Absurdity of evolution

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Absurdity of evolution

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Post by EarthScienceguy »

How is evolution even possible in light of the following?

1. Haldane's Dilemma

The cost of substitution Cs is 30 and it is paid off in installments (Ps)of 0.1 each generation. At that rate, it takes (Cs/Ps) 300 generations to pay the cost of substituting one gene. Haldane's conclusion was over the long term the average rate of gene substitution is no better than one gene every 300 generations. (Crow and Kimura, 1970 p 244-252; Crow 1968 p 168-173; Ewens 1979 p 252-256; Merrell 1981 p 187-193)

In a human-like population with a nominal generation time of 20 years 10 000 000/(20x300) = 1667nucleotides could have been changed. That is 0.000047% of the human genome. For 1% of the human genome to be changed in this fashion would take 210,000,000,000 years.

Haldane's dilemma ended the idea of selection causing evolution.

How is there time for evolution?
How can there be evolution without selection?

2. Kimura's Neutral theory of evolution

Kimura is credited with coming up with the solution to Haldane's dilemma. He suggests that neutral mutations is the way that most of the genome was changed.

Error catastrophe is when harmful mutations accumulate too fast and genetic deterioration becomes unavoidable. The standard genetic model the one model taught in every evolutionary textbook -predicts that error catastrophe occurs when the mutation rate gets much above one harmful mutation per progeny. (that is 0.5 harmful mutations per gamete per generation) At that rate, each progeny typically has one more harmful mutation than its parents. Above this threshold, the species would rapidly accumulate harmful mutations from generation to generation.

Kimura estimates that amino-acid altering mutations are roughly ten times more likely to be definitely harmful than neutral. (kimura 1983, p 199; King and Jukes 1969 p 795) That would indicate that the expressed neutral mutations cannot be more common than 0.05 per gamete per generation.

The neutral theory predicts that the neutral substitution rate is equal to the neutral mutation rate per gamete. (Kimura 1983 p 46-48) Therefore, expressed neutral mutations are substituted no faster than 0.05 per generation. In ten million years, a human-like population could substitute no more than 25000 expressed neutral mutations. That amounts to 0.00007% of the genome. So that means if 1% of the human genome were to change it would 14,000,000,000 it is closer to the age of the universe.

How would evolution have time to occur?

3. Punctuated Equilibria

Punctuated Equilibria was developed in response to seeing cladogenesis in the fossil record and not anagenesis. Punctuated equilibria has three central postulates.

Postulate 1: Most evolution occurs in short, rapid bursts (called punctuation events) followed by stasis. This produces a large morphological gap.

Postulate 2: Most evolution occurs at speciation (in other words, punctuation events are closely tied to speciation)

Postulate 3: Speciation has no inherent directionality. A daughter species tends to originate in a random, non-adaptive direction from the parent species.

Punctuated equilibria destroy the idea of discernable phylogeny in the fossil record. Punctuationists declare that evolution is a labyrinthine bush, not an identifiable tree.

How can evolution be true if phylogeny is not discernable in the fossil record?

Remine, Walter The biotic message
Last edited by EarthScienceguy on Tue Nov 09, 2021 4:19 pm, edited 1 time in total.

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Re: Absurdity of evolution

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Post by The Barbarian »

It's not just observed speciations that refute your interpretation. It's that for example, the evolution of a new digestive organ in a population of relocated lizards (in about 20 years' time) shows that major evolutionary changes can occur rather quickly if the selection is strong enough.

(sound of goalposts being frantically repositioned)
EarthScienceguy wrote: Tue Nov 16, 2021 12:39 pm As you learned in the different thread these lizards of yours did not produce any new function they simply enhanced an existing function.
Sorry, you're wrong. These lizards can now effectively ferment plant material, and use the fermented product to gain nutrition. Which they could not do before. But that aside, you've again hit a wall, because you don't know what biological evolution is.
And as you just learned polymorphism is not a mutation.
And once again,because you don't know what biological evolution is, you've hit another wall:

Polymorphism, by strict definitions which hardly anybody pays attention to anymore, is a place in the DNA sequence where there is variation, and the less common variant is present in at least one percent of the people of who you test. That is to distinguish, therefore, polymorphism from a rare variant that might occur in only one in 1,000 people. A polymorphism, it has to occur in at least one in 100 people. Polymorphisms could be not just single-letter changes like a C instead of T. They could also be something more elaborate, like a whole stretch of DNA, that is either present or absent. You might call that a copy number variant; those are all polymorphisms. But this is basically a general term to talk about diversity in genomes in a species.
Francis S. Collins, M.D., Ph.D.

https://www.genome.gov/genetics-glossary/Polymorphism

A variation in the DNA sequence that occurs in a population with a frequency of 1 % or higher is termed a polymorphism [26]. The higher incidence in the population suggests that a polymorphism is naturally occurring, with either a neutral or beneficial effect. Polymorphisms can also be of one or more nucleotide changes, just like mutations. The SNP exemplifies the commonest polymorphism, thought to arise every 1,000 base pairs in the human genome, and is usually found in areas flanking protein-coding genes [27] – regions now recognized as critical for microRNA binding and regulation of gene/protein expression [28]. However, SNPs can also occur in coding sequences, introns, or in intergenic regions [27]. SNPs are used as genetic signatures in populations to study the predisposition to certain traits, including diseases [29].
The anatomy of the problem

In the era of advanced DNA sequencing tools and personal genomics, these earlier definitions of mutation and polymorphism are antiquated. Before multiple parallel sequencing was developed, it was impossible to sequence multiple times the genome of the same patient. For these reasons at that time it was required to use a reference sequence coming from the assembly of multiple genomes. In the preparation of the consensus sequence, an arbitrary threshold of 1 % was established to distinguish common (polymorphism) from rare (mutation) variants [26].

The 1 % or higher frequency associated with a polymorphism is an arbitrary number [30] recommended by scientists prior to the era of Next Gen Sequencing. The threshold being arbitrary, redefining the population itself may affect the classification, with rare variants becoming polymorphisms or polymorphisms becoming rare variants according to the population analyzed.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4502642/

So a polymorphism is a mutation that has a frequency of at least .01 in the population. It's just an arbitrary point at which one assumes the variation is a "normal" part of the population genome. But as the article notes, that means polymorphisms can be come "mutations" and mutations can become "polymorphisms." This goes back again to not understanding the terminology. You would do a lot better if you spent some time reading up on this.

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Re: Absurdity of evolution

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Post by The Barbarian »

EarthScienceguy wrote: Tue Nov 16, 2021 3:15 pm Again polymorphism is only considered a mutation if it changes the phenotype.
You're wrong again. Most mutations don't do anything noticable at all.

When parents pass their genes down to their children, an average of 60 errors are introduced to the genetic code in the process, according to a new study. Any of those five dozen mutations could be the source of major differences in a person's appearance or behavior as compared to his or her parents and altogether, the mistakes are the driving force of evolution.

Sixty mutations may sound like a lot, but according to the international team of geneticists behind the new research, it is actually fewer than expected. "We had previously estimated that parents would contribute an average of 100 to 200 mistakes to their child," Philip Awadalla, a geneticist at the University of Montreal who co-led the project, said in a press release. "Our genetic study, the first of its kind, shows that actually much fewer mistakes, or mutations, are made."

https://www.livescience.com/33347-mutan ... tions.html

So why don't we see all those mutations changing phenotypes? It's because most mutations don't do much of anything at all. Changing one amino acid in a protein generally doesn't affect its activity in any measurable way.

This is why there are so many different cytochrome C molecules, but they all do exactly the same thing. There are, however, highly conserved portions of cytochrome C, which are common throughout living things. This is because mutations at that point will alter the activity of the molecule. Which would be lethal, given the role of cytochrome C in oxidative phosphorylation, which is found in all living things. Some parts can change quite a bit without altering the activity. Other parts need to be what they are.

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Re: Absurdity of evolution

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Post by EarthScienceguy »

[Replying to Difflugia in post #0]
Did you even read that? It doesn't even mention phenotype. It is wrong about at least one other thing, though (it claims that "polymorphisms" aren't affected by natural selection; that's not part of the definition, either) and probably more (it's rather sloppy in general).

It also agrees with me.
Did you read the entire thing?

The big chart which explains the difference between polymorphism and mutation. Did you see that big chart?

My definition for the difference between polymorphism and mutations came from the guys at the research gate so there must be a significant difference between polymorphism and mutations.

Do you really want to define a mutation as a difference between males and females? Or Hair color or any of the millions of characteristics progeny receive from their parents. If you are calling that mutations that cause evolution then why is polymorphism not considered the driving force of evolution?

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Re: Absurdity of evolution

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Post by EarthScienceguy »

[Replying to The Barbarian in post #51]
So a polymorphism is a mutation that has a frequency of at least .01 in the population. It's just an arbitrary point at which one assumes the variation is a "normal" part of the population genome. But as the article notes, that means polymorphisms can be come "mutations" and mutations can become "polymorphisms." This goes back again to not understanding the terminology. You would do a lot better if you spent some time reading up on this.
So you want to call the difference between males and females and the difference in hair colors mutations? So what is the driving force of evolution? Polymorphism if polymorphism is a mutation it should be the driving force of evolution because there would be more polymorphism mutations than any other type of mutation.

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Re: Absurdity of evolution

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Post by EarthScienceguy »

[Replying to The Barbarian in post #52]
When parents pass their genes down to their children, an average of 60 errors are introduced to the genetic code in the process, according to a new study. Any of those five dozen mutations could be the source of major differences in a person's appearance or behavior as compared to his or her parents and altogether, the mistakes are the driving force of evolution.
Really because these are articles say that duplication is a major force if not the driving force of evolution.

https://pubmed.ncbi.nlm.nih.gov/2364042 ... 0organisms.

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Re: Absurdity of evolution

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Post by The Barbarian »

So a polymorphism is a mutation that has a frequency of at least .01 in the population. It's just an arbitrary point at which one assumes the variation is a "normal" part of the population genome. But as the article notes, that means polymorphisms can be come "mutations" and mutations can become "polymorphisms." This goes back again to not understanding the terminology. You would do a lot better if you spent some time reading up on this.[/quote]
EarthScienceguy wrote: Wed Nov 17, 2021 10:46 am So you want to call the difference between males and females and the difference in hair colors mutations?
How do you think sex differences are the result of mutations? Tell us about that. And yes, hair color is an example of mutation.

Cosmet Dermatol 2002 Jul;1(2):62-5.
Red hair--a desirable mutation?
Abstract
Red hair is one of the most striking variants of human hair coloration and has historically been of profound social importance. Red hair in man is due to certain loss of function mutations of one of the peptide products of the pro-opiomelanocortin (POMC) gene, the melanocortin-1 receptor (MC1R, MIM 155555). Such functional mutations enable the melanocyte to produce red-yellow pheomelanin in preference to the default, black-brown eumelanin. This paper reviews the path of discovery of the MC1R in control of animal coat colour, the subsequent role of MC1R in human physiology and possibly wider role of MC1R in human skin carcinogenesis and human development through history.


As you learned, mutations that have a frequency of at least 0.01 in a population are often called polymorphisms.
So what is the driving force of evolution? Polymorphism if polymorphism is a mutation it should be the driving force of evolution because there would be more polymorphism mutations than any other type of mutation.
No, that's wrong. For example, every human has dozens of mutations that are not present in either parent. So there are hundreds of billions of them, none of them with frequencies that would qualify as polymorphisms.

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Re: Absurdity of evolution

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Post by Difflugia »

EarthScienceguy wrote: Wed Nov 17, 2021 10:43 amDid you read the entire thing?
Yes. That's why I know that it's sloppy.
EarthScienceguy wrote: Wed Nov 17, 2021 10:43 amThe big chart which explains the difference between polymorphism and mutation. Did you see that big chart?
Yes. Part of that is wrong (the bit about "natural selection does not affect alleles that brings polymorphism", which is also a bit rough on grammar). It doesn't say anything about phenotype or that a polymorphism isn't also a mutation, though.
EarthScienceguy wrote: Wed Nov 17, 2021 10:43 amMy definition for the difference between polymorphism and mutations came from the guys at the research gate so there must be a significant difference between polymorphism and mutations.
Research Gate is just a collection of resources. The "guys at Research Gate" are collectors.
EarthScienceguy wrote: Wed Nov 17, 2021 10:43 amDo you really want to define a mutation as a difference between males and females? Or Hair color or any of the millions of characteristics progeny receive from their parents.
If you mean the genetic differences between individuals that are responsible for those traits, then yes, technically those are all the result of past mutation.
EarthScienceguy wrote: Wed Nov 17, 2021 10:43 amIf you are calling that mutations that cause evolution then why is polymorphism not considered the driving force of evolution?
As long as you mean "along with natural selection," nobody said that it wasn't.
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Re: Absurdity of evolution

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Post by JoeyKnothead »

EarthScienceguy wrote: Wed Nov 17, 2021 10:43 am ...
Do you really want to define a mutation as a difference between males and females?
Considering that males come about by coding for it, yes.

Unless one considers "god did it" a more likely explanation.
Or Hair color or any of the millions of characteristics progeny receive from their parents.
If hair color weren't the result of mutation, we should see differences across the human spectrum. There's just not many blond Africans. Or blond Asians.
If you are calling that mutations that cause evolution
Mutations by themselves don't cause evolution. Selective pressures must also come into play.
then why is polymorphism not considered the driving force of evolution?
As we noticed from your provided link...

https://www.thethirdwayofevolution.com/

There is some disagreement on the particulars, but no doubt that evolution is fact.

So let's declare for argument's sake that polymorphism is not the driving force for evolution.

Your own source still accepts the fact of evolution.
Discovery is finding things that exist.
Invention is using things discovered.

Create that path and engineer a metamorphosis.

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Re: Absurdity of evolution

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EarthScienceguy wrote: Tue Nov 16, 2021 4:02 pmYou are not understanding what the dilemma is.
The number of loci in a vertebrate species has been estimated at about 40,000. 'Good' species, even when closely related, may differ at several thousand loci, even if the differences at most of them are very slight. But it takes as many deaths, or their equivalents, to replace a gene by one producing a barely distinguishable phenotype as by one producing a very different one. If two species differ at 1000 loci, and the mean rate of gene substitution, as has been suggested, is one per 300 generations, it will take 300,000 generations to generate an interspecific difference. It may take a good deal more, for if an allele a1 is replaced by a10, the population may pass through stages where the commonest genotype is a1a1, a2a2, a3a3, and so on, successively, the various alleles, in turn, giving maximal fitness in the existing environment and the residual environment.[5]
This is the problem. For the new trait to become fixed the entire population that does not have the new trait has to die off. The population has to rebound to a point in which another beneficial mutation can happen again. Haldane calculated this to be 300 generations.
There do not absolutely have to be die-offs, as I will explain in the cow example, and because Haldane is being too linear, what's not being included in the calculation is that this process is happening on multiple genes at once, each becoming slightly more prevalent over time if it is good, during good times. Then, in lean times, when there is a die-off, the lucky individuals that posses the most beneficial traits will be the winners.
EarthScienceguy wrote: Tue Nov 16, 2021 4:02 pmSo all the cats would have to die off so that just the short-haired cats remain. In nature that is what has to happen for a trait to become fixed in a species. So your bull example is nothing more than a bunch of bull. Because for to be an example of refutation of Haldane's dilemma all bulls would have to like like your bull and that is a bunch of bull.
In one generation, if I dose every female with that sperm, all of my new cattle now carry the trait. If I buy the sperm again, in two generations, half will now express the trait and the remaining half will be carriers. Now that I have an expressor bull of my own, probably many, I use those exclusively. Even if I never culled females, in this third generation, 3/4 will be expressors and the remaining 1/4 will be carriers. I can easily now cull 1/4 of the females. This is all assuming the gene is recessive.

There doesn't always have to be extra death, and the amount of death that occurs naturally by predators (simulated by my harvesting my own cattle for meat) is more than enough to accomplish selection.

You are talking to an actual animal breeder. I know my stuff. I have done what you are claiming can't be done, and though you shouldn't just trust me, this is frustrating. The only difficult part of modern animal breeding and fixing traits in your population is the frankly BS insistence from the breeding community that you never inbreed, when not inbreeding (in a pure breed, which admits no new individuals from the random outside population) only delays and exacerbates the problem of bad recessives. So I have to go out and find new cats that are "not related" to my cats (even though they are, it's a pure breed) and buy them or trade for them to appease the foolish notion that not inbreeding is somehow fighting against the problem.
Difflugia wrote: Tue Nov 16, 2021 4:02 pm
Purple Knight wrote: Tue Nov 16, 2021 3:52 pmI believe what he's saying is that every individual trait that makes a pug different from a wolf actually existed out there in the wild before we put them all together and pieced together an abomina- *cough* I mean a pug, from a wolf.
You may be right, but then the last assertion doesn't make sense. If what we're calling the SNP was actually put into the genome by Jesus in the first place, then it still wouldn't matter if it affected phenotype or not. It either arose sometime after the first pair of wolves stepped off the Ark, in which case it's a mutation, or it was one of the four possible variants of any given wolf gene in that pair of platonic ideal wolves. Clean animals at least get the benefit of 14 (or even 28, depending on how you read it) possible variants for any given gene, but I'm pretty sure wolves don't have cloven hooves or chew the cud.
I didn't get a lot of meaning out of that last bit either, but I assumed it was an attempt to define evolution out of existence because I didn't see what else it could be. I'm familiar with the rebuttal as it is used against the case of the moths, so I'm giving it its strongest form. Yes, they will say, the population changed, and is now almost all black, but this is an example of polymorphism, because there were black ones before. For it to be real evolution, they will want a situation where the moths become black without that gene being present in the population previously.

And to be fair, it's kinda sorta possible. Most of the bad traits people breed for in dogs are recessive, so we simply have to imagine that each starter wolf carried exactly half of the bad genes we force upon our hapless dogs for our amusement.

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Re: Absurdity of evolution

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Post by Difflugia »

Purple Knight wrote: Wed Nov 17, 2021 2:45 pmThe only difficult part of modern animal breeding and fixing traits in your population is the frankly BS insistence from the breeding community that you never inbreed, when not inbreeding (in a pure breed, which admits no new individuals from the random outside population) only delays and exacerbates the problem of bad recessives. So I have to go out and find new cats that are "not related" to my cats (even though they are, it's a pure breed) and buy them or trade for them to appease the foolish notion that not inbreeding is somehow fighting against the problem.
That's an interesting problem. With a small population and artificial selection, I'd think that you'd want to inbreed as much as possible, but be diligent about identifying and tracking carriers of novel deleterious mutations and removing them and offspring from the pool (neutering).
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