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

originally posted by: cooperton

originally posted by: Venkuish1

1) Nowhere in your OP you identified which part comes from the paper

lol what? it's even in their abstract:

"the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, 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."

I use the 10e77 and multiply it by other known factors

I admire this someone who gave you a star

considering you got 8 stars for saying that density and weight are interchangeable, I think the star system has lost its purpose

originally posted by: NovemberHemisphere

The 1 in 10^77 probability is based on a fundamental misunderstanding of protein selection. In this scenario proteins are selected by function not structure, different structures have been shown to sometimes give the same function.

They said in the paper the odds of making any functional group is 1 in 10^64. So there's not even enough time in the universe to have made one functional group, regardless of function

Your arguments ok this thread (and the other threads you are taking part) have been refuted again and again.

You have misrepresented the paper and the author by giving the impression the author has come to a conclusion that he never made in the first place. Instead it was your conclusion who you copy pasted from your reddit account.

My points which I will include again are the following:

1) Nowhere in your OP you identified which part comes from the paper and which part is yours and you didn't event mention the conclusion of yours has come from your reddit thread and it's not the conclusion of the author. You didn't mention at all you had a reddit account where you created similar threads.

2) You have only linked the abstract of the scientific paper and not the whole article which you can easily find online (from sciencedirect). This way the reader couldn't find out what the paper is about and the conclusions of the author.

3) In another post of yours you even made a statement of how is it possible this scientific paper allowed to be published giving the impression again it shouldn't have been published under normal circumstances as it comes to the conclusion there is not enough time in the world for mutations to have created new proteins. This is a complete misrepresentation of what the author has said.

4) We don't know whether the 'math' produced and the article is yours or has come from someone else in your reddit thread given this thread is a copy paste of your thread in reddit.

5) You have presented the figure given by the author as being a fact although it is an estimation (that's a key point). You base your entire thread on misrepresenting just one scientific paper

This is a complete misrepresentation of the author and everyone can see it. In your mind you want desperately to come to a conclusion there isn't enough time for mutations to create new proteins. This isn't what the author said and you didn't include the power in your OP but just the abstract. You completely forgot to include the rest of the it like the following paragraph

Within these constraints, though, specific residue assignments were essentially random, resulting in numerous disruptive changes throughout the encoded proteins. This is an example of the reverse approach, in that it uses a natural sequence as a starting point but, because the produced variants carry extensive disruption throughout the structure rather than just local disruption, they provide reliable information on the stringency of functional requirements. The prevalence of functional chorismate mutases among sequences carrying the specified hydropathic pattern was estimated to be just one in 10^24

And no you are wrong as you had the conversation with the other two posters who were saying that heavier and more dense are used interchangeably in every day life and this is true in relation to object dink in water. Every day terminology could be slightly different.

originally posted by: Venkuish1

You have misrepresented the paper and the author by giving the impression the author has come to a conclusion that he never made in the first plac.

I used his data to make a conclusion along with other known estimates such as mutation rates and the approximation of all bacteria on the planet. Where specifically was my math wrong?

Your arguments ok this thread (and the other threads you are taking part) have been refuted again and again.

Where specifically was my math shown to be wrong? You haven't refuted anything lol, you haven't shown why any of my calculations were incorrect, you're just yelling that they must be wrong because they defy your belief system.

originally posted by: cooperton

They said in the paper the odds of making any functional group is 1 in 10^64. So there's not even enough time in the universe to have made one functional group, regardless of function

They said in what paper? There is a very clear misunderstanding here of how and why proteins form in the first place and what motivates them to fold or find function. You can pretend to be as certain as you want to, but neither the science or the math checks out. Your theory is just chalk full of assumptions- you can't provide any corroborating sources to any of it.

originally posted by: cooperton

originally posted by: Venkuish1

You have misrepresented the paper and the author by giving the impression the author has come to a conclusion that he never made in the first plac.

I used his data to make a conclusion along with other known estimates such as mutation rates and the approximation of all bacteria on the planet. Where specifically was my math wrong?

Your arguments ok this thread (and the other threads you are taking part) have been refuted again and again.

Where specifically was my math shown to be wrong? You haven't refuted anything lol, you haven't shown why any of my calculations were incorrect, you're just yelling that they must be wrong because they defy your belief system.

You have been misrepresenting the paper and his author and anyone can see what was written hasn't come from the author but from your erroneous assumptions despite the fact you tried hard.

There is nothing in the scientific literature which provides the assumptions and conclusions you have made. Not a single paper arguing there is not enough time for mutations to create new proteins.

You have misunderstood how proteins form and how they fold to become functional and what kind of tasks they perform. Not even once you have mentioned the amount of proteins that are found in a human cell which is enormous and on the tens of thousands per cell showing clearly the opposite of your debunked conclusion which you have come up with by misrepresenting the author of the paper.

sitn.hms.harvard.edu...

There are 20,000 to over 100,000 unique types of proteins within a typical human cell. Why so many? Proteins are the workhorses of the cell. Each expertly performs a specific task. Some are structural, lending stiffness and rigidity to muscle cells or long thin neurons, for example. Others bind to specific molecules and shuttle them to new locations, and still others catalyze reactions that allow cells to divide and grow. This wealth of diversity and specificity in function is made possible by a seemingly simple property of proteins: they fold.

a reply to: cooperton

Your argument here is as good as the one you made earlier in the threads when you claimed the universal law of gravitation is off by 2,000% which isn't true. There is a hidden mass in the galaxies called dark matter.

Same is true with your understanding of evolution where viruses don't evolve to become other typeof viruses which shows why you don't understand the basics.

And the same is true when you and other creationists are asking why monkeys haven't evolved to become humans (because we have descended from monkeys).

There is a fundamental misunderstanding of all concepts and principles in science which results from lack of basic education and the belief in the alternative but debunked arguments offered by creationism.

a reply to: cooperton

New enzyme discovered...


phys.org...#:~:text=The%20new%20enzyme%3A%20PET46&text=Structurally%2C%20the%20enzyme%20diffe rs%20significantly,that%20degradation%20can%20be%20continuous.

Using a metagenomic approach, the research team has identified and biochemically described the PET-degrading enzyme PET46 from a non-cultured deep-sea microorganism for the first time. This involved identifying the gene from a deep-sea sample based on similarities to known sequences, synthesizing the corresponding coding gene, producing the protein in the bacterium Escherichia coli and then studying it biochemically and structurally.

PET46 has many unusual properties and adds to the scaffold diversity of PET-active enzymes. Structurally, the enzyme differs significantly from those previously discovered. For example, it has the ability to degrade both very long-chain PET molecules, known as polymers, and short-chain PET molecules, known as oligomers, which means that degradation can be continuous.

Among other things, PET46 uses a completely different mechanism for substrate binding than previously known PET-degrading enzymes. The researchers describe an unusual 'lid' of 45 amino acids above the enzyme's active center as crucial for binding. In other PET enzymes, aromatic amino acids close to the active site are typical.

Do you see how bogus your logic is? You argued that the chance of formation of biologically useful proteins is impossible just like all other creationists do. Here you have another new useful protein that debunks your great 'math' based on your great 'assumptions'.

originally posted by: NovemberHemisphere

"They said in the paper the odds of making any functional group is 1 in 10^64."

They said in what paper? There is a very clear misunderstanding here of how and why proteins form in the first place and what motivates them to fold or find function. You can pretend to be as certain as you want to, but neither the science or the math checks out. Your theory is just chalk full of assumptions- you can't provide any corroborating sources to any of it.

I showed you the source:

" The prevalence of low-level function in four such experiments indicates that roughly one in 10(64) signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences."

link

So this is essentially saying that the odds of forming any working domain at all is 1 in 10^64, whereas the odds of forming a working domain that performs a specifically needed function is 1 in 10^77.

originally posted by: Venkuish1

You have been misrepresenting the paper and his author and anyone can see what was written hasn't come from the author

I used the numbers that they calculated for the probability of randomly mutating a working functional group on a protein. This is how science works, you use data from researchers who have done the work in specific fields, and apply it to the real world.

originally posted by: Venkuish1
a reply to: cooperton

New enzyme discovered...


phys.org...#:~:text=The%20new%20enzyme%3A%20PET46&text=Structurally%2C%20the%20enzyme%20diffe rs%20significantly,that%20degradation%20can%20be%20continuous.

Yeah a new enzyme was discovered, so what? It wasn't shown to have evolved in a lab setting. A novel functional group emerging through random mutation in a lab has never been seen before, this is due in part because the rarity of such an event is estimated to be about 1 in 10^64

originally posted by: cooperton

originally posted by: NovemberHemisphere

"They said in the paper the odds of making any functional group is 1 in 10^64."

They said in what paper? There is a very clear misunderstanding here of how and why proteins form in the first place and what motivates them to fold or find function. You can pretend to be as certain as you want to, but neither the science or the math checks out. Your theory is just chalk full of assumptions- you can't provide any corroborating sources to any of it.

I showed you the source:

" The prevalence of low-level function in four such experiments indicates that roughly one in 10(64) signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences."

link

So this is essentially saying that the odds of forming any working domain at all is 1 in 10^64, whereas the odds of forming a working domain that performs a specifically needed function is 1 in 10^77.

originally posted by: Venkuish1

You have been misrepresenting the paper and his author and anyone can see what was written hasn't come from the author

I used the numbers that they calculated for the probability of randomly mutating a working functional group on a protein. This is how science works, you use data from researchers who have done the work in specific fields, and apply it to the real world.

originally posted by: Venkuish1
a reply to: cooperton

New enzyme discovered...


phys.org...#:~:text=The%20new%20enzyme%3A%20PET46&text=Structurally%2C%20the%20enzyme%20diffe rs%20significantly,that%20degradation%20can%20be%20continuous.

Yeah a new enzyme was discovered, so what? It wasn't shown to have evolved in a lab setting. A novel functional group emerging through random mutation in a lab has never been seen before, this is due in part because the rarity of such an event is estimated to be about 1 in 10^64

You argued there is not enough time for the formation of biologically useful proteins to be created (and you generalised to proteins). That's not true as we know because reality has proven you wrong and proteins are abundant in our world. As the matter of fact an new enzyme has been found and enzymes are proteins. Why does it have to be created in a lab setting?? It was created naturally just as it happens with enzymes and proteins in general.

The math you are using is bogus and based on false assumptions as it has already been explained to you.

See link above

There are 20,000 to over 100,000 unique types of proteins within a typical human cell. Why so many? Proteins are the workhorses of the cell. Each expertly performs a specific task. Some are structural, lending stiffness and rigidity to muscle cells or long thin neurons, for example. Others bind to specific molecules and shuttle them to new locations, and still others catalyze reactions that allow cells to divide and grow. This wealth of diversity and specificity in function is made possible by a seemingly simple property of proteins: they fold.

The fact that there are tens of thousands of proteins in the human cell it should be alarming to you and the other creationists who try to argue this nonsense. It directly proves how flawed these arguments are and the math used to make these erroneous estimations.

For once again, the author never came to the conclusion there is not enough time for proteins to have been formed. That's your own conclusion based on the lack of understanding of the basics. I can even assume you found this estimation from someone else on the internet. But at least you were consistent because you copy pasted your thread in reddit to appear as if it was the logical conclusion of the paper for which you provided only the abstract.

originally posted by: cooperton
I showed you the source:

" The prevalence of low-level function in four such experiments indicates that roughly one in 10(64) signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences."

link

So this is essentially saying that the odds of forming any working domain at all is 1 in 10^64, whereas the odds of forming a working domain that performs a specifically needed function is 1 in 10^77.

I used the numbers that they calculated for the probability of randomly mutating a working functional group on a protein. This is how science works, you use data from researchers who have done the work in specific fields, and apply it to the real world.

Cool, just wanted to make sure I'm addressing the correct source. As I stated earlier, multiple structures have been shown to cause the same function- carbonic anhydrases are a group of proteins that all catalyze the same reaction, but have different structures clearly indicating that they did some how evolve independently. That is not the leading theory on how things initially get started, though.


Basically the idea that life started with proteins first is not a working theory- it started with "proteinoid microsphere" theories in the context of historical ideas about abiogenesis, which is basically the idea that life forms from decomposing organic material (people in antiquity noticed how maggots would appear on rotting meat, etc.). In modern science we now know that we can start with a ribozyme (that’s only 30 or so nucleotides long) and it’ll catalyze proteins/select functions for those proteins. The protein-first hypothesis is not popular among scientists and the article you linked further demonstrates how very unlikely the protein-first theory is. The leading hypothesis is RNA-first, followed by peptide/RNA. We know that there was substantial chemical evolution of RNA first, then peptides, or RNA and peptides underwent chemical evolution together- that's where our current understanding is- figuring out what RNA evolved from and how.

The problems associated with the RNA world hypothesis are well known, but there are far more problems with the protein-first hypothesis. The RNA first hypothesis does not necessarily imply that RNA was the first replicating molecule to appear on the Earth (although a new paper by Benner and colleagues argues that this was, in fact, the case). The more universal understanding is that the RNA ecosystem comprised a stage of evolution preceding the RNA/protein/DNA world we now inhabit. In this way, the hypothesis is not incompatible with other models- for example- it has been hypothesized that RNA was preceded by a nucleic acid analogue, one theory is in which glycerol replaces ribose in the phosphodiester backbone, though pathways for the prebiotic synthesis of many such analogues are even less plausible than for RNA itself.


There are a lot of proponents of the protein-first hypothesis, however, it seems highly unlikely that proteins synthesized proteins prior to the advent of the ribosome, as this would suggest an infinite regression series. You don't run into this problem with non-coding RNAs such as ribosomal RNA and tRNA, as these were able to replicate prior to the evolution of ribosomal protein synthesis. The RNA-first hypothesis is extremely difficult to verify and no one has been able to produce self-replication of RNA, but there is still a lot of evidence to mull over with RNA-first hypothesis. Conversely, the other hypotheses on the origin of life are pretty much hopeless in terms of evidence. The RNA first hypothesis is also a logical inevitability- something had to start efficiently replicating to begin evolving and proteins do not have this ability. We know that A)- Random sequences are an abundant source of bioactive RNAs or peptides and B)- Random sequences rapidly evolve into de novo promoters (www.nature.com...). It was found that 175 de novo genes arose while concurrently- eight times as many genes arose through duplication over 3.4 million years of evolution. If this rate is consistent, multiplied by a thousand is 175,000 de novo genes for the majority of time that life has been evolving on this planet. That’s 3.4 billion years out of the 4.5 billion or so age of the Earth- if modern humans have around 30,000 functional genes that are 98.7% identical to bonobo genes, then there is more than enough time for every single one of them to emerge de novo.



As with any unproven science, progress to understanding is sporadic, with insights coming in far and few from around the world. Your statistical inference alone is not enough to evaluate the data for this hypothesis. Most amino acids are very interchangeable, instead of 20 amino acids to work from, there are 4 categories of amino acids: nonpolar, polar neutral, polar acidic, polar alkaline. There are amino acids with unique functions, but the majority of amino acids are interchangeable. The article you linked only claims to add evidence that functional folds require highly extraordinary sequences- again alluding to ribozymes being necessary.


Anyone (including you) who claims to know what the chances are of something happening, when it has obviously already happened, is making postdictions, not predictions. All you are doing is taking a result that you already know occurred and are trying to assess it's probability after the fact. You're using a paper literally titled "*Estimating* the prevalence of protein sequences adopting functional enzyme folds" as smoking gun evidence for your claims.... "Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function". Probabilities are extremely dynamic, they change as time moves; situations and scenarios occur and disappear throughout all of history. In the article you linked, it is stated that the experiment was "to assess a working beta-lactamase domain. An alignment of homologous domain sequences is used to deduce the pattern of hydropathic constraints along chains that form the domain fold". Do you really not understand how highly specific that is? They used aligned homologous domain sequences just to get an *ESTIMATE*. There currently exists no realistic way to calculate the probability of a protein having any function whatsoever.



The interactions we are discussing depend on all levels of structure and function. There is no way to know about all of the highly unique scenarios that existed throughout the Earth's cataclysmic history. It may interest you to know that a phage display of a library of antibodies has been created in the past to find ones with catalytic function. Beta lactam hydrolase function was experimentally searched for and out of a library of 2.7 x 109 antibodies, 5 demonstrated beta lactamase ability (pubmed.ncbi.nlm.nih.gov...).

Yes there is. Study Francis Galton and his correspondence with Darwin. Natural selection can occasionally lead to accelerated and novel speciation.