Abiogenesis and Probabilities

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Abiogenesis and Probabilities

Post #1

Post by DrNoGods »

I'm creating a new thread here to continue debate on a post made by EarthScience guy on another thread (Science and Religion > Artificial life: can it be created?, post 17). This post challenged probability calculations in an old Talkorigins article that I had linked in that thread:

http://www.talkorigins.org/faqs/abioprob/abioprob.html

Are the arguments (on creationist views) and probabilities presented reasonable in the Talkorigins article? If not, why not?
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Re: Abiogenesis and Probabilities

Post #411

Post by Difflugia »

EarthScienceguy wrote: Wed Nov 03, 2021 3:48 pmThe only thing this paper is good for, is a laugh.
My college degree major was computer science and my minor was biology. My day job is writing data analysis software for automated elemental and molecular analysis equipment. This is exactly my area of expertise. If you want to bluff and snort, pick a different topic.
EarthScienceguy wrote: Wed Nov 03, 2021 3:48 pmIt is nothing like mathematical principles. If someone does not believe trigonometric identities are true. They can measure the angles and sides themselves and prove it themselves.
Thanks to the US National Institutes of Health, that exactly describes molecular phylogenetic analysis. Any researcher that uses NIH grant money in genomic research must submit any generated sequences to the GenBank database. Many other researchers, particularly those outside of the US, do so voluntarily. As a result, anyone can access the database and download the sequences of millions of genes from hundreds of thousands of organisms. The software you need to analyze the data is free to download and runs easily on my crappy laptop. I wrote about it just shy of two years ago in another thread that you also posted in.

There are enough data in that database to prove or disprove many facets of evolutionary theory and anyone can download the data and do the analysis themselves. Once you figure out the software (I use PHYLIP and MUSCLE) and the GenBank search interface, you can formulate experiments on the data that potentially nobody else has ever thought of and then run them yourself. You can think of the most damning and evolutionarily impossible gotchas that Jesus might have coded into the genomes of various yeasts and flatworms, then look for them.

Pick any genes from any organisms you want. Generate phylogenetic trees and analyze the relationships, or just eyeball the data if you don't trust any of that fancy science with its lah-di-dah data analysis.

Be careful, though. If you learn enough about phylogenetic analysis to start understanding your results, I'd wager that you won't be a creationist anymore. I dare you.
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Re: Abiogenesis and Probabilities

Post #412

Post by The Barbarian »

EarthScienceguy wrote: Wed Nov 03, 2021 12:23 pm [Replying to The Barbarian in post #404]
No. As you learned, the HPAS1 allele maintains normal hemoglobin content even for people at very high altitudes. It does this by adding some functions to the cardiovascular and repiratory system to allow a normal amount of hemoglobin to carry sufficient oxygen.
You are speaking in generalities.
I'm correcting your misconception. The mutation does not 'reduce hemoglobin'; it keeps it at a normal level. Would you like me to show you that, again?

We examined three significant tag single-nucleotide polymorphisms (SNPs, rs13419896, rs4953354, and rs4953388) in the EPAS1 gene in Sherpas, and compared these variants with Tibetan highlanders on the Tibetan Plateau as well as with non-Sherpa lowlanders. We found that Sherpas and Tibetans on the Tibetan Plateau exhibit similar patterns in three EPAS1 significant tag SNPs, but these patterns are the reverse of those in non-Sherpa lowlanders. The three SNPs were in strong linkage in Sherpas, but in weak linkage in non-Sherpas. Importantly, the haplotype structured by the Sherpa-dominant alleles was present in Sherpas but rarely present in non-Sherpas. Surprisingly, the average level of serum erythropoietin in Sherpas at 3440 m was equal to that in non-Sherpas at 1300 m, indicating a resistant response of erythropoietin to high-altitude hypoxia in Sherpas.
https://journals.plos.org/plosone/artic ... ne.0050566

Mol Biol Evol. 2017 Apr; 34(4)
Down-Regulation of EPAS1 Transcription and Genetic Adaptation of Tibetans to High-Altitude Hypoxia
We showed that the Tibetan-enriched EPAS1 variants down-regulate expression in human umbilical endothelial cells and placentas. Heterozygous EPAS1 knockout mice display blunted physiological responses to chronic hypoxia, mirroring the situation in Tibetans. Furthermore, we found that the Tibetan version of EPAS1 is not only associated with the relatively low hemoglobin level as a polycythemia protectant, but also is associated with a low pulmonary vasoconstriction response in Tibetans. We propose that the down-regulation of EPAS1 contributes to the molecular basis of Tibetans’ adaption to high-altitude hypoxia.

Remember when I said that fitness counts only in terms of environment? That's what Darwin pointed out, too.
Yes, I know that is why the phrase "survival of the fittest" is a tautology.
As you learned, natural selection is not a tautology, since it doesn't actually depend on survival, but reproduction.

You don't seem to know what evolutionary theory is. Explain to me how it would predict that everyone in at least China would have the same function. BTW, if it was deleterious at lower altitudes, that would be consistent with evolutionary theory, which again points out that fitness only counts in terms of the environment. But there is no selective reason for a neutral mutation to spread through a population. I asked you several times what you think the scientific definition of biological evolution is. Perhaps that's the problem. But you seem unwilling to say.
So then why did you claim that this HPAS1 allele mutation was evolution?
Because it is. As I mentioned, you still seem to be unaware of what biological evolution is. Have you figured out what it is, yet? You seem very reluctant to tell us what you think it is.
Or do you not believe in Dollo's law?
You've perhaps misunderstood what it is:
The statement is often misinterpreted as claiming that evolution is not reversible,[3] or that lost structures and organs cannot reappear in the same form by any process of devolution.[4][5] According to Richard Dawkins, the law is "really just a statement about the statistical improbability of following exactly the same evolutionary trajectory twice (or, indeed, any particular trajectory), in either direction".[6] Stephen Jay Gould suggested that irreversibility forecloses certain evolutionary pathways once broad forms have emerged: "[For example], once you adopt the ordinary body plan of a reptile, hundreds of options are forever closed, and future possibilities must unfold within the limits of inherited design."[7]
https://en.wikipedia.org/wiki/Dollo%27s ... ersibility

For example, if all Tibetans where homozygous for the HPAS1 mutation, we would still expect a population of Tibetans moving to lower altitudes to lose that adaptation over time. It's just that it would be highly unlikely for the new HPAS1 allele to be identical to the one normally present in Han Chinese. Dolo's law basically says that the same sequence of mutations is unlikely to occur, but it of course does not rule out similar mutations with the same effect. But since the unmutated allele is still present in some Tibetans, a more likely result would be that mutation increasing in the new population. Again, you don't seem to actually know what biological evolution is. Why not look it up and we'll talk about it?

They just couldn't survive very well eating only plants. So when they were moved to a location without sufficient prey, they evolved new adaptations to survive on plants alone.

Why don't you test that and move the lizards back to their original environment and see if these lizards lose this "new evolutionary structure."
Or is this another violation of Dollo's law?
That would likely not be a violation of Dollo's law, since the mutation, if they became established in the population, would not happen precisely as they did. For example, humans retain an appendix, even though humans don't ferment plant material as many other mammals do. The organ merely became vestigial for that function. Probably, you'd see the cecal valve evolving that way, to a vestigial form for fermentation of plant material. Of course, it's possible that the adapted lizards might find a suitable source of plant food in their old environment and continue as a separate population from the usual wall lizards.

As far as Dollo's law being violated for real, it happens from time to time...
https://onlinelibrary.wiley.com/doi/ful ... 11.01221.x

If you're unable to find the scientific definition of biological evolution, would you like me to tell you what it is? And please make sure you understand what "vestigial" means in biology before you comment on it. Fair enough?

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Re: Abiogenesis and Probabilities

Post #413

Post by EarthScienceguy »

[Replying to Difflugia in post #0]
My college degree major was computer science and my minor was biology. My day job is writing data analysis software for automated elemental and molecular analysis equipment. This is exactly my area of expertise. If you want to bluff and snort, pick a different topic.
I do not have a degree in computer science and I am not even saying that algorithm is incorrect. What I am saying the philosophy behind the algorithm is incorrect and is not testable because it cannot be observed.

Take for example duplication events, for evolution to be internally consistent theory chromosomes and genomes must be duplicated and changed. We see that nowhere in nature but only in phylogenetic programs. In nature, we only see severe problems associated with duplicated chromosomes.

Evolution is also supposed to be irreversible and yet in nature the changes that we see are reversible.

Adaptation is based on environmental stressors. How can this be known when we are still debating what killed the dinosaurs and the other 5 major extinctions that are part of deep time theology let alone regional stressors.

Even if the basic theory of evolution did not have major problems. Your program could not possibly do what you are saying it can do because we do not have enough information about the past.

Thanks to the US National Institutes of Health, that exactly describes molecular phylogenetic analysis. Any researcher that uses NIH grant money in genomic research must submit any generated sequences to the GenBank database. Many other researchers, particularly those outside of the US, do so voluntarily. As a result, anyone can access the database and download the sequences of millions of genes from hundreds of thousands of organisms. The software you need to analyze the data is free to download and runs easily on my crappy laptop. I wrote about it just shy of two years ago in another thread that you also posted in.

There are enough data in that database to prove or disprove many facets of evolutionary theory and anyone can download the data and do the analysis themselves. Once you figure out the software (I use PHYLIP and MUSCLE) and the GenBank search interface, you can formulate experiments on the data that potentially nobody else has ever thought of and then run them yourself. You can think of the most damning and evolutionarily impossible gotchas that Jesus might have coded into the genomes of various yeasts and flatworms, then look for them.
And people have. Take for example the supposed chimp to human evolution. Chimps have 48 chromosomes and humans have 46 chromosomes. Your phylogenetic tree predicts or was inputted either one that there was a telomere to telomere fusion in chromosome 2. One of the many problems with that belief is that mammals do not fuse chromosomes telomere to telomere because of the functional genes on the ends of chromosomes.

If the input data is incorrect the output is going to be incorrect no matter what the algorithm is.

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Re: Abiogenesis and Probabilities

Post #414

Post by Difflugia »

EarthScienceguy wrote: Thu Nov 04, 2021 10:47 amI do not have a degree in computer science and I am not even saying that algorithm is incorrect. What I am saying the philosophy behind the algorithm is incorrect and is not testable because it cannot be observed.
What do you mean that "it cannot be observed?" What is "it?" What is "observed?" The pattern in the data is what we're looking for. If evolution happened and we were omniscient, we'd be able to see pattern of speciations and extinctions that we could draw as a (mostly) binary tree. When a speciation event occurs, a node gains two children. All terminal nodes represent either an extinction or the present moment. If our ideas about inheritance and mutation are correct, we should be able to almost completely derive that same pattern from molecular genome data by sequencing organisms that are alive now. That in itself says nothing of mechanism, but we can map the derived pattern onto the actual, historical pattern that we know from our omniscience.

We're not omniscient, though. Instead, what we have to do is, first, see if we can derive the same data in multiple independent ways, and second, think of all the historical narratives that might be responsible for the pattern and ensure that they're all worse at explaining the pattern than evolution is. The first was covered when scientists realized that the molecular data gave the same results as cladistic data, but with much, much better resolution. The second is covered by showing that the pattern is present in all genetic data, even when the genes are otherwise funtionally identical. Most mitochondrial genes, for example, have identical functions in at least all mammals, and many are identical across nearly all eukaryotes. If the phylogenetic pattern were the result of similar design as many creationists assert, for example, then mitochondrial genes should show a different pattern than the apparent evolutionary one in nuclear genes. They don't. The pattern's the same, even when the differences can be shown to be the result of neutral drift.

Your objection seems to be that since this paper in particular hasn't proven that the homologous genes were in fact the result of gene duplication, then the paper is invalid. That's false. If the author had replaced every instance of "duplicate gene" with "genetic pattern indistinguishable from a duplicate gene," then we in science would have rolled our eyes, but it wouldn't have affected the conclusion or its importance. It's like failing to say "alleged thief" for someone with a hand in the cookie jar and in the process of signing a confession, but that hasn't been convicted yet. Yes, we know that there's a series of vanishingly improbable events that could explain what we're seeing, but the failure to acknowledge it can't damage the power of the evidence.

As I said before, your claim was that "most of the time duplication is lethal." Scientists have shown that duplications happen and the resulting genes are ubiquitous within the genome. With things like bacteria, yeasts, and Drosophila, they've been in the room when they happen. They're a bit of a problem with personal genetic testing. Now, if you're going to claim that some apparent gene duplications weren't really gene duplications, that still doesn't buy anything for your thesis. Even if you're absolutely right, there's just some unidentified mechanism that can mimic gene duplication and you're back where you started unless you can posit a way to identify the difference.
EarthScienceguy wrote: Thu Nov 04, 2021 10:47 amTake for example duplication events, for evolution to be internally consistent theory chromosomes and genomes must be duplicated and changed. We see that nowhere in nature but only in phylogenetic programs. In nature, we only see severe problems associated with duplicated chromosomes.
I assumed before that you just meant in humans, but you mean at all? Like across all organisms? How about tetraploid frogs and apples? Or is that not what you mean. It's hard to tell what you mean.
EarthScienceguy wrote: Thu Nov 04, 2021 10:47 amEvolution is also supposed to be irreversible and yet in nature the changes that we see are reversible.
What does that even mean? Who said that "evolution is irreversible?" Gene loss is, for obvious reasons, irreversible, but any duplication or SNP is potentially reversible.
EarthScienceguy wrote: Thu Nov 04, 2021 10:47 amAdaptation is based on environmental stressors. How can this be known when we are still debating what killed the dinosaurs and the other 5 major extinctions that are part of deep time theology let alone regional stressors.
What point do you think this makes?
EarthScienceguy wrote: Thu Nov 04, 2021 10:47 amEven if the basic theory of evolution did not have major problems. Your program could not possibly do what you are saying it can do because we do not have enough information about the past.
It does exactly what I said it does. BLAST finds similar genes in a database according to a set of alignment rules. That's it. If you're going to claim that they weren't the result of past gene duplication, that's up to you to demonstrate. I've been trying to explain why your incorrect "I think X" arguments are likely wrong, but even if I can't, my inability to figure out why you think something inexplicable doesn't somehow transform it into a valid argument.
EarthScienceguy wrote: Thu Nov 04, 2021 10:47 amAnd people have. Take for example the supposed chimp to human evolution. Chimps have 48 chromosomes and humans have 46 chromosomes. Your phylogenetic tree predicts or was inputted either one that there was a telomere to telomere fusion in chromosome 2.
"My" phylogenetic tree doesn't predict that, but sequencing chromosome 2 showed genes orthologous to those on chimpanzee chromosomes 12 and 13, an anomalous region of telomeres in the middle of the chromosome, and a broken centromere in the region corresponding to chimpanzee chromosome 13. Those are easy to explain with a "telomere to telomere fusion," but extraordinarily difficult otherwise.
EarthScienceguy wrote: Thu Nov 04, 2021 10:47 amOne of the many problems with that belief is that mammals do not fuse chromosomes telomere to telomere because of the functional genes on the ends of chromosomes.
You're going to have to flesh that out a bit; "lol nope" isn't really much of an argument.
EarthScienceguy wrote: Thu Nov 04, 2021 10:47 amIf the input data is incorrect the output is going to be incorrect no matter what the algorithm is.
What do you think that means? Are the sequences in the database incorrect or falsified? The computations for the distance calculations and tree generation are based on a relatively simple set of rules. The fact that the rules find the expected pattern nearly every single time is powerful evidence that both the methods of data collection and the analysis rules are valid.
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Re: Abiogenesis and Probabilities

Post #415

Post by JoeyKnothead »

EarthScienceguy wrote: Thu Nov 04, 2021 10:47 am I do not have a degree in computer science and I am not even saying that algorithm is incorrect. What I am saying the philosophy behind the algorithm is incorrect and is not testable because it cannot be observed.
If ya ain't saying the algorithm is incorrect, then you can't posit any reliable argument that the results're wrong.
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Re: Abiogenesis and Probabilities

Post #416

Post by EarthScienceguy »

[Replying to The Barbarian in post #0]
I'm correcting your misconception. The mutation does not 'reduce hemoglobin'; it keeps it at a normal level. Would you like me to show you that, again?

We examined three significant tag single-nucleotide polymorphisms (SNPs, rs13419896, rs4953354, and rs4953388) in the EPAS1 gene in Sherpas, and compared these variants with Tibetan highlanders on the Tibetan Plateau as well as with non-Sherpa lowlanders. We found that Sherpas and Tibetans on the Tibetan Plateau exhibit similar patterns in three EPAS1 significant tag SNPs, but these patterns are the reverse of those in non-Sherpa lowlanders. The three SNPs were in strong linkage in Sherpas, but in weak linkage in non-Sherpas. Importantly, the haplotype structured by the Sherpa-dominant alleles was present in Sherpas but rarely present in non-Sherpas. Surprisingly, the average level of serum erythropoietin in Sherpas at 3440 m was equal to that in non-Sherpas at 1300 m, indicating a resistant response of erythropoietin to high-altitude hypoxia in Sherpas.
https://journals.plos.org/plosone/artic ... ne.0050566

Mol Biol Evol. 2017 Apr; 34(4)
Down-Regulation of EPAS1 Transcription and Genetic Adaptation of Tibetans to High-Altitude Hypoxia
We showed that the Tibetan-enriched EPAS1 variants down-regulate expression in human umbilical endothelial cells and placentas. Heterozygous EPAS1 knockout mice display blunted physiological responses to chronic hypoxia, mirroring the situation in Tibetans. Furthermore, we found that the Tibetan version of EPAS1 is not only associated with the relatively low hemoglobin level as a polycythemia protectant, but also is associated with a low pulmonary vasoconstriction response in Tibetans. We propose that the down-regulation of EPAS1 contributes to the molecular basis of Tibetans’ adaption to high-altitude hypoxia.
The hemoglobin concentration is not as high in Tibetan's as in others that do not have the same allele as the Tibetan's. So the Tibetan's with this high altitude allele, their hemoglobin is not as high or is reduced from the level of those without that allele.

But if we go by the article that you are citing the EPAS1 allele does reduce the hemoglobin that is what a polycythemia protectant is. And there are even drugs that you can take to reduce the hemoglobin.
Jakafi is a prescription medicine used to treat adults with polycythemia vera who have already taken a medicine called hydroxyurea and it did not work
https://www.jakafi.com/polycythemia-ver ... lsrc=aw.ds
So also according to your article, the EPAS1 allele also has "low pulmonary vasoconstriction" so it keeps the pulmonary artery from constricting. Which also usually happens at high altitudes to those that do not have the EPAS1 allele. Your article does not indicate how the EPAS1 allele makes the body believe that it has enough oxygen so that it does not constrict the pulmonary artery.

My guess is that the EPAS1 allele maintains the heme oxygenase-2 system at a consistent level. The heme oxygenase-2 system senses the oxygen in the blood and produces carbon dioxide when blood is adequately oxygenated. When the blood is not adequately oxygenated the heme oxygenase-2 system does not produce carbon dioxide and the body then constricts the pulmonary artery and increases hemoglobin production.

So where are the new structures you were speaking of?
Yes, I know that is why the phrase "survival of the fittest" is a tautology.
As you learned, natural selection is not a tautology, since it doesn't actually depend on survival, but reproduction.
If a species does not reproduce then it does not survive. Reproduction is basic to survival, so that would still make it a tautology. Try again.
You don't seem to know what evolutionary theory is. Explain to me how it would predict that everyone in at least China would have the same function. BTW, if it was deleterious at lower altitudes, that would be consistent with evolutionary theory, which again points out that fitness only counts in terms of the environment.

But there is no selective reason for a neutral mutation to spread through a population.
Ok, so far you have said:

1. That evolution is not irreversible if the environmental results push the way it came. Like a reversible chemical reaction can go in both directions.
2. That survival does not depend on reproduction.
3. That neutral mutations cannot spread through a population.

You have just falsified evolution yourself.

1. If you are saying that evolution is not irreversible then you are indicating that there is no such thing as fixation of traits in a species.
2. If you are saying that survival does not dependent on reproduction then there would be no way for traits to spread through a population.
3. If you are saying that neutral mutations cannot spread through a population then you have no answer to Haldane's dilemma.

Evidently, it is you who do not believe in evolution.
The statement is often misinterpreted as claiming that evolution is not reversible,[3] or that lost structures and organs cannot reappear in the same form by any process of devolution.[4][5] According to Richard Dawkins, the law is "really just a statement about the statistical improbability of following exactly the same evolutionary trajectory twice (or, indeed, any particular trajectory), in either direction".

[6] Stephen Jay Gould suggested that irreversibility forecloses certain evolutionary pathways once broad forms have emerged: "[For example], once you adopt the ordinary body plan of a reptile, hundreds of options are forever closed, and future possibilities must unfold within the limits of inherited design."[7]
https://en.wikipedia.org/wiki/Dollo%27s ... ersibility
So which is it. These are totally different ideas.

If evolutionary pathways are forever closed then that would be that evolution is irreversible.

If it is a statement about statistical improbability then the door is left open. But if it is like other probability statements in evolution then it is really closed and irreversible.

That would likely not be a violation of Dollo's law, since the mutation, if they became established in the population, would not happen precisely as they did. For example, humans retain an appendix, even though humans don't ferment plant material as many other mammals do. The organ merely became vestigial for that function. Probably, you'd see the cecal valve evolving that way, to a vestigial form for fermentation of plant material. Of course, it's possible that the adapted lizards might find a suitable source of plant food in their old environment and continue as a separate population from the usual wall lizards.
So are you trying to suggest that ht appendix does not have a function? That would be against modern science.
Research in recent years has shown that the human appendix has lymphoid cells, which help the body fight infections. This strongly suggests that the appendix plays a role in the immune system.

The appendix has been found to play a role in mammalian mucosal immune function. It is believed to be involved in extrathymically derived T-lymphocytes and B-lymphocyte-mediated immune responses. It is also said to produce early defences that help prevent serious infections in humans. https://www.news-medical.net/health/Why ... endix.aspx


As far as Dollo's law being violated for real, it happens from time to time...
https://onlinelibrary.wiley.com/doi/ful ... 11.01221.x
Recently, Goldberg and Igic (2008) suggested that violation of Dollo's law is a “spectacular claim” (p. 2730) and that many of these examples may simply be the result of “devastating flaws” (p. 2727) in the methods used. Specifically, they suggested that previous studies were compromised by assumptions about state frequencies at the root of these phylogenies and by failure to account for the possible impact of the character on patterns of diversification (speciation and extinction).
When you all settle this debate amongst yourselves let me know.
And please make sure you understand what "vestigial" means in biology before you comment on it. Fair enough?
It would be fair if you would tell me which definition you are using. Because like most things in evolutionary theology the definition of a vestigial organ is a moving target. So which definition are you using? How are you defining the evolution of vestigial organs?

1. Vestigial organs are the organs that have no apparent function and are considered to be the residual parts from the past ancestors.” https://byjus.com/biology/vestigial-organs/
2. Vestigial organs are organs, tissues or cells in a body which are no more functional the way they were in their ancestral form of the trait. It is authentication of evolution and hence, were helpful in explaining adaptation. https://byjus.com/biology/vestigial-organs/
3. “a bodily part or organ that is small and degenerate or imperfectly developed in comparison to one more fully developed in an earlier stage of the individual, in a past generation, or in closely related forms.” The Merriam-Webster’s Dictionary
4. Vestigial organs and body parts refer to those that have little or no purpose in humans. They are a vestige left over from our ancestors. https://universityhealthnews.com/daily/ ... dont-need/
5. A "vestigial structure" or "vestigial organ" is an anatomical feature or behavior that no longer seems to have a purpose in the current form of an organism of the given species. https://www.thoughtco.com/about-vestigi ... es-1224771

So which definition is your theological preference?

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Re: Abiogenesis and Probabilities

Post #417

Post by The Barbarian »

EarthScienceguy wrote: Thu Nov 04, 2021 4:44 pm The hemoglobin concentration is not as high in Tibetan's as in others that do not have the same allele as the Tibetan's.
No, that's wrong. They have about the same hemoglobin content as you do.
So the Tibetan's with this high altitude allele, their hemoglobin is not as high or is reduced from the level of those without that allele.
The new allele prevents them from having a greatly increased concentration of hemoglobin, which happens to people without that allele at high elevations. You have it backwards.
But if we go by the article that you are citing the EPAS1 allele does reduce the hemoglobin that is what a polycythemia protectant is.
No, it prevents an elevated level of hemoglobin, thanks to that new and useful mutation.
And there are even drugs that you can take to reduce the hemoglobin.
But because those with that new mutation don't have elevated levels of hemoglobin, they don't need the drugs. You and I would, because we don't have that mutation.
So where are the new structures you were speaking of?
You're confusing the HPAS-1 mutation with the lizards. You see, a useful mutation sometimes produces a new structure. But there are other traits besides anatomical ones. So this useful new trait is biochemical.
Yes, I know that is why the phrase "survival of the fittest" is a tautology.
As you learned, natural selection is not a tautology, since it doesn't actually depend on survival, but reproduction.
If a species does not reproduce then it does not survive.


As you learned, some traits are harmful to the individual's survival, but still produce more offspring. So you were wrong about that, too.
Reproduction is basic to survival, so that would still make it a tautology.
Nope. And if you thought about it for a minute, I bet you would realize why:
The term "fitness" is used in evolutionary biology in relation to selection. A particular version of a genetic trait may have more or less fitness than an alternative version of that trait. So for instance, say there's a gene that, in primates, codes for a protein essential for the implantation of a fertilized egg. Now, imagine a version of that gene that does not function at all. That would be a trait that has a different fitness than the 'wild' or 'normal' type. Specifically, it would have less fitness. Or, imagine that the run of the mill protein that helps with implantation works 90 percent of the time, but a new version comes along via mutation (by chance) that works 98 percent of the time. That version of the gene would potentially be selected for. It would have higher fitness.

So fitness is linked to selection. Something being selected for is something with higher fitness. So, to say "Natural Selection is survival of the fittest" where "the fittest" means "more genetic fitness" is a false tautology. It is a tautology because it says "fitness equals fitness" and it is a false tautology because natural selection does not usually mean more fit. Usually, it means elimination of the not-as-fit. Most mutations lead to broken, not fitness-enhanced, genetic variance. So, really, "Natural selection is the elimination of less-fit alleles" is way, way more correct, but still only partially correct.

https://scienceblogs.com/gregladen/2009 ... s-survival

You could invoke natural selection and say that reproduction rates change when selected for or against, and therefore reproductive rates are changed when affected by natural selection.
You could invoke Newton's First Law and say that when acted on by an outside force objects change velocity , therefore objects changing velocity have been acted on by an outside force.

But neither of these is a tautology. In fact, we can (and do) make predictions based on natural selection, and they can be verified to be true. Indeed, this has been mathematically demonstrated; population geneticists use the Hardy-Weinberg equation to detect natural selection for given alleles. Try again.

You don't seem to know what evolutionary theory is. Explain to me how it would predict that everyone in at least China would have the same function. BTW, if it was deleterious at lower altitudes, that would be consistent with evolutionary theory, which again points out that fitness only counts in terms of the environment.

But there is no selective reason for a neutral mutation to spread through a population.
Ok, so far you have said:
I said it would be useful and clear up a lot of what appears to be misconceptions on your part, if you would tell us what you think the scientific definition of biological evolution is. So far, you've been dodging that repeated question. I gather you either don't have any idea and don't want to admit it, or you do know, and realize that admitting what it is, would damage your argument. Want to bite the bullet and tell us what you think?
1. That evolution is not irreversible if the environmental results push the way it came. Like a reversible chemical reaction can go in both directions.
That would be pretty rare. It would require the same specific mutations to be reversed. Which does happen in point mutations,but not in more complex adaptive evolution like those lizards which evolved a new structure. But the same trait that was lost, could be regained by other mutations.
2. That survival does not depend on reproduction.
That was your statement. I pointed out that natural selection, by enhancing reproduction, could also reduce likelihood of survival for those with a useful mutation. Reproductive success does not depend on increased survival of an organism. You have that backwards, too.
3. That neutral mutations cannot spread through a population.
No. I said there was no selective reason for a neutral mutation to spread though a population. It can happen, but not by natural selection.
You have just falsified evolution yourself.
You've merely invented odd ideas and insist that I believe them.
1. If you are saying that evolution is not irreversible then you are indicating that there is no such thing as fixation of traits in a species.
Perhaps you don't know what "fixation" means in population genetics. What do you think it means? Hint: it doesn't have anything to do with reversible mutations.
2. If you are saying that survival does not dependent on reproduction then there would be no way for traits to spread through a population.
That was your statement. As you now realize, you got that one backwards. Reproductive success does not mean greater survival for individual having reproductive success. In many cases, they actually die sooner than individuals that are not reproductively successful.
3. If you are saying that neutral mutations cannot spread through a population
That was your statement, not mine. Neutral mutations can spread though a population, but not by natural selection.
then you have no answer to Haldane's dilemma.
Not that I expect an answer by now, but would you mind telling us what you think Haldane's Dilemma says?
Evidently, it is you who do not believe in evolution.
This goes back to you not knowing what biological evolution is. In fact, evolution is constantly observed and documented in many ways by biologists. It's not just big changes like those new cecal valves in lizards. Seriously, you've be a lot more effective fighting evolution, if you knew what it is. Worth learning?
The statement is often misinterpreted as claiming that evolution is not reversible,[3] or that lost structures and organs cannot reappear in the same form by any process of devolution.[4][5] According to Richard Dawkins, the law is "really just a statement about the statistical improbability of following exactly the same evolutionary trajectory twice (or, indeed, any particular trajectory), in either direction".

[6] Stephen Jay Gould suggested that irreversibility forecloses certain evolutionary pathways once broad forms have emerged: "[For example], once you adopt the ordinary body plan of a reptile, hundreds of options are forever closed, and future possibilities must unfold within the limits of inherited design."[7]
https://en.wikipedia.org/wiki/Dollo%27s ... ersibility
So which is it.
They are both true. Even if an adaptation involves only three mutations, each with a probability of 0.1, there's only one chance in 1,000 that a reversal is possible, even without a number of other complicating factors (we can discuss those if you like). On the other hand, even if almost all of the basic HOX genes of a sea urchin and a turtle are the same basic design, no population of turtles will ever evolve into an echinoderm, because there are no viable ways for reptiles to evolve transitional stages. Such transitional forms exist, but can't form from reptiles. Would you like to learn why?
If evolutionary pathways are forever closed then that would be that evolution is irreversible.
You're still not clear on how mutations work. A single point mutation in a population (which is by definition evolution) can be reversed by a mutation that restored the former nucleotide.
That would likely not be a violation of Dollo's law, since the mutation, if they became established in the population, would not happen precisely as they did. For example, humans retain an appendix, even though humans don't ferment plant material as many other mammals do. The organ merely became vestigial for that function. Probably, you'd see the cecal valve evolving that way, to a vestigial form for fermentation of plant material. Of course, it's possible that the adapted lizards might find a suitable source of plant food in their old environment and continue as a separate population from the usual wall lizards.
So are you trying to suggest that ht appendix does not have a function?
I'm pointing out that you don't know the definition of "vestigial." Look it up.

That would be against modern science.



As far as Dollo's law being violated for real, it happens from time to time...
https://onlinelibrary.wiley.com/doi/ful ... 11.01221.x
Recently, Goldberg and Igic (2008) suggested that violation of Dollo's law is a “spectacular claim”
Too bad for them then. Back mutations are a documented fact:
https://medical-dictionary.thefreedicti ... k+mutation
And please make sure you understand what "vestigial" means in biology before you comment on it. Fair enough?
It would be fair if you would tell me which definition you are using.
The one used in evolutionary theory since Darwin first discussed it.
Because like most things in evolutionary theology the definition of a vestigial organ is a moving target.
No, you're wrong about that, too. It appears that you're using the flexible creationist definition. The scientific one is quite clear and unequivocal. I don't expect you to say, but I'd be interested in what you think the scientific definition of vestigial is. Early on, the term was "rudimentary", but they mean the same thing in biology. So is this one more definition you don't know, and won't venture a guess about?
How are you defining the evolution of vestigial organs?
Works the same way as other evolution. Since you've continued to refuse to tell us what you think the scientific term for evolution is, is it time for me to tell you so you know?
1. Vestigial organs are the organs that have no apparent function and are considered to be the residual parts from the past ancestors.” https://byjus.com/biology/vestigial-organs/
No, that's wrong. And it's been wrong since Darwin pointed out that "rudimentary" did not mean "no function."
2. Vestigial organs are organs, tissues or cells in a body which are no more functional the way they were in their ancestral form of the trait. It is authentication of evolution and hence, were helpful in explaining adaptation. https://byjus.com/biology/vestigial-organs/
This is good. Do you see the difference?
3. “a bodily part or organ that is small and degenerate or imperfectly developed in comparison to one more fully developed in an earlier stage of the individual, in a past generation, or in closely related forms.” The Merriam-Webster’s Dictionary
Wrong.
4. Vestigial organs and body parts refer to those that have little or no purpose in humans. They are a vestige left over from our ancestors. https://universityhealthnews.com/daily/ ... dont-need/
5. A "vestigial structure" or "vestigial organ" is an anatomical feature or behavior that no longer seems to have a purpose in the current form of an organism of the given species. https://www.thoughtco.com/about-vestigi ... es-1224771
Nope. That's wrong, too. Your theological preference for informal sources tripped you up again.

Here's the proper definition: "A structure that no longer serves its original function." Darwin pointed out that such structures often become adapted for other purposes, and are often not useless.

I've just handed you a definition. Do you suppose you might step up and give us the definition of those other terms I've asked you to define? Tell you what; if you don't know the definitions of any or all of the rest, just say so, and I'll explain them to you. Or you could tell us what you think they are. Which will it be?

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Re: Abiogenesis and Probabilities

Post #418

Post by EarthScienceguy »

[Replying to The Barbarian in post #417]
1. Vestigial organs are the organs that have no apparent function and are considered to be the residual parts from the past ancestors.” https://byjus.com/biology/vestigial-organs/
No, that's wrong. And it's been wrong since Darwin pointed out that "rudimentary" did not mean "no function."
2. Vestigial organs are organs, tissues or cells in a body which are no more functional the way they were in their ancestral form of the trait. It is authentication of evolution and hence, were helpful in explaining adaptation. https://byjus.com/biology/vestigial-organs/
This is good. Do you see the difference?
3. “a bodily part or organ that is small and degenerate or imperfectly developed in comparison to one more fully developed in an earlier stage of the individual, in a past generation, or in closely related forms.” The Merriam-Webster’s Dictionary
Wrong.
4. Vestigial organs and body parts refer to those that have little or no purpose in humans. They are a vestige leftover from our ancestors. https://universityhealthnews.com/daily/ ... dont-need/
5. A "vestigial structure" or "vestigial organ" is an anatomical feature or behavior that no longer seems to have a purpose in the current form of an organism of the given species. https://www.thoughtco.com/about-vestigi ... es-1224771

Nope. That's wrong, too. Your theological preference for informal sources tripped you up again.

Here's the proper definition: "A structure that no longer serves its original function." Darwin pointed out that such structures often become adapted for other purposes, and are often not useless.
I will answer this last part because evidently, you cannot defend your position with actual researched facts.

Point out to me the definition that is from any creation journal. You can't because they are not.

biology online defines vestal organ like this: refers to an organ or part (for example, the human appendix) which is greatly reduced from the original ancestral form and is no longer functional or is of reduced or altered function. https://www.biologyonline.com/dictionary/vestigial

The medical dictionary; vestigial organ any organ that during the course of evolution has become reduced in function and usually size. https://medical-dictionary.thefreedicti ... gial+organ

New World Encyclopedia In evolutionary biology and comparative anatomy, "vestigiality" in a species describes organs (vestigial organs), structures (vestigial structures), behaviors, and biochemical pathways that have seemingly lost all or most of an original function present in ancestor species. These structures are typically in a degenerate, atrophied, or rudimentary condition, and are often called vestigial organs, despite some of them not being actual organs.

Like seriously can you cite anyone that uses that definition. And could you explain why there was a change in the definition? It is not really kosher to make uncited statements in response to cited statements if they are different.

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Re: Abiogenesis and Probabilities

Post #419

Post by EarthScienceguy »

[Replying to The Barbarian in post #417]
The term "fitness" is used in evolutionary biology in relation to selection. A particular version of a genetic trait may have more or less fitness than an alternative version of that trait. So for instance, say there's a gene that, in primates, codes for a protein essential for the implantation of a fertilized egg. Now, imagine a version of that gene that does not function at all. That would be a trait that has a different fitness than the 'wild' or 'normal' type. Specifically, it would have less fitness. Or, imagine that the run of the mill protein that helps with implantation works 90 percent of the time, but a new version comes along via mutation (by chance) that works 98 percent of the time. That version of the gene would potentially be selected for. It would have higher fitness.

So fitness is linked to selection. Something being selected for is something with higher fitness. So, to say "Natural Selection is survival of the fittest" where "the fittest" means "more genetic fitness" is a false tautology. It is a tautology because it says "fitness equals fitness" and it is a false tautology because natural selection does not usually mean more fit. Usually, it means the elimination of the not-as-fit. Most mutations lead to broken, not fitness-enhanced, genetic variance. So, really, "Natural selection is the elimination of less-fit alleles" is way, way more correct, but still only partially correct.
https://scienceblogs.com/gregladen/2009 ... s-survival
Elimination of the less fit still means survival of the fittest genes. It is not a tautology because fitness equals fitness but because fitness equals survival. Therefore "survival of the fittest" is a tautology.

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Re: Abiogenesis and Probabilities

Post #420

Post by The Barbarian »

EarthScienceguy wrote: Tue Nov 09, 2021 12:00 pm Elimination of the less fit still means survival of the fittest genes.
So now, it's about genes surviving, not individuals? You're getting closer. Remember when you learned that fitness doesn't mean "survive", but rather "leave your genes to the next generation?"
That's what evolution is about. Have you learned what the scientific definition is yet, or do you want me to show you what it is?
It is not a tautology because fitness equals fitness
You're still not getting it. Fitness means "more likely to leave viable offspring." And notice that because it's only a matter of likelihoods, it can't be reduced to "fitness equals survival." As you saw in the case of peacocks, fitness can actually work against survival of the individual.
but because fitness equals survival.
But it doesn't. It only increases the likelihood of leaving viable offspring.
Therefore "survival of the fittest" is a tautology.
Bad assumption, faulty conclusion. Are there any definitions I've asked you about, that you'd care to give us now? There are quite a few of them, you've refused to tell us about, or even tell us what you think they might be. And this is holding you back in understanding the issue.
Last edited by The Barbarian on Tue Nov 09, 2021 9:19 pm, edited 1 time in total.

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