There's not enough time in the world for mutations to create new proteins

originally posted by: cooperton

originally posted by: quintessentone

Yet there may be average mutation rates, then there may be rare mutation rates. Maybe nobody can get the math right because it's all just theory.

They need trillions and trillions of multipliers though. The mutation rate could be trillions of times more likely and all the time in the world is still remarkably short.

27,000,000,000,000,000,000,000,000,000,000,000,000,000,000 years is a lot of time. No one so far has argued the details of the numbers, because I got the numbers from peer-reviewed journals - their gospel.

Sinner is a big word with many definitions and/or interpretations from different belief systems.

To me it means a deviation from archetype. Archetype being Christ's philosophy. Deviate from the user manual and you're susceptible to the issues that coincide with not being joined to the perfect.

So all other people's of the world believing in their creationist theories, spirits and/or Gods, or multiple gods eminating from one God, are deviating from the user manual? No, they make their own user manual and theirs is not a deviation from THEIR archetype.

Christ's philosophy was born from intermingling of other people's philosophies/religions including retaining some aspects of Judaism including there being only one God/Creator, if we are to believe in Jesus' world travels and learning how others live and worship, which I believe since Jesus originally strayed away, or questioned his religious teachings in Judaism.

However, it appears not all people's believe in a singular one power or creator as in Hindiusm:

In Hinduism, dharma denotes behaviours that are considered to be in accord with Ṛta—the "order and custom" that makes life and universe possible. This includes duties, rights, laws, conduct, virtues and "right way of living". The concept is believed to have a transtemporal validity, and is one of the four Puruṣārthas.

en.wikipedia.org...#:~:text=In%20Hinduism%2C%20dharma%20denotes%20behaviours,one%20of%20the%20four%20Puru%E1%B9%A3%C4%81rthas.

Transtemporal validity: (or taking the passing of time out of the equation - sorry for all the text but this read is interesting)

In order for phenomenal consciousness to be to the moments as the projector is to the frames of the film it would have to have access to all the moments, just as the projector has access to all of the frames, and the whole problem is that there is no part or aspect of the observer that has
access to anything other than the specific moment in which that version of that observer exists. However, if phenomenal consciousness were an emergent property not of the body, but of the system of moments as a whole, it would be perfectly positioned to experience moment after
moment, and reality would be exactly as it seems to us to be. This is closely akin to Chalmers' deduction about the necessary nature of phenomenal consciousness, which places it on a par with the fundamental physical properties of the universe

I suggest that a theory of consciousness should take experience as fundamental ... we will take experience itself as a fundamental feature of the world, alongside mass, charge, and space­time. If we take experience as fundamental, then we can go about the business of constructing a theory of experience.

As Mermin proposes, “... consciousness is beyond the scope of physical science, at least as we understand it today.” (1998,7). Nonetheless, clearly our accustomed concept of the universe seems nothing like the right kind of thing to give rise to consciousness. The idea of a space­time of stars and galaxies giving rise to sentience seems plainly ludicrous. This universe, however, is only one tiny and likely infinitesimal aspect of the totality of all possible universes, the Everettian universe as multiverse, and this is not physical in the ordinary sense of the word. It is the simultaneity of all possible physical universes, thus it is total indeterminacy. Ascribing phenomenal consciousness to a cosmos of space and galaxies plainly is absurd, but ascribing it to the totality of all possibilities is an entirely different kind of concept.

Neither the transtemporal phenomenal consciousness nor the body­mind of an observer constitutes a transtemporal observer, only in the juxtaposition of these two aspects of the observer, the experiencer and the experienced, does observation take place. Thus the definition
of an observer must include both transtemporal phenomenal consciousness and a body­mind system which registers and records the structured sensory experiences it has produced; the latter being the basic process of access consciousness, the production of an accessible information structure, the observation that is experienced. Therefore the only possible observer of the passage of time is a composite entity having both temporal and transtemporal properties, both phenomenal consciousness and access consciousness. On this view this is the missing piece to the puzzle which has made the comprehension of the nature of the observer, and observation, so problematic. Subjective transtemporal reality is the phenomenon occuring in the juxtaposition of the inherent duality of access consciousness and phenomenal consciousness, that which is experienced and that which experiences the experienced. Each transtemporal observer is a phenomenon encompassing both. The result is observation as a process, the experiential life of the transtemporal observer

philsci-archive.pitt.edu...

If we think of ourselves as being transtemporal observers then we have a new way of theorizing quantum mechanics and perhaps God's grand design, then your math calculations are not necessary nor are evolutionary theories spanning millions to billions of years.

Knowing more about all this science and the math odds make people who believe in evolution, a faith based dogma equal to those that believe in some form of creation. Both ideologies have scientific support, basically a person worlds perspective decides which one they emotionally want to believe more at this point, not pure logic.

However if the creationists are wrong, they go back to the ground just like the evolutionist when they die with no hope of life after death. BUT if the evolutionists are wrong they end up in the same spot, however the creationist picks up eternal life from God.

So I lose nothing if I am wrong, but the unbeliever loses forever if he is wrong, due to his judgement........what a huge gamble just based on emotionality of a theoretical dogma.

Place your bets !

a reply to: Blue_Jay33

Unless we believe ourselves to be the creators of everything.

a reply to: cooperton

So that's a roundabout way of saying,

No, sinners should not have children.

And, yes a child through no fault of its own can miss out on God's gift?

originally posted by: cooperton
Just like scientists can defame the name of science, that doesn't mean we throw out science entirely just because of a few mis-representative emissaries.

Throw it out entirely, maybe not. Disregard much that doesn't fit a predetermined narrative, absolutely. Not trying to pick on you personally, just making a broad observation.

For example. I know a guy who loves technology. Is always so impressed with the latest cameras, or cell phones. Is amazed at how far we've come in medicine, surgery, etc.

But, because of his religion, and what its lead him to believe without any actual attempts at understanding it, evolution is absolute bull#. It's from the devil trying to take glory away from God.

So, basically. Trust the science when it's something you like, disregard it and attribute it to a cult when it doesn't.

And as far as a few mis-representative emissaries, no doubt there are bad actors in many fields, but many can be found in "creationist science".

The science community, and therefore the world at large, will accept proven evidence.

Creationists accept nothing if it's not in the bible or can be manipulated out of it.

a reply to: TerraLiga

Ancient believers in Amun (creator par excellence, of matter out of nothing) were creationists long before there was a Christian Canon of Scripture. I don't think they manipulated anything out of the Bible.

originally posted by: TerraLiga

Creationists accept nothing if it's not in the bible or can be manipulated out of it.

Name the empirical evidence that I am ignoring.

a reply to: cooperton

That would take more time than I have available.

Let's start with the age of the universe (currently under review, but measured in billions of years, not thousands).
The age of the Earth.
That biology, given the conditions and time, could occur by chance.
Humans and dinosaurs existed together.
That your god, above all others before it and since, not only exists but is the only god.

Let's start with those.

a reply to: cooperton

Name the empirical evidence that I am ignoring.

Anything that doesn't agree with you.

www.ncbi.nlm.nih.gov...

Titled: Protein evolution speed depends on its stability and abundance and on chaperone concentrations.

I get only enough of this to know it refutes the premise and provides a different answer. Not the answer, just a different one.

Significance.

Some biological evolution is slow (millions of years), and some is fast (months to years). The speed at which a protein evolves depends on how stable a protein’s folded structure is, how well it avoids aggregation, and how well-chaperoned it is. What are the mechanisms? We compute fitness landscapes by combining a model of protein-folding equilibria with sequence-change dynamics. We find that adapting to a new environment is fastest for proteins that are least stably folded, because those sit on steep downhill parts of fitness potentials. The modeling shows that cells should adapt to warmer environments faster than to colder ones, explains why increasing a protein’s abundance slows cell evolution, and explains how chaperones accelerate evolution by mitigating this effect

Abstract:

Proteins evolve at different rates. What drives the speed of protein sequence changes? Two main factors are a protein’s folding stability and aggregation propensity. By combining the hydrophobic–polar (HP) model with the Zwanzig–Szabo–Bagchi rate theory, we find that: (i) Adaptation is strongly accelerated by selection pressure, explaining the broad variation from days to thousands of years over which organisms adapt to new environments. (ii) The proteins that adapt fastest are those that are not very stably folded, because their fitness landscapes are steepest. And because heating destabilizes folded proteins, we predict that cells should adapt faster when put into warmer rather than cooler environments. (iii) Increasing protein abundance slows down evolution (the substitution rate of the sequence) because a typical protein is not perfectly fit, so increasing its number of copies reduces the cell’s fitness. (iv) However, chaperones can mitigate this abundance effect and accelerate evolution (also called evolutionary capacitance) by effectively enhancing protein stability. This model explains key observations about protein evolution rates.

You used an example of proteins that evolve really slow, but failed to acknowledge varied rates of evolution due to other factors like environment. Because you refuse to acknowledge environment causes adaptation. That's the definition of a false dilemma.

And also seems like something the prototypical devil would do. Purposely avoid things that refute their claim and mislead people with fallacy anyway. It is manipulative and deliberately deceptive at very least.

The snake-head scoffs at their ideas being contested, will refuse to acknowledge other answers as valid, and then continue to push their own will and agenda, even after being discredited.

originally posted by: Degradation33
Adaptation is strongly accelerated by selection pressure, explaining the broad variation from days to thousands of years over which organisms adapt to new environments. (ii) The proteins that adapt fastest are those that are not very stably folded, because their fitness landscapes are steepest.

You bolding this part alone shows You don't know what the paper I posted in the original post is referring to. Your bolded part here is referring to selection of traits, which of course can happen relatively quickly with allele drift, think of black and white people, the difference is allele drift. They're still human though, and these alleles always existed within the human genome.



The paper I posted is not referring to selection, which is different than mutation


Your paper does mention the need for mutations, but it doesn't emphasize the fact that a simple mutation is incapable of adding a functional sequence. The difference is between a simple mutation, and the realistic amount of mutations needed to add an active site to a protein. The other reason my paper has remarkably lower odds is because it also takes into consideration the improbability of mutating a specific gene that would so happen to generate a relevant function to the organism. That's why my paper I posted emphasizes:

"this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10e77, adding to the body of evidence that functional folds require highly extraordinary sequences."
source

You used an example of proteins that evolve really slow, but failed to acknowledge varied rates of evolution due to other factors like environment. Because you refuse to acknowledge environment causes adaptation. That's the definition of a false dilemma.

Now that you realize the difference between a single mutation and the plethora of mutations needed to create a new active group on a protein, will you consider changing your mind? Especially since you said:

And also seems like something the prototypical devil would do. Purposely avoid things that refute their claim and mislead people with fallacy anyway.

Will you admit your paper is not relevant to actual active site generation in proteins? This is the part that actually allows a protein to perform an enzymatic reaction thereby having a biochemical effect on the body. This has to be the case because there are multitudes of interdependent enzymes that work together in the body... Also further lending creedence to the idea that these could not have evolved in step-by-step manner because the entirety of a biochemical cascade is needed for proper functioning.

The number of stars you received despite mis-representing actual biological reality shows how many blind followers there are in evolution, desperate for their beliefs to be right.

originally posted by: TerraLiga
a reply to: cooperton

That would take more time than I have available.

Let's start with the age of the universe (currently under review, but measured in billions of years, not thousands).
The age of the Earth.
That biology, given the conditions and time, could occur by chance.
Humans and dinosaurs existed together.

Let's start with those.

You didn't list empirical evidence, you just suppose that the mainstream theory is automatically right lol. You have to give the empirical evidence that supports those assertions, do it in your own words. Stay on topic and only refer to the point "biology could occur by chance". You see how degradation33 at least tried to use a relevant article to try to debate me? Rather than just using generic phrases found in kids books.

a reply to: cooperton

You didn't least empirical evidence, you just suppose that the mainstream theory is automatically right lol. You have to give the empirical evidence that supports those assertions, do it in your own words.

Just speaking for myself (non-specialist, non-polymath):

I live in a culture which is heavily influenced by memes (a word coined by Dawkins, Biologist). The memes are bits of information floating around that we pick up. The info may be accurate or wildly inaccurate. Whatever the case may be, our thinking and even Worldview are influenced.

We do not know the source of each meme so as to offer the citation.

Bottom line:

I realize this seems lame, but I would rather believe a consensus (majority opinion) of actual specialists rather than not. And I live in hope that when facts become clearer in these specialized disciplines that they get passed down to people like me.

originally posted by: pthena

Just speaking for myself (non-specialist, non-polymath):

I live in a culture which is heavily influenced by memes (a word coined by Dawkins, Biologist). The memes are bits of information floating around that we pick up. The info may be accurate or wildly inaccurate. Whatever the case may be, our thinking and even Worldview are influenced.

We do not know the source of each meme so as offer the citation.

Bottom line:

I realize this seems lame, but I would rather believe a consensus (majority opinion) of actual specialists rather than not. And I live in hope that when facts become clearer in these specialized disciplines that they get passed down to people like me.

Yes I don't mean to denigrate people who rely on expert advice because they haven't taken biology courses or studied it vigorously, I only use that as a defense if someone is calling me an idiot while also not being able to even assess what I am saying or explain their own scientific beliefs with evidence. Terraliga does this a lot. He doesn't actually know how to debate science, but calls me dumb merely because I am expressing an opinion different than the mainstream. So naturally I will point out the irony that he is just blindly believing experts (which is an appeal to authority fallacy). Notice how he doesn't debate the actual numbers, or the empiricism.

a reply to: cooperton

just blindly believing experts (which is an appeal to authority fallacy)

I'll have to look that up.

The way I see it is that objections offered to your presentation give you the chance to present more. Some things are easier to explain as answers to questions.

Example: Khalil Gibran's The Prophet

originally posted by: pthena

I'll have to look that up.

The way I see it is that objections offered to your presentation give you the chance to present more. Some things are easier to explain as answers to questions.

Example: Khalil Gibran's The Prophet

Yes good point and also one of my favorite books. I'm only hard on someone though if they are mean-spirited. I'll still even answer their question / objection though. When I really got into debating these sorts of topics I was shocked how many people do rely on mostly blind belief, and were unwilling to reconsider based on new evidence.

For example, Soft tissue in dinosaur bones is enough to show the evolutionary timeline is wrong, yet I had trained archaeologists/geologists yelling at me that it's not soft tissue, despite it still being obviously stretchy cartilage. If they were objective this should excite them, new evidence that will have to change things. But I realized soon that many are just as dogmatic as in the days of Galileo

a reply to: cooperton

I'm only hard on someone though if they are mean-spirited.

I'm trying to tone down my own mean-spiritedness. At the moment I'm fighting scared-spiritedness.

I read the whole Wikipedia article on appeal to authority fallacy. There was a link to Asch_conformity_experiments.

The Asch conformity experiments are often interpreted as evidence for the power of conformity and normative social influence,[14][15][16] where normative influence is the willingness to conform publicly to attain social reward and avoid social punishment.[17] From this perspective, the results are viewed as a striking example of people publicly endorsing the group response despite knowing full well that they were endorsing an incorrect response.[18][19]

Similarly, Jerry M. Burger admits the normative influence effect of the experiment in Chapter 21 of Noba online book.[20] He mentioned that people follow the crowd to avoid potential criticism. During Asch's experiment, participants choose the wrong answer to keep the association with the group. The demonstration in this experiment broadens people's understanding of the large application of normative influence. To stay consistent with other group members, people may follow a trend that is apparently wrong. Moreover, the behavior of normative conformity may reduce when the individual response is not accessible to other people.[21] This phenomenon further stresses the social role in normative influence.
...
[ order of appearance in article switched for clarity ]
Written responses
Asch also varied the method of participants' responding in studies where actors verbalized their responses aloud but the "real" participant responded in writing at the end of each trial. Conformity significantly decreased when shifting from public to written responses.[4]

My hopes are somewhat renewed by that paragraph that I quoted last.

People have a chance to disengage occasionally and examine their perceptions and conclusions in private. Less social pressure. According to the Gospel accounts Jesus did that too. That's the only example that comes quickly to the top of my head.

a reply to: cooperton

That's was actually pretty good.

I'll be honest on this, I don't fully grasp what you're arguing. I don't know crap about proteins. I'm not a molecular biologist. I just looked up "How fast can proteins mutate" or something like that into Google and plucked the first response that said something that seemed good enough.

I honestly didn't really read it.

So this time I searched "How fast can mutations create new proteins" in google and got this.

www.ncbi.nlm.nih.gov...

Phenotypic mutations contribute to protein diversity and shape protein evolution

How is that wrong, how does it not apply, and what am I still missing? I really don't know.

You do things like take the total number of bacteria on earth and then use an expected rate and then plug numbers until it's something irrefutable for intelligent design. The way you go about it and use statistics and results to validate other things seems erroneous to say the least. But it's super technical so how would anyone know?

So please cut all the freaking psychobabble and explain the argument more simply. For the simpleton. In simple terms what are you trying to say is impossible without god?

Are you saying proteins could never reach the point of drift because there's too many possibilities for initial configuration and that could never happen by chance?

What is the dilemma that requires God to fix?

Please dumb it down.

I can get really technical and wordy with geology. So if you care to debate the age of the earth that's one I wouldn't get massacred on, or have to look up things like "active site". That's some complex molecular biology stuff. I don't want to read that much. Wow though.


On a side note.

They said No Man's Sky was going to be so large nobody would be able to find another civilization or previously visited planet. And it happened right away, within a week. 2⁶⁴ = 18,446,744,073,709,551,616, astrominical odds cut through like butter. 18.4 Quintillion to one.

And all you really need is the first freak anamoly. All we need do is get to LUCA.

I maintain that using even astronomical statistical odds to negate something's likelihood of occurring is still a false dilemma. Against all odds can still happen quickly.

For meta-fun:

Maybe those freak statistical anomalies are the closest thing to a supercausal intelligence you will get.

Perhaps design is through random anamoly (statistical glitches) and not of a specific intelligence. It makes the random less random, without specific intent. No design, just a random interjection now and then.

One could say god's "supercausal" glitchy existence made No Man's Sky immediately defy all the predicted odds too. Albeit randomly and without intended consequence.

Or you can say it is influenced by consciousness.

You could even add human intention to that and say, "The Hubris of the game designers believing no one would find each other made that random glitch more likely to happen."

But now your saying intent controls wave collapse. Which is a whole new metaphysical can of worms.

Of course, you're left to ask, "Is this really happening from outside the causal universe, or am I just viewing significant randomness as divine again?"

a reply to: Degradation33

Maybe those freak statistical anomalies are the closest thing to a supercausal intelligence you will get

I'm fairly certain that that is pretty much the theme of Philip Pullman's His Dark Materials trilogy.

It's been a few years since I've read it but I was very much struck by Dr. Mary Malone's explanation in the second book, that the alethiometer worked the same as I Ching.

But then the author is an atheist. And I'm confused. Maybe it doesn't matter what we label ourselves to be.

a reply to: cooperton

Coop, you have made this religious pursuit your life's work. Your belief that the chances of biology forming from chemistry is zero forms the basis of everything you post. Would you not agree that if your 'discoveries' are valid you should publish them for professional scrutiny? Why, for the life of me I simply do not understand, would you post your theories on a conspiracy website?

The summary of your disagreements with the professional consensus is probability and time - neither of which you agree with. I have a passing knowledge of chemistry and biology, but my particular sport (now sadly passed on a professional capacity) is physics, which uses probability and time as two cornerstones forming the basis of knowledge. You casually dismiss these possibilities as if the general scientific community is foolish.

I propose that instead of proving negatives, you prove the existence of your god, therefore putting this entire debate to bed.

originally posted by: Degradation33

explain the argument more simply. For the simpleton. In simple terms what are you trying to say is impossible without god?

Are you saying proteins could never reach the point of drift because there's too many possibilities for initial configuration and that could never happen by chance?

Yeah That's what I am saying, new code will not be able to make it to the point of being selected or not due to the immense probability against the initial configuration from ever forming. That's what they are referring to in the probabilities described in this paper. The active site is a portion on a protein that allows it to form together with other proteins to create functional machinery, as well as make reactions happen such as creating energy from calories.

Therefore, those odds would have to hit many, many times, making it even more astronomically implausible. Creating a host of co-operative micromolecular machinery to allow independent life in a cell is not possible for the following logic. If you wanted to build an engine, it requires multiple pieces all working in proper synchrony. It's the same with proteins in our cells:



This motor-like protein is made up of many smaller proteins that fit together to allow it to act as a motor. These protein pieces are precision fit, with various "active sites" that allow them to stay together and perform a function. So this will not function if you are missing a piece, which begs the question, how did it evolve into existence in a piece-by-piece manner? One portion of it is useless without the rest of the pieces.


The probability of creating an active site by mutations is very difficult due to how specific these active sites need to be in order to perform a precise function. An active site on a protein requires about 300 DNA units on average to be able to code for its production. The odds of this paper are actually referring to a much smaller than average active site, so these are the highest probabilities you will see for active site formation.The thing with active sites also is that they often have to be complete to have proper function, so there would be nothing that would naturally select this developing strand until it was complete, thereby offering no favorable advantage to selecting this beyond base probability.

What makes these odds even more insurmountable, is that protein chains do not grow spontaneously in water, so now it is very apparently impossible for life to come from non-life because there's no known mechanism that would be capable of even sequencing proteins without the proteins that exist in cells to bond them together... It would be like creating a Ford truck except there's no Ford truck factory and you don't know how to make any of its parts and you're also deaf and blind.

So this time I searched "How fast can mutations create new proteins" in google and got this.

www.ncbi.nlm.nih.gov...

Phenotypic mutations contribute to protein diversity and shape protein evolution

How is that wrong, how does it not apply, and what am I still missing? I really don't know.

That isn't referencing the mutation of an active site, it is referring to mistakes that happen when the protein is being made from the code. This and the other paper are referring to mutations in their simplest sense, but this sort of simplicity cannot create the complexity such as the ATP synthase video shown above, or this thing that transports materials around the cell:



The active site is what allows its feet here to be able to temporarily bond and unbond to the scaffolding that it's walking on. The active site is around 380 amino acids (protein pieces) long, meaning the genetic code that codes for it is around 1,140 DNA pieces long. This would be a much larger active site than the one used in the reference paper, meaning it would be even less probable to form. plugging that into the probability formula of hitting a sequence of 1,140 DNA pieces, given a 1/4 odds due to 4 possible options of DNA pieces: (1/4)^1140 = 1-in-pretty-much-infinity... Online calculators can't even register the number because it's so low.



So if these new DNA sequences to create working active sites cannot be made by chance, then they must have been made by something intelligent. I believe the Creator is extra-dimensional, able to create whatever as easily as we create vast landscapes in our dreams every night. This is good news, we have purpose and meaning in life, and this intelligent Creator allows us perpetuity of consciousness after death.