Unrealized Genomes as the Ultimate Falsification of the Evolution Theory

[niwrad]

!

Moderator Note

 As per the rules no advertisement to external blogs, the discussion should be facilitated here. 

 

The linked article examines the fundamental assumption of the evolution theory by which, just because each new organism has subtly different genome than its parents, this will eventually lead to genomes with information for previously nonexistent, functional and niche occupying structures, such as organs. For that purpose, first it compares two libraries. One library contains ‘realized genomes’ — i.e. all genomes that could have been formed during the entire history of life on Earth. Another library contains ‘unrealized genomes’ — i.e. all possible genomes that a genome of a certain size allows, reduced by the number of realized genomes. Finally, it calculates the waiting time required for finding the genome containing information for insect wings and it concludes that it would take 10^871 years for that to happen.

[Arete]

It doesn't make sense to analyze all possible nucleotide combinations due to selection. A common misconception made by proponents of irreducible complexity. 

[Strange]

1 hour ago, niwrad said:

Finally, it calculates the waiting time required for finding the genome containing information for insect wings and it concludes that it would take 10^871 years for that to happen.

This appears to be a version of the idiotic "tornado in a junkyard" argument. Presumably, it is based on ignorance or misrepresentation of how genes and/or evolution works.

[John Cuthber]

The OP may find this explanation interesting

 

[niwrad]

Since the link is removed I will c/p the article here:

In a nutshell, the Evolution Theory is surprisingly simple. We start with unicellular, amoeba-like organism. This organism produces offspring and in each new generation subtly different genomes are produced. The process continues, which results in lots of different genomes. Eventually, in one of the genomes, information for new biological structure arises. This structure allows an organism to occupy a new ecological niche. Because of that, the organism has better chances of survival and reproduction, which consequently increases the frequency of its genes in the genetic pool of its population. Increased gene frequency or population separation by genetic drift leads to gene fixation and speciation  (the formation of new species ). With new reproduction cycles, we again have slightly different genomes. The above process repeats itself, and gives rise to new species and genomes with information for all of the proteins, protein complexes, organs and organ systems that exist today but were not present in the first organism.

So, the basic Theory of Evolution is surprisingly simple. But, there is obviously something suspicious with this simplicity. What? Well, it is the assumption that just because each new organism has subtly different genome than its parents, this will eventually lead to genomes with information for previously nonexistent, functional and niche occupying structures, such as organs. However, even a quick look at biological reality shows that this assumption doesn’t hold. For e.g.,  in the last 300,000 years more than 110 billion humans have lived on Earth. Since due to mutations each human genome is unique, that means that human population produced 110 billion different genomes. But has this caused humans to start to develop some new, previously nonexistent and functional organs that will occupy ecological niches humans previously could not occupy? Well, obviously not. After an enormous number of different genomes produced, humans are anatomically, morphologically and physiologically practically identical, without any traces of new organs starting to develop.

But here’s how a standard narrative of the Evolution Theory looks like:

“When the first forests arose on earth, new niches for terrestrial animals were created. Spore-feeders and others who depended on plants and/or the animals living around them would have to adapt too to make use of them. In a world with no flying animals, it would probably just be a matter of time before some arthropods who were living in the trees evolved paired structures with muscle attachments from their exoskeleton and used them for gliding, one pair on each segment.“

So, there you have it. Just because “new niches were created“, new organs for occupying those niches must have started to develop. And not only that, but it was “just a matter of time” before this happens. In other words, just because some wingless insects produced offspring with subtly different genomes, the information for previously nonexistent, functional and niche occupying organs must have appeared in these genomes. Now, is such an assumption realistic? Well, let’s put it to the test and find out.

For the purpose of testing, first we are going to compare two libraries. One library contains ‘realized genomes’ — i.e. all genomes that could have been formed during the entire history of life on Earth. Another library contains ‘unrealized genomes’ — i.e. all possible genomes that a genome of a certain size allows, reduced by the number of realized genomes.

Whenever an organism reproduces and produces an offspring with subtly different genome, all that happens is the appearance or realization of one specific genome that resides in the library of all possible genomes. Meaning, it doesn’t matter whether parents pass a hundred, a thousand or even a million mutations to their offspring, the fact is that every reproduction cycle results in only one genome – that it results in only one combination of nucleotides, which resides in the library of all possible combinations that a genome of a certain size allows. So basically, the size of the library of ‘realized genomes’ is equal to the maximum number of organisms that have ever lived of Earth. Let’s assume that at any point during the entire history of life, the number of organisms was equal to the number of atoms comprising the Earth’s total mass, which is 10^50, and that these organisms were reproducing once every Planck time. This is the smallest measurable unit of time and is about 10^-44 seconds. Since the first life appeared about 4 billion years (10^17 seconds) ago, this gives us an upper bound of 10^50*10^44*10^17=10^111 organisms, which is, as we said, also the size of the library of ‘realized genomes’. This is of course a highly exaggerated number, but we just want to show what numbers are beyond physical possibility and also give an advantage to the assumption we are testing.

Now that we know how big is the library of realized genomes, we can compare it to the library of unrealized genomes and determine the difference between the two. We will be using the insect genome as a determiner, or more precisely, the smallest insect genome, which contains 91 million base pairs of nucleotides(bp). (Hanrahan SJ1, Johnston JS., 2011). Since there are 4 nucleotide bases (A, T, G and C), we get that the number of all possible genomes that insect genome allows is 4^(91,000,000), or ≈10^54,787,459. If we now subtract the above upper bound (10^111) from this number we get that the library of unrealized genomes is 54,787,348 orders of magnitude greater than the library of realized genomes. To put this difference in perspective, consider that the difference between the diameter of an electron and the diameter of the Universe is only 41 orders of magnitude. In other words, the library of realized genomes is the size of an electron, while the library of unrealized genomes is the size of 10^54,787,307 universes.

Now, how is this difference related to the above evolutionary assumption by which the genome with the information for insect wings will eventually appear just because some wingless insects produce offspring with subtly different genomes? Well, the information for insect wings can reside either in the library of realized genomes or in the library of unrealized genomes. So what the above assumption actually assumes is that this information resides in the tiny library of realized genomes and not in the ridiculously big library of unrealized genomes. And given the enormous difference between the two libraries, assuming something like that is not only unrealistic but also ridiculous. We will now demonstrate this by comparing the library of genomes to The Library of Babel.

The Library of Babel, a short story by Argentine author Jorge Luis Borges, describes an infinite universe in the form of a library containing all possible 410-page books derived from a set of 25 characters (22 letters, the period, the comma, and space), seemingly arranged in random order. The librarians that inhabit this universe seek to comprehend the library. Since the library is infinite and the number of possible books is finite, the library must contain books with all possible useful information including biographies of any person, predictions of the future, critiques of obscure economic theories, poetic descriptions of clouds, translations of any book in all languages and thousands of slight imperfections of any book (e.g., a treatise on the sky that gets everything correct except stating that the sky is red). Since the crushing majority of books in the library contain gibberish and the books appear to be randomly distributed, the library is utterly useless and the librarians are despondent.

The library of genomes is like Borges’ library. Individual insect genomes are books, while useful information in these books – like biographies, is the equivalent of information for insect wings. The genome of the first amoeba didn’t contain this information, which is why the process of random modification of the genome during reproduction must find it. But assuming something like that is as absurd as assuming the Borges’ librarians will find a book that contains some useful information on problems that emerge in their environment. Let’s say, for instance, that one librarian is looking for a new job, which is why he needs a book containing his biography. This is equivalent to the situation where wingless insects require the genome with information for wings in order to occupy the forest niche. And now, the librarian believes that it is “just a matter of time” before he finds his biography. This search is equivalent to the formation of subtly different genomes during the reproduction of wingless insects – who thereby search for the required genome.

In the process of searching, both librarians and insects will obviously find or “realize” a certain number of genomes (books). But assuming that they will find the required ones is ridiculous. The fact is that reqierd genome or book must reside somewhere in the library of genomes and Borges’ library, but the difference between those that are in reach of the searching process and those that are not, is so big that insects or librarians would not find the required ones even if they search until the end of the universe. We will now demonstrate this mathematically, by calculating the waiting time required for finding the genome with information for insect wings.

Searching for librarian’s biography or information for insect wings is not searching for only one book or genome. The biography text can be written in many different ways, or with many typographical errors, but will still express a comprehensible and accurate librarian’s biography. The same is true for genomes. They can tolerate a lot of variance (different combinations of nucleotides), but still express the same phenotype, i.e. functional insect wings.

In that regard, in the first step of our calculation, we want to know how many different combinations of nucleotides will code for functional wings, and how many will not. Or in other words, we want to know the number of functional DNA sequences – those that can occupy the forest niche, and the number of nonfunctional ones – those that cannot occupy the niche. But before that, we need to know the size of these sequences. The fact is that biological structures, such as wings, are the culmination of the interaction of many different genes over many generations of cell division, but since we want to give an advantage to the above evolutionary assumption, let’s assume some super primitive insect wings, which are coded with only three average eukaryotic genes. Since the average eukaryotic gene size is 1,346 bp (Yubo Hou and Senjie Lin, 2009), this gives us DNA sequence of size 4,038 bp.

Now that we know the size, we can determine the number of functional DNA sequences. For that purpose we will use the replacement tolerance, i.e. the degree by which functional genes can tolerate random nucleotide replacements before losing their functions. Some gens can tolerate many such replacements, whereas other genes (ultra and highly conserved) must be very precise to retain their function, and even a few replacements are detrimental. In our calculation we will be using an extremely high replacement tolerance of 60 percent. Such tolerance means that when our three genes code for functional primitive insect wings, 2,422 of their 4,038 nucleotides can undergo random replacements and this would still not be detrimental for insects’ flying function. In the context of many ultra and highly conserved genes in living systems, such replacement tolerance in not realistic, but our goal is to give every possible advantage to the above evolutionary assumption.

With the 60 percent replacement tolerance, and with the DNA sequence of size 4,038 bp, we get that the number of sequences that will code for primitive insect wings is 4^(4,038*0.6) or ≈10^1,458. To put that in perspective, there are only 10^80 elementary particles in the observable universe. So we are talking about really an enormous number of functional sequences. These sequences are the equivalent of all possible different texts that express a comprehensible and accurate librarian’s biography. However, now we must also calculate the number of nonfunctional sequences, i.e. all DNA sequences that won’t code for primitive insect wings but are either junk (contain gibberish – like crushing majority of books in the Borges’ library) or they code for various ‘non-flying’ functions. We get the number of those by simply subtracting the number of functional sequences(10^1,458) from the total number of possible DNA sequences(4^4,038). Doing the subtraction, we get ≈10^2,431. So this is the number of all nonfunctional DNA sequences, i.e. those that won’t code for insect wings. If we now divide this number by the number of functional sequences — (10^2,431/10^1,458), we get that for every functional sequence there are 10^973 nonfunctional ones.

By determining this ratio we can finally calculate the waiting time required for finding the genome with information for insect wings. Previously we have mentioned that Planck’s time is the smallest measurable unit of time. If we assume that organisms can generate new DNA sequences once every Planck time and that their number is equal to the number of atoms comprising the Earth’s total mass, they would be able to generate 10^44*10^50=10^94 different sequences per second or 31556926*10^94=3.16*10^101 different sequences per year. At that speed, the required waiting time would be 10^973/3.16*10^101≈10^871 years. For comparison, our planet Earth was formed only 4.6*10^9 years ago.

As we can see, even with many generous assumptions in favor of the above evolutionary assumption, the waiting time required for the appearance of the genome with information for previously nonexistent, functional and niche occupying organs is 862 orders of magnitude longer than the time since Earth’s formation. So, what is in evolutionary narrative “just a matter of time” in practice is “never.” And not just never in terms of Earth’ age and computational capacity, but also of universes’. Namely, suppose all 10^80 elementary particles in the universe are DNA sequences. Now suppose we can rearrange all of these sequences once every Planck time. And suppose we did this until the heat death of the universe in 10^100 years. That’s 10^150 Planck time units. We still only get 10^80*10^150=10^230 combinations. And that’s not even close to the 10^973 figure. That is why the above evolutionary assumption is not only unrealistic but also ridiculous.

The assumption that just because each new organism realizes different genome, this will eventually lead to genomes with information for previously nonexistent, functional and niche occupying structures, is behind all evolutionary explanations. It doesn’t matter if one tries to explain the origin of wings, eyes, bacterial flagellum, immune system, metabolic pathway, heart, kidneys… one always has to assume that genomes with information for these structures and systems reside in the tiny library of realized genomes and not in the ridiculously big library of unrealized genomes. And given the sheer complexity of many biological structures in comparison to insect wings, the required waiting time of 10^871 years is extremely short. That is why, from the perspective of science, logic and reason, no one can assume that information for these structures resides in the library of realized genomes. The enormous difference between this library and the library of unrealized genomes therefore represents the ultimate falsification of the Evolution Theory.

10 hours ago, Arete said:

It doesn't make sense to analyze all possible nucleotide combinations due to selection. A common misconception made by proponents of irreducible complexity. 

Your general statement has nothing to do with the arguments of the article.

8 hours ago, John Cuthber said:

The OP may find this explanation interesting

 

This is not topic about evolutionary explanations or the evolution process. It is about the fundamental assumption behind the evolution theory by which just because each new organism realizes different genome, this will eventually lead to genomes with information for previously nonexistent, functional and niche occupying structures, such as organs.

[Arete]

The argument assumes all mutations have an equal probability of being passed to the next generation, which unless the population is in Hardy-Weinberg equilibrium, is untrue. It also assumes that all mutations are equally likely, which even a rudimentary understanding of the translation of codons into amino would provide, not to mention the processes of exaptation, recombination, chromosomal duplication, gene regulation, codon usage bias, horizontal gene transfer, etc. 

Honestly, the flaws in the argument are numerous, foundational and show a very poor grasp of basic genetics. I mean even in the first sentence, it describes the first life form as "amoeba-like". Amoeba are eukaryotes. 

Edited February 26, 2019 by Arete

[niwrad]

3 minutes ago, Arete said:

The argument assumes all mutations have an equal probability of being passed to the next generation, which unless the population is in Hardy-Weinberg equilibrium, is untrue. It also assumes that all mutations are equally likely, which even a rudimentary understanding of the translation of codons into amino would provide, not to mention the processes of exaptation, recombination, chromosomal duplication, gene regulation, codon usage bias, horizontal gene transfer, etc. 

Honestly, the flaws in the argument are numerous, foundational and show a very poor grasp of basic genetics. 

The argument assumes nothing of the sort. It is based of the simple and factual premise that every reproduction cycle results is a subtly different genome. In that way, one genome is realized - a genome that resides in the library of all possible genomes. Like I have said, your generic statements have nothing to do wit the arguments in the article.

[John Cuthber]

38 minutes ago, niwrad said:

It is about the fundamental assumption behind the evolution theory

Your  posts show that you do not understand the theory.

You really need to learn about it before trying to say it is wrong.

[Arete]

 

26 minutes ago, niwrad said:

 It is based of the simple and factual premise that every reproduction cycle results is a subtly different genome. 

That's not a fact - e.g. polyploidy. 

If you aren't equally weighting all mutations, none of the math in the entire post makes any sense. 

This probabilistic numerology argument is not new and founded in foundational misunderstandings of genetics and evolution: 

DNA encodes amino acids in triplicates of base pairs called codons. There are 64 possible codons, encoding 20 amino acids, and stop. The translation of codons into amino acids is highly redundant, with numerous codons denoting each amino acid. 61 encode amino acids, and three encode stop. There are no untranslatable codons. This has a number of implications: 

 1) All possible DNA sequences can be translated into proteins. There is no such thing as a "gibberish" DNA code. 

2) Because of the redundancy, multiple changes can occur without affecting the translation of the sequence. 

3) Arguments from low probability are not apt. Given all possible arrangements of nucleotides can encode proteins, there are no null sequences. Consider it more like a dice throw. Rolling one hundred sixes in a row has a probability of (1/6)¹⁰⁰ or 1.5 x 10^-78. Except ALL combinations of 100 throws have this probability and if you perform the experiment, an outcome is inevitable. Claiming that the low probability makes the outcome impossible ex post facto is not sensible.

If you're open to it, a major component missing from the argument posed is explained by the concept of fitness landscapes, which allows one to model the adaptation of a population given different likelihoods of each possible mutation proliferating in a population through time.  The entire landscape would be all of your "unrealized genomes" but because of the weighting of selection on certain regions of the landscape, some mutations are more likely to fix than others. Step size on the landscape can change drastically if large scale mutation like translocation, duplication or deletion occurs (i.e. not all changes are incremental). See 

• https://www.sciencedirect.com/science/article/pii/S0022519396900491
• https://www.mitpressjournals.org/doi/abs/10.1162/106365602317301754
• https://onlinelibrary.wiley.com/doi/abs/10.1002/(SICI)1097-0134(199712)29:4<461::AID-PROT6>3.0.CO;2-B etc. 

Edited February 26, 2019 by Arete

[niwrad]

45 minutes ago, John Cuthber said:

Your  posts show that you do not understand the theory.

You really need to learn about it before trying to say it is wrong.

Why would I have to "understand the theory"if my article is not about the theory, but about the assumption behind it? The evolution theory is build on the assumption that the genomes with information for functional and niche occupying structures, such as organs, reside in the library of realized genomes and not in the library of unrealized genomes. Given the fact that the latter library is 54,787,348 orders of magnitude greater than the former library, this renders the assumption absurd to the point of ridicule, which is expressed mathematically in the article. So, it is not about the evolution theory, it is about its assumption.

43 minutes ago, Arete said:

That's not a fact - e.g. polyploidy. 

If you aren't equally weighting all mutations, none of the math in the entire post makes any sense. 

This probabilistic numerology argument is not new and founded in foundational misunderstandings of genetics and evolution: 

DNA encodes amino acids in triplicates of base pairs called codons. There are 64 possible codons, encoding 20 amino acids, and stop. The translation of codons into amino acids is highly redundant, with numerous codons denoting each amino acid. 61 encode amino acids, and three encode stop. There are no untranslatable codons. This has a number of implications: 

 1) All possible DNA sequences can be translated into proteins. There is no such thing as a "gibberish" DNA code. 

2) Because of the redundancy, multiple changes can occur without affecting the translation of the sequence. 

3) Arguments from low probability are not apt. Given all possible arrangements of nucleotides can encode proteins, there are no null sequences. Consider it more like a dice throw. Rolling one hundred sixes in a row has a probability of (1/6)¹⁰⁰ or 1.5 x 10^-78. Except ALL combinations of 100 throws have this probability and if you perform the experiment, an outcome is inevitable. Claiming that the low probability makes the outcome impossible ex post facto is not sensible.

If you're open to it, a major component missing from the argument posed is explained by the concept of fitness landscapes, which allows one to model the adaptation of a population given different likelihoods of each possible mutation proliferating in a population through time.  

So, you have decided to completely ignore the article, and instead, to just copy/paste stuff completely unrelated to it? Ok, it is your choice.

Edited February 26, 2019 by niwrad

[Strange]

20 minutes ago, niwrad said:

Why would I have to "understand the theory

“I don’t know anything about how electric cars work but I’m sure we can make a better one based on cheese”

[niwrad]

8 minutes ago, Strange said:

“I don’t know anything about how electric cars work but I’m sure we can make a better one based on cheese”

I can repeat the question for you: why would I have to know how electric cars work if my claim is that electric cars cannot run without a traction battery?

I do not understand why you are trolling this topic so much?

[Strange]

12 minutes ago, niwrad said:

I can repeat the question for you: why would I have to know how electric cars work if my claim is that electric cars cannot run without a traction battery?

That summarises the problem perfectly. If you can't understand why that would be a problem, then you have bigger problems than trying to understand how genetics or evolution works.

But go ahead, submit this paper to a peer reviewed journal in the field. Let us know how you get on.

12 minutes ago, niwrad said:

I do not understand why you are trolling this topic so much?

I'm not the one posting pseudo-scientific nonsense.

43 minutes ago, niwrad said:

So, you have decided to completely ignore the article, and instead, to just copy/paste stuff completely unrelated to it?

So you have decided to completely ignore people pointing out errors in your assumptions and understanding.

[Dagl1]

23 minutes ago, niwrad said:

I can repeat the question for you: why would I have to know how electric cars work if my claim is that electric cars cannot run without a traction battery?

I do not understand why you are trolling this topic so much?

For the sake of trying to be helpful, could you in a few sentences give me a detailed argument of what you think the problem is (I understand that you think the realized vs unrealized library size ratio is unrealistic, but I don't really get how that is a problem)?

 

[Carrock]

1 hour ago, niwrad said:

I can repeat the question for you: why would I have to know how electric cars work if my claim is that electric cars cannot run without a traction battery?

I would be unable to explain in a way you could understand that electric cars can run without a traction battery.

[studiot]

2 hours ago, niwrad said:

I can repeat the question for you: why would I have to know how electric cars work if my claim is that electric cars cannot run without a traction battery?

I was going to say that electric cars with no battery have been around a long time.

Even the late victorians/edwardians had them.

But Carrock beat me to it. +1

 

[Strange]

But forex niwrad has never been strong on facts.

Edited February 26, 2019 by Strange
Silly me. Wrong user name.

[Arete]

9 hours ago, niwrad said:

So, you have decided to completely ignore the article, and instead, to just copy/paste stuff completely unrelated to it? Ok, it is your choice.

It might be useful to correct the secondary school level biological error in the first sentence of your wall of text copypasta, but hey, you do you. 

[Phi for All]

!

Moderator Note

Too many mistakes that need to be corrected before any of this can be taken seriously. And it looks like we have a sockpuppet of a banned account as well, so this is closed for non-compliance with basic rules.

 

[swansont]

10 hours ago, niwrad said:

Why would I have to "understand the theory"if my article is not about the theory, but about the assumption behind it? The evolution theory is build on the assumption that the genomes with information for functional and niche occupying structures, such as organs, reside in the library of realized genomes and not in the library of unrealized genomes.

!

Moderator Note

I will be blunt: this is BS. This characterization that there is a "library of realized genomes" and "library of unrealized genomes" is, so far as I can tell, a concoction of your own making (top google hit for one of those phrases is this thread, second is your blog and there are only 10). IOW it is NOT part of the basis of evolutionary theory.

Meaning you have constructed a straw-man argument, and nobody here is going to let you pretend that you haven't.

In addition, you show you are not aware of, or reject correction on, numerous errors present in your argument. Closed.

 

edit: x-post with Phi