengineered process than the generally accepted evolutionary process, and that the ability of proteins to attain their native conformations must have evolved by natural selection of sequences that fold quickly and correctly (“evolution solved the protein folding problem” ) becomes more and more remotely possible.

And more mechanisms are in play helping protein folding insider the ribosome:
Some recently published results, include studies of the role of the exit tunnel in nascent chain folding. For small protein domains, the ribosome itself can provide the kind of sheltered folding environment that chaperones provide for larger proteins. That the small zinc-finger domain ADR1a folds cotranslationally as the tether connecting it to the ribosome grows in length from ∼20 to ∼30 residues. ADR1a buried deep in the vestibule of the exit tunnel, provides a clear demonstration that small proteins or protein domains can fold within the ribosome, as predicted by computational studies Although the zinc finger is one of the smallest independently folding protein domains, it has been estimated that ∼9% of all structural domains found in the PDB are less than 40 residues long, and ∼18% are less than 60 residues long. Folding of protein domains wholly or partly inside the exit tunnel may thus be not too uncommon, despite its relatively constrained geometry. But even MORE REMARKABLY: In the upper part of the tunnel, results suggest that A2062 and A2451 can communicate in both directions for translation stalling, mostly through dynamically coupled C2063, C2064, and A2450.

My comment: This is truly awe-inspiring. The functional group A2451, which is not only of crucial importance as described above for peptyde bond catalysis, but when the translation process is stalled, it signals to a dynamically coupled group in the exit tunnel of the product, the polypeptide chain: " we have a problem here" !! and the ribosome takes action.

If all this is not evidence of a bioengineered process, i don't know, what is!!

Tl;Dr - "I think Ribosomes are very awesome and I can't fathom how they could be a thing without God"

That's literally it. Appeal to ignorance/incredulity/GOTG. Nothing more.

Also, posting large amounts of copy/pasta from work that ISN'T yours is usually considered flooding and/or spam. Citing references is obviously fine, but it's nice if you sometimes have an original thought of your own.

You're still failing to address any of the replies to you, this forum isn't a soundboard for you to preach from, nor is it a stepladder from which to spout forth unfounded and unproven assertions. If your next reply doesn't address at least some (read - any) of the criticisms already levied against you then come what may, I will either restrict your ability to post here, OR, dismantle you piece by piece.

As you were, chaps.

Analogy to Irreducible complexity/Intelligent design.

I have an elderly friend. She used to be my landlady when I was (a Creationist) at Bible college. She thought magicians, illusions and card tricks etc. were of the devil. Her basis was largely that it simply could not be done/explained naturally. [i.e. how could s/he possibly disappear from here and appear over there?). I enjoy doing magic myself, and used to show her tricks – mainly card tricks. She would immediately confirm that it was from the devil and that I should leave it alone. I would then proceed to show her exactly how I did it. Her response was that, well maybe that was just a trick, but lots of other ones are real magic. I repeated this with different tricks and got the same response. The truth was, that if SHE could not work it out, it was therefore impossible (naturally) and therefore the devil or demons were involved in deceiving people. My evidence based conclusion was that as tricks are intentioned/defined to deceive and do what you can’t explain, she would have to see and have revealed, every trick ever, in order to be convinced there was no evil magic master. ‘Pearl before swine’, ‘waste of time’, ‘no hope’ all spring to mind. Open mindedness or seeking answers is not about just going up to a scientific paper (and people who have done all the work), and just looking for a mistake or hole. Peer review will do that, have no fear. Why not try to take experiments or research and take it to the next level and try to work things out instead of leaving it to the other scientists (many of whom are Christians) to work out. The number of times that IC has been shown not to be (irreducibly complex) should make you realize that there most likely are natural explanations ahead. So, like a fortune teller or one who predicts the future, be careful what you claim, lest it catch up to you.



I like you.

I do have a soft spot for you, Rationalist. You have often been very patient with people (and others have been less patient with you). I commend you for this tolerance. You are a lone, tireless advocate of your faith and ID and with those as pre-conception/starting points, (not science or the truth), you stick well to it, but leave yourself open to criticism based on your pre-conception/motive and unnecessary god inclusions/conclusions.



There were/are/will always be new things to fathom.

ID and IC (i.e. teleological) arguments can sound amazing and very compelling to non-specialists and especially when embellished with adjectives, comparisons to things that do not involve billions of years, miss much out, exaggerate and using unknown or unverifiable stats to bolster it with. But without positive evidence or facts or science, what else is there to convince with? Rainbows, snow drops, the movements of the stars and planets and so much more was once PROOF of God to most people. Because we had no current explanation.



A NEW magic trick/ID/IC finding, it must be real.

You have stated in your posts that the things you propose, ‘cannot’ have natural explanations. Quite a claim (without an, ‘if’). That is good, because it shows your confidence (if not evidence). And this is open to science to fill such gaps and show that you may be wrong. But (like my magician watcher), you have merely ignored new explanations and moved onto something else, and will continue to do so. Only when everything is totally and fully explained, (which is obviously never) can you be satisfied. This is totally, ‘god of the gaps’ and your infinite jump to, and regular inclusion of, God in your arguments/conclusion (your pre-conception) and failure to properly engage with specialist responses does not help your case as someone who is open mindedly sharing knowledge and research or wanting any answer that does not correspond to your beliefs. Your actions and declarations are typically conspiracy based and tick all of the boxes.



Crying wolf on each new apparent gap.

If all of the scientists could not fathom out a particular mechanism for something, it still means very little and does not imply anything, not least your god and there are multiple explanations, with natural ones most likely. Science lives for and thrives and depends upon gaps to fill and some take a long time, but God was no more present in the explanation when the problem arose than when the natural explanation was found and is no more so now. Some gaps of knowledge in the past existed for centuries, but it was not proof of a god and those who thought it was, have since been shown that they were wrong as the gaps were (as always, naturally) filled. To continue to find gaps, claim god and then continually have them filled, naturally, and ignore them is crying wolf and people will see your game (if they haven’t already) and see right through it. Lack of knowledge in an area is not proof of God or anything and we have so often found this to be the case, with a natural explanation.



Parasites and who exposes who?

Your case study, like many, are good examples of complex structures. Question (to demonstrate open mindedness and searching for truth): How many times have gaps in scientific knowledge regarding evolution been discovered by a Creationist? So, regarding many of Michael Behe’s IC examples which have many hundreds of explanatory papers; there is nothing stopping a scientist who is a creationist from doing some research and discovering a natural explanation to something. Many believing Christians who are scientists contribute a lot to such findings. In fact, as far as I know, for every error that a scientist has inadvertently made, (or non-scientist that has been fraudulent for financial or notoriety gain) it has been someone who accepts evolution (and not creation) that has uncovered or exposed it. What does that say? That creationists aren’t following science very much and they are just parasitic, trolling through other people’s hard work for petty gain.



Here’s something I don’t know (Creationist). Let’s find out how (scientist).

Try to find some positive evidence for a/your God and make predictions and test it and then you have some science that people can work with. I can share examples with you that would work if it helps, because there are multiple ways to tangibly test a god/supernatural/unexplained force.



Engagement warning.

I suggest that anyone who engages with Otangelo Grasso considers what they are getting into in terms of time, effort, motive and response and consider what you hope to gain from it and strap themselves in. You have been notified and may appear on his site!



Here is some correspondence between Otangelo and bio-chemist professor Larry Moran. And Otangelo has been a regular Youtube discussion person on several shows:



https://sandwalk.blogspot.com/2017/02/trying-to-educate-creationist-otangelo.html



Who are YOU?

There are those who sit back and wonder at the mystery of things. Many of us.



There are those who simply and lazily or like sheep or parasites, just attribute things to the unknown and many like to give this unknown a name, having done little if anything themselves.



There are others who also try or want to find out in as much detail as they can about how things work. They have, over the centuries, unfolded the mystery of so much, which has often allowed us to make progress and make the understanding of science so much more exciting.



A starter for you on this post topic, but you need to target specialists.

It would be great if you engaged with this process, with an open agenda, acknowledging and correcting and updating and accepting new knowledge to those people and on your site. Here’s one of those (this is a sneak, pre-publication preview) on the post topic and please do read the many other past, present and future articles addressing this (that don’t support your gaps of natural impossibility) and include them on your site and remove any of your arguments that they cover/explain:

https://www.biorxiv.org/content/10.1101/2020.09.01.277582v1.full.pdf

I am not engaging otherwise in your article as it presents no evidence to consider (just alleged gaps) and I know so little about it, but I can assist in helping get you in contact with the authors or any of the authors in their research if it helps. They are your target audience on more complex areas, not lay folk. After you have engaged with specialists and demonstrated that you understand, have read the literature on it and have baffled them with your brilliance and they sing your praises, bring/share it here. People like evidence and compelling research. Not someone who just points and says, ‘well how do you explain that then?’.



A lack of responses definitely does not equate to, ‘people have no responses’, but a wrong site to share it.

If people do not respond to your posts, it may well be that there are no specialists who are here/able to respond or that people think you have nothing or little to present. No response on multiple sites does not mean people have no reply, but that it is not the place to post it. I do emphasise that there are multiple research papers, mostly peer reviewed, that do directly address the things you raise, and I’d be very keen to see you reflect, fairly, those responses after you read them.



Poetic licence (to be nice).

You use statistics which are totally unknowns. So often, the erroneous stats did not even apply if the scenario that is presented were true, which they are so often not. It is emotionalising the case to try to convince people of something which is not there by scientific presentation. I don’t even know how you could present a paper on a lack of knowledge, rather than additional knowledge, which is what you are trying to do. ‘Here is a possible explanation’ rather than your, ‘I can’t explain this’ is the way to go. If you can’t present a positive knowledge case to peer review, why should people take you seriously or not equally consider any other conspiracy or proposal lacking evidence?



Note to admins.

re:, ‘He_who_is_nobody’’s comment. Rationalist has been deemed to try to hijack aspects of this site with multiple posts and this thread or post may be better moved to his own area where people can choose to engage. If he has any evidence (not supposed gaps or lack of knowledge) to present, he should be free to do so in the appropriate place.



I’m being picked on because…

I am hard pressed to think of any Creationist who truly or independently came to the creation conclusion based on a sound scientific education and understanding and with no theological influential play involved and who understands evolution even at a fairly low level. Creationism is virtually by definition, a lack of understanding or acceptance or acknowledgement of real science. It is either forced, deceptive, deceived and/or to follow one’s belief system or interpretation and has an immoveable starting point of God and/or inerrancy.

If you feel you are being picked on for being a creationist, some reasons/explanations may be found in this post and you would be very wrong to assume or claim that it is for any reasons related to your faith (other than your unnecessary theological links added on to some biology). There are no doubt many people of faith here, and an argument is an argument, wherever it comes from. You do paint a very biased picture and squeeze god in as much as you can, which detracts from any reasonabnle point you might otherwise have. If God is obvious, you don’t need to say or force it, and neither do you need to exaggerate points. I do sense that you feel that you are a martyr, by sticking to your stance and being persistent and spreading across different forums, and there may even be creationists who support you and interpret your, ‘just sticking to the point and ignoring other points’, as good and holding the fort for your beliefs/ID, but to this, I do want to highlight that you are simply avoiding science and playing god of the gaps and not actually presenting any evidence and ignoring the relevant points made by those who know what they are talking about. Your words and copied notes can sound sciency and technical, but when engaging with specialists, (which is what you should be doing if you think you have good points on specialist topics), then you have fallen a long way short.

Just wondered if you have this related educational video (and many mentioned publications) on your site for people to also consider? It also explains a lot, iof not most or all of what you claim are gaps in knowledge on the formation and evolution of molecules. I don’t blame you for omitting it and painting a very lop sided image, because your agenda rejects it for theological and not scientific reasons and theology trumps science for you. Straw manning just puts people off and will lead to them not trusting you for representing things honestly.

BrachioPEP said:

Analogy to Irreducible complexity/Intelligent design.

Click to expand...

You can find below answer and reply at my library:




Claim:The number of times that IC has been shown not to be (irreducibly complex) should make you realize that there most likely are natural explanations ahead.
Reply: Irreducible Complexity: The existence of irreducible interdependent structures in biology is an undeniable fact

https://***************************...uctures-in-biology-is-an-undeniable-fact#2133

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.

1. A codified information transmission system depends on: a) A code as a system of rules where a symbol, letters, words, or even sounds, gestures, or images, are assigned to something else. Assigning meaning of characters through a code system requires a common agreement of meaning. Statistics, Semantics, Synthax, and Pragmatics, b) Information encoded through that code, c) An information storage system, and d) an information transmission system, that is encoding, transmitting, and decoding.
2. We see that precisely in living cells, where information is encoded through the histone code which is a set of rules, stored in amino acid sequences in the histone tail. They are used to orchestrate gene expression. The assignment of codified meaning to combinatorial amino acid sequences 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 gene expression is done through the orchestration of histone code readers, writers, erasers, and permit the loosening and tightening chromatin, and in consequence, the RNA polymerase machinery to express specific genes. This system had to be set-up all at once. That is the software - the histone code "language", as well as the hardware, that is the histone tails upon which the "message" is written, the readers, writers, and erasers.
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.

The oxygen-evolving complex (OEC) of photosystem II is irreducible complex.
1. One of the most important and fundamental biochemical reactions on which all advanced life-forms depend is performed by the oxygen-evolving complex (OEC) in oxygenic photosynthesis, responsible for catalyzing the light-driven oxidation of water to molecular oxygen in plants, algae, and cyanobacteria. It is also described as "undoubtedly one of the most remarkable inventions in all of biology." OEC is surrounded by 4 core proteins of photosystem II at the membrane-lumen interface. It remains a fundamental mystery of how this complicated, four-electron transfer process originated. Enigmatic is how the precise geometry and unique mechanism of the OEC came about. Key differences exist between oxygenic and anoxygenic photosynthetic machinery with no apparent homologs or transitional forms that would provide clues to their development. Foremost among these differences is the presence and key role of manganese at the site of water oxidation in photosystem II. This is distinct from bacterial anoxygenic reaction centers, which rely on redox-active periplasmic proteins as electron donors.
2. According to peer-reviewed scientific papers, each of the four extrinsic proteins, (PsbO, PsbP, PsbQ, and PsbR) of plants are ESSENTIAL, and each was tested upon mutated form, and the mechanism was found inefficient and compromising the OEC function. Furthermore, a water network around the Mn4CaO5 cluster and D1 protein subunit of PSII is also indispensable, and
3. That means evolutionary intermediates are non-functional. There is a precise fit and size matching of the residues with the individual atoms of the clusters. This is evidence, that this most fundamental biochemical reaction could not have emerged by evolutionary, step-wise mechanisms, and therefore, Darwin's theory has been falsified and refuted. The only plausible alternative to darwinian evolution is intelligent design.

The cell is irreducibly complex
https://******************************/t1299-abiogenesis-the-cell-is-irreducibly-complex

Abiogenesis? Impossible !!


The cell is the irreducible, minimal unit of life 5
https://sci-hub.tw/https://link.springer.com/chapter/10.1007/978-3-319-56372-5_8

Chemistry and the Missing Era of Evolution: A. Graham Cairns-Smith
We can see that at the time of the common ancestor, this system must already have been fixed in its essentials, probably through a critical interdependence of subsystems. (Roughly speaking in a domain in which everything has come to depend on everything else nothing can be easily changed, and our central biochemistry is very much like that.
https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/18260066

chemist Wilhelm Huck, professor at Radboud University Nijmegen
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity
https://sixdaysblog.com/2013/07/06/protocells-may-have-formed-in-a-salty-soup/


I like you.
Reply: Thanks :=))

Claim: I do have a soft spot for you, Rationalist. You have often been very patient with people (and others have been less patient with you). I commend you for this tolerance. You are a lone, tireless advocate of your faith and ID and with those as pre-conception/starting points, (not science or the truth), you stick well to it, but leave yourself open to criticism based on your pre-conception/motive and unnecessary god inclusions/conclusions.
Reply: My scientific approach is attempting to remove my bias as much as possible, and start with the evidence, and attempting to come to rational, case-adequate conclusions based on the evidence.


Claim: There were/are/will always be new things to fathom.
ID and IC (i.e. teleological) arguments can sound amazing and very compelling to non-specialists and especially when embellished with adjectives, comparisons to things that do not involve billions of years, miss much out, exaggerate and using unknown or unverifiable stats to bolster it with. But without positive evidence or facts or science, what else is there to convince with? Rainbows, snow drops, the movements of the stars and planets and so much more was once PROOF of God to most people. Because we had no current explanation.
Reply: I think theistic claims are not based on gaps ( sometimes we commit that error imho, admitted), but there are many positive claims and evidence can be provided, to bolster the claim of ID: 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.

God of the gaps and incredulity, a justified refutation of ID arguments?
https://***************************...edulitya-justified-refutation-of-id-arguments


Claim: A NEW magic trick/ID/IC finding, it must be real.
You have stated in your posts that the things you propose, ‘cannot’ have natural explanations. Quite a claim (without an, ‘if’). That is good, because it shows your confidence (if not evidence). And this is open to science to fill such gaps and show that you may be wrong. But (like my magician watcher), you have merely ignored new explanations and moved onto something else, and will continue to do so. Only when everything is totally and fully explained, (which is obviously never) can you be satisfied. This is totally, ‘god of the gaps’ and your infinite jump to, and regular inclusion of, God in your arguments/conclusion (your pre-conception) and failure to properly engage with specialist responses does not help your case as someone who is open mindedly sharing knowledge and research or wanting any answer that does not correspond to your beliefs. Your actions and declarations are typically conspiracy based and tick all of the boxes.
Reply: My claims are based on what we DO know, not the opposit. As an example:

Chance of intelligence to set up life:
100% We KNOW by repeated experience that intelligence produces all the things, as follows:
factory portals ( membrane proteins ) factory compartments ( organelles ) a library index ( chromosomes, and the gene regulatory network ) molecular computers, hardware ( DNA ) software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes ) information retrieval ( RNA polymerase ) transmission ( messenger RNA ) translation ( Ribosome ) signaling ( hormones ) complex machines ( proteins ) taxis ( dynein, kinesin, transport vesicles ) molecular highways ( tubulins ) tagging programs ( each protein has a tag, which is an amino acid sequence informing other molecular transport machines were to transport them.) factory assembly lines ( fatty acid synthase ) error check and repair systems ( exonucleolytic proofreading ) recycling methods ( endocytic recycling ) waste grinders and management ( Proteasome Garbage Grinders ) power generating plants ( mitochondria ) power turbines ( ATP synthase ) electric circuits ( the metabolic network ) computers ( neurons ) computer networks ( brain ) all with specific purposes.

Chance of unguided random natural events producing just a minimal functional proteome, not considering all other essential things to get a first living self-replicating cell,is:

Let's suppose, we have a fully operational raw material, and the genetic language upon which to store genetic information. Only now, we can ask: Where did the information come from to make the first living organism? Various attempts have been made to lower the minimal information content to produce a fully working operational cell. Often, Mycoplasma is mentioned as a reference to the threshold of the living from the non-living. Mycoplasma genitalium is held as the smallest possible living self-replicating cell. It is, however, a pathogen, an endosymbiont that only lives and survives within the body or cells of another organism ( humans ). As such, it IMPORTS many nutrients from the host organism. The host provides most of the nutrients such bacteria require, hence the bacteria do not need the genes for producing such compounds themselves. As such, it does not require the same complexity of biosynthesis pathways to manufacturing all nutrients as a free-living bacterium.

The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells. It has complete biosynthetic pathways for all 20 amino acids. These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins. 14 That would be the size of a book with 400 pages, each page with 3000 characters. They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells. If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. This probability is hard to imagine but an illustration may help.

Claim: Crying wolf on each new apparent gap.
If all of the scientists could not fathom out a particular mechanism for something, it still means very little and does not imply anything, not least your god and there are multiple explanations, with natural ones most likely.
Reply: 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.

Genesis, vs secular science explanations of origins
https://******************************/t1642-creation-believe-it-or-not-part-1
We have observed atoms having forced that keep them together. We have not explained what that force is, and why it persists. It is assumed to persist for various reasons, but no cause has ever been found, scientifically. The very mechanisms of life: DNA, replication of DNA and other microbiological processes have been observed, but never explained, because their very activity is driven by data processes, which have no known independent cause or source. The force of gravity has been observed, characterized, and tested, but its source of energy has never been explained through naturalistic processes or observation. Logic and mathematics themselves have been analyzed and understood, but what is never explained through naturalistic or materialistic methods or science is why they exist, or what enforces them. They “just are”, and that assumption is the biggest gap materialists make as they seek to explain everything without God. The very foundations of reasoning are the concepts that things are repeatable, and therefore testable and predictable, yet there is no explanation for why things are consistent, from a materialistic perspective. Believers in the one true God, on the other hand, have answers for all of those questions, and it is because we have answers to those questions that we can advance scientific understanding and practical application to our universe and to daily life. There is nothing in the theistic worldview that negates or limits scientific discovery, because we expect a consistent level of logic, predictability, order, material processes and that God wants us to intelligently utilize our world, the senses, and brains we are endowed with. We discover laws of physics, math, and science, and understand they exist and persist because there is a lawgiver. They are there for our benefit, and we are free to discover them and utilize them. To suggest otherwise is merely a statement from ignorance. Ignorance of the existence of God.

Claim: Science lives for and thrives and depends upon gaps to fill and some take a long time, but God was no more present in the explanation when the problem arose than when the natural explanation was found and is no more so now. Some gaps of knowledge in the past existed for centuries, but it was not proof of a god and those who thought it was, have since been shown that they were wrong as the gaps were (as always, naturally) filled. To continue to find gaps, claim god and then continually have them filled, naturally, and ignore them is crying wolf and people will see your game (if they haven’t already) and see right through it. Lack of knowledge in an area is not proof of God or anything and we have so often found this to be the case, with a natural explanation.
Reply: Question: what is the better explanation for the origin of the following things?

https://******************************/t2245p25-abiogenesis-the-factory-maker-argument#7904

- factory portals with fully automated security checkpoints and control
- factory compartments
- a library index and fully automated information classification, storage, and retrieval program
- computer hardware
- software, a language using signs and codes like the alphabet, an instructional blueprint,
- information retrieval systems
- information transmission systems
- translation systems
- complex robotlike machines
- taxis adapted for cargo transport and delivery, with GPS systems
- highways
- tagging programs informing taxis were to transport goods
- factory assembly lines
- error check and repair systems
- recycling machines
- waste grinders and management
- power generating plants
- power turbines
- electric circuits

Chance, or intelligent design ?

The cell is a factory - adios materialism.

1. Computer hard-drives with high capacity of digital data storage, software programs based on languages using statistics, syntax, semantics, pragmatics, and apobetics, and the elaboration of complex instructional blueprints through those software programs, and data transmission systems (encoding, sending, decoding), all operated through computers and interlinked computer networks, which prescribe, drive, direct, operate and control interlinked compartmentalized factory parks making products for specific purposes, full of autonomous, robotlike high-tech production lines, high-efficiency power plants, complex high-tech robots with autoregulation and feedback loops, producing products with minimal error rates, that are transported through GPS driven transport carriers to their destination, all driven through energy made by high rotative turbines and power plants, are always set up by intelligent agents designing those things for purposeful goals.

2. Science has unraveled, that cells, strikingly, contain, and operate through all those things. Cells are cybernetic, ingeniously crafted cities full of factories. Cells contain information, which is stored in genes (books), and libraries (chromosomes). Cells have superb, fully automated information classification, storage, and retrieval programs ( gene regulatory networks ) which orchestrate strikingly precise and regulated gene expression. Cells also contain hardware - a masterful information-storage molecule ( DNA ) - and software, more efficient than millions of alternatives ( the genetic code ) - ingenious information encoding, transmission, and decoding machinery ( RNA polymerase, mRNA, the Ribosome ) - and highly robust signaling networks ( hormones and signaling pathways ) - awe-inspiring error check and repair systems of data ( for example mind-boggling Endonuclease III which error checks and repairs DNA through electric scanning ). Information systems, which prescribe, drive, direct, operate, and control interlinked compartmentalized self-replicating cell factory parks that perpetuate and thrive life. Large high-tech multimolecular robotlike machines ( proteins ) and factory assembly lines of striking complexity ( fatty acid synthase, non-ribosomal peptide synthase ) are interconnected into functional large metabolic networks. In order to be employed at the right place, once synthesized, each protein is tagged with an amino acid sequence, and clever molecular taxis ( motor proteins dynein, kinesin, transport vesicles ) load and transport them to the right destination on awe-inspiring molecular highways ( tubulins, actin filaments ). All this, of course, requires energy. Responsible for energy generation are high-efficiency power turbines ( ATP synthase )- superb power generating plants ( mitochondria ) and electric circuits ( highly intricate metabolic networks ). When something goes havoc, fantastic repair mechanisms are ready in place. There are protein folding error check and repair machines ( chaperones), and if molecules become non-functional, advanced recycling methods take care ( endocytic recycling ) - waste grinders and management ( Proteasome Garbage Grinders )

3. Chemist Wilhelm Huck, professor at Radboud University, Netherlands: A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity. Cells, containing all those things are irreducibly complex. Without energy, information, or the basic building blocks fully synthesized, there would be no life. All this is best explained as a product of a super-intellect, an agency equipped with unfathomable intelligence - through the direct intervention, creative force, and activity of an intelligent cognitive agency, a powerful creator.


Claim: Parasites and who exposes who?
Your case study, like many, are good examples of complex structures. Question (to demonstrate open mindedness and searching for truth): How many times have gaps in scientific knowledge regarding evolution been discovered by a Creationist? So, regarding many of Michael Behe’s IC examples which have many hundreds of explanatory papers; there is nothing stopping a scientist who is a creationist from doing some research and discovering a natural explanation to something. Many believing Christians who are scientists contribute a lot to such findings. In fact, as far as I know, for every error that a scientist has inadvertently made, (or non-scientist that has been fraudulent for financial or notoriety gain) it has been someone who accepts evolution (and not creation) that has uncovered or exposed it. What does that say? That creationists aren’t following science very much and they are just parasitic, trolling through other people’s hard work for petty gain.
Reply: If you think only creationists reject evolution, you might know better after this:
Why Darwins theory of evolution does not explain biodiversity
https://***************************...ry-of-evolution-does-not-explain-biodiversity

Where Do Complex Organisms Come From?
https://******************************/t2316-evolution-where-do-complex-organisms-come-from


Claim: Here’s something I don’t know (Creationist). Let’s find out how (scientist).
Reply: Norman Geisler:
The creation-evolution debate is not religion versus science or the Bible versus science, it's about good science versus bad science. Likewise, it's not faith versus reason, its about reasonable faith, versus unreasonable faith.

Any worldview is limited in that it does not grant absolute truth, but only yields degrees of probability or likelihood. Bayesian inference is a method of statistical inference in which Bayes' theorem is used to update the probability of a hypothesis as more evidence or information becomes available. Bayesian inference has found application in a wide range of activities, including science, theology, and philosophy. After careful examination, all we can do is come to instant-deduction to the best explanation.

Claim: Try to find some positive evidence for a/your God and make predictions and test it and then you have some science that people can work with. I can share examples with you that would work if it helps, because there are multiple ways to tangibly test a god/supernatural/unexplained force.
Reply: How to recognize the signature of (past) intelligent actions
https://***************************...nize-the-signature-of-past-intelligent-action

Either reality, our physical existence emerged by a lucky accident, spontaneous events of self-organization by unguided natural events in an orderly manner without external direction, purely natural processes and reactions, or through the direct intervention and creative force of an intelligent agency, a powerful creator.

Can:

randomness
unpredictable events
lack of orderly patterns
unfollow or intelligible patterns or combinations
improbable events
unpredictable movements
unplanned events
accidents
Spontaneous generations
control-less events
chaos
unguided
directionless

do the following ?

1. Produce objects in nature very similar to human-made things?
2. Make something based on mathematical principles?
3. Generate systems and networks functioning based on logic gates?
4. Create something purposefully made for specific goals?
5. Come up with specified complexity, the instructional blueprint, or a codified message?
6. and upon this, create irreducible complex and interdependent systems or artifacts composed of several interlocked, well-matched parts contributing to a higher end of a complex system that would be useful only in the completion of that much larger system?
7. Create order or orderly patterns
8. Invent hierarchically arranged systems of parts
9. Create artifacts that use might be employed in different systems ?(as the wheel, used in cars and airplanes )
10. Fine-tune systems and things?

That is all that we observe in the natural world, and it seems to me, intelligence explains following much better than no intelligence:

1. Machines, production lines, factories, and factory parks
2. Physical laws
3. The gene regulatory network
4. The eye to see, the ear to listen, the nose to smell, the brain to think
5. The genetic and epigenetic information
6. The flagellum, the Cell, the eye, etc.
7. Fibonacci curves are seen in Seashells, plants, cactus, etc.
8. Atoms - molecules - molecular machines - cells - multicellular organisms,
9. Sonar systems used in bats, dolphins, whales
10. The BigBang, cosmological constants, the fundamental forces of the universe, our galaxy, the earth ?

I have not enough faith to be an atheist.


Engagement warning.
I suggest that anyone who engages with Otangelo Grasso considers what they are getting into in terms of time, effort, motive and response and consider what you hope to gain from it and strap themselves in. You have been notified and may appear on his site! Here is some correspondence between Otangelo and bio-chemist professor Larry Moran. And Otangelo has been a regular Youtube discussion person on several shows:

https://sandwalk.blogspot.com/2017/02/trying-to-educate-creationist-otangelo.html


Claim: Who are YOU?
There are those who sit back and wonder at the mystery of things. Many of us. There are those who simply and lazily or like sheep or parasites, just attribute things to the unknown and many like to give this unknown a name, having done little if anything themselves. There are others who also try or want to find out in as much detail as they can about how things work. They have, over the centuries, unfolded the mystery of so much, which has often allowed us to make progress and make the understanding of science so much more exciting.
Reply: The science fathers were Christians.
https://******************************/t1452-what-good-has-the-christian-faith-brought-to-us
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



Claim: A starter for you on this post topic, but you need to target specialists.

It would be great if you engaged with this process, with an open agenda, acknowledging and correcting and updating and accepting new knowledge to those people and on your site. Here’s one of those (this is a sneak, pre-publication preview) on the post topic and please do read the many other past, present and future articles addressing this (that don’t support your gaps of natural impossibility) and include them on your site and remove any of your arguments that they cover/explain:

https://www.biorxiv.org/content/10.1101/2020.09.01.277582v1.full.pdf

I am not engaging otherwise in your article as it presents no evidence to consider (just alleged gaps) and I know so little about it, but I can assist in helping get you in contact with the authors or any of the authors in their research if it helps. They are your target audience on more complex areas, not lay folk. After you have engaged with specialists and demonstrated that you understand, have read the literature on it and have baffled them with your brilliance and they sing your praises, bring/share it here. People like evidence and compelling research. Not someone who just points and says, ‘well how do you explain that then?’.
Reply: Sure. Put them in touch with me.


A lack of responses definitely does not equate to, ‘people have no responses’, but a wrong site to share it.

Claim: If people do not respond to your posts, it may well be that there are no specialists who are here/able to respond or that people think you have nothing or little to present. No response on multiple sites does not mean people have no reply, but that it is not the place to post it. I do emphasise that there are multiple research papers, mostly peer reviewed, that do directly address the things you raise, and I’d be very keen to see you reflect, fairly, those responses after you read them.
Reply: I have done so with Dimiter Kunnev, and he has not engaged, and not replied to my inquiries. He just has accused me of doing cherry picking. See here:
A reply to Dimiter Kunnev
https://***************************...-through-ribosomes-amazing-nano-machines#8008



Claim: You use statistics which are totally unknowns.
Reply: No. They are known.

https://***************************...g-through-unguided-natural-random-events#5399

Bit by Bit: The Darwinian Basis of Life
Gerald F. Joyce Published: May 8, 2012
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001323
Even the sequence of a simple ribozyme of 40 mer has 10^24 possible compositions. To represent all of these compositions at least once, and thus to establish a certainty that this simple ribozyme could have materialized, requires 27 kg of RNA chains, which classifies spontaneous emergence as a highly implausible event.

For an enzyme to be functional, it must fold in a precise three-dimensional pattern. A small chain of 150 amino acids making up an enzyme must be tested within the cell for 10^12 different possible configurations per second, taking 10^26 ( 1,000,000,000,000,000,000,000,000,000) years to find the right one. This example comprises a very, very, very small degree of the chemical complexity of a human cell.

Claim:So often, the erroneous stats did not even apply if the scenario that is presented were true, which they are so often not. It is emotionalising the case to try to convince people of something which is not there by scientific presentation. I don’t even know how you could present a paper on a lack of knowledge, rather than additional knowledge, which is what you are trying to do. ‘Here is a possible explanation’ rather than your, ‘I can’t explain this’ is the way to go. If you can’t present a positive knowledge case to peer review, why should people take you seriously or not equally consider any other conspiracy or proposal lacking evidence?
Reply: Such a paper has just been published in the journal of theoretical Biology. It has gone through regular peer review, and posits explicitly intelligent design.

Using statistical methods to model the fine-tuning of molecular machines and systems
https://www.sciencedirect.com/science/article/pii/S0022519320302071?via=ihub

Claim: I’m being picked on because…I am hard pressed to think of any Creationist who truly or independently came to the creation conclusion based on a sound scientific education and understanding and with no theological influential play involved and who understands evolution even at a fairly low level.
Reply: See here:

Where Do Complex Organisms Come From?
https://******************************/t2316-evolution-where-do-complex-organisms-come-from

How does biological multicellular complexity and a spatially organized body plan emerge?
https://***************************...ty-and-a-spatially-organized-body-plan-emerge

BrachioPEP said:

Just wondered if you have this related educational video (and many mentioned publications) on your site for people to also consider? It also explains a lot, iof not most or all of what you claim are gaps in knowledge on the formation and evolution of molecules. I don’t blame you for omitting it and painting a very lop sided image, because your agenda rejects it for theological and not scientific reasons and theology trumps science for you. Straw manning just puts people off and will lead to them not trusting you for representing things honestly.

Click to expand...

i made a video reply to that video.