Abiogenesis and Probabilities

[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?

[EarthScienceguy]

[Replying to Difflugia in post #394]

That's wrong. Most of the time gene duplication is neutral, even if both copies are expressed. In fact, gene duplication events seem to increase organism robustness and life expectancy in the short term.

The "paper" you referenced used "BlastP" to predict their results that is what the P stands for Predicts. The predicted means that there is no experimental evidence that the protein is produced by the isolate that was sequenced. Brian Thomas Foley Los Alamos National Laboratory

I will back off of the lethal, and go to a more conservative mostly deleterious to lethal as is the case with all mutations.

Duplications cause genetic diseases like

1. Pallister Killian syndrome
2. Down syndrome
3. Edwards' syndrome have an extra chromosome 18 present in all cells. This is called full Edwards' syndrome. The effects of full Edward's syndrome are often more severe. Sadly, most babies with this form will die before they are born.
4. Patau's syndrome
5. trisomy 18
6. MECP2 duplication syndrome
7. Trisomy 13

Can you name any duplications that are beneficial that are not part of some phylogenetic story but based on actual observation?

[EarthScienceguy]

[Replying to Difflugia in post #400]

That's what Jean Baptiste Lamarck thought. He was wrong, too. The Soviets demonstrated that rather ironically.

That would be what we call in science a prediction based on a proposed hypothesis .

[Difflugia]

The "paper" you referenced used "BlastP" to predict their results that is what the P stands for Predicts.

You unironically quote Answers in Genesis, but you put scare quotes around a "paper" published in PLOS Genetics?

The predicted means that there is no experimental evidence that the protein is produced by the isolate that was sequenced.

That's really reaching and isn't a valid point pretty much no matter how one looks at it. The most charitable interpretation of your statement is that you're making a declaration that similar genes weren't produced by duplication events. That turns your entire argument into a circular one in which beneficial genes that evolutionary theory assigns to duplication events actually came about by some other means. However, if obvious homologs weren't actually the result of gene duplication, then your claim that gene duplications are primarily deleterious is meaningless and we need to focus on your unspecified mechanism instead. Does the finger of God produce primarily deleterious mutations (or whatever you call them)?

I will back off of the lethal, and go to a more conservative mostly deleterious to lethal as is the case with all mutations.

Duplications cause genetic diseases like

1. Pallister Killian syndrome
2. Down syndrome
3. Edwards' syndrome have an extra chromosome 18 present in all cells. This is called full Edwards' syndrome. The effects of full Edward's syndrome are often more severe. Sadly, most babies with this form will die before they are born.
4. Patau's syndrome
5. trisomy 18
6. MECP2 duplication syndrome
7. Trisomy 13

With one exception, those are duplications of entire chromosomes, which is not what gene duplication refers to. And yes, if a gene that serves a regulatory function based on concentration is duplicated, the result would likely be deleterious. In that one instance, nobody is surprised.

Can you name any duplications that are beneficial that are not part of some phylogenetic story but based on actual observation?

In your mind, what does "actual observation" entail here if not a "phylogenetic story"? If the "actual observation" of a genome shows historical gene duplication events that were beneficial, but you deny that they were duplication events, then on what basis are you claiming that duplication events are deleterious? If you deny the validity of scientific observation, how would you identify a duplication event to claim that it's deleterious?

That would be what we call in science a prediction based on a proposed hypothesis .

You scientists sure are a pedantic bunch.

[The Barbarian]

Your quote said exactly what I said.

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.

That EPAS1 reduces the hemoglobin concentration in upper elevations.

No. It maintains normal hemoglobin concentrations, thereby avoiding high altitude sickness of those people lacking the new adaptation, who must increase their hemoglobin. You have it precisely backwards.

Your quote says nothing about the new function that you say the Tibetans have. But it seems that there is definitely no selective advantage at lower altitudes.

Remember when I said that fitness counts only in terms of environment? That's what Darwin pointed out, too.

And it seems that this function must be deleterious at lower elevations otherwise evolutionary theory would predict that everyone in at least China would have the same function.

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 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.

Not long ago, scientists discovered that a population of lizards, moved to a new environment, rapidly evolved a new digestive organ (among other things)
Examination of the lizard’s digestive tracts revealed something even more surprising. Eating more plants caused the development of new structures called cecal valves, designed to slow the passage of food by creating fermentation chambers in the gut, where microbes can break down the difficult-to-digest portion of plants. Cecal valves, which were found in hatchlings, juveniles and adults on Pod Mrcaru, have never been reported for this species, including the source population on Pod Kopiste.
https://www.sciencedaily.com/releases/2 ... 112433.htm

They are not new structures. They are enlarged structures that have already existed.

This goes back to my point about you being unaware of what biological evolution actually is. Evolution produces nothing de novo; it's always a modification of something already there. So this new structure (a cecal valve has never been seen in these lizards before) evolved by modifying a portion of the digestive tract. That's how it always works. Would you be interested in a simple introduction to the theory, to make this easier on everyone?


It's quite accessible, even to a non-biologist.

The lizard could eat plants before they were released on the island.

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

This is also evidence of creationism and that all animals were once plant-eating.

If you think about it, the first heterotrophs had to be plant-eaters. Evolutionary theory would require that. However, creationism cannot support such a claim, since they insist that all animals were created as is, and did not evolve. So spiders obviously could not have been plant-eaters.

If the lizards were taken back to their original habitat then these cecal valves would go away.

For the same reason that Tibetans, if they moved to lower elevations, would eventually lose their new adaptation and evolve normal HPAS1 alleles; no selective purpose to the new version in lower elevations.

And how about telling us what you think the scientific definition of biological evolution is? It might clear up a lot of the difficulties.

[The Barbarian]

[Replying to Difflugia in post #400]

That's what Jean Baptiste Lamarck thought. He was wrong, too. The Soviets demonstrated that rather ironically.

That would be what we call in science a prediction based on a proposed hypothesis .

The Soviets banned Darwinian theory because it was too much like capitalist economics. Soviet agriculture and biology are still recovering from that stupidity.

[JoeyKnothead]

"Under evolutionary theory, this thing can't happen" does not exclude those many times it does.

Sure, footballs won't never be em too much good for the baseball playing. But the ability to produce viable, competitive offspring'll always be in vogue.

[EarthScienceguy]

[Replying to Difflugia in post #403]

That's really reaching and isn't a valid point pretty much no matter how one looks at it. The most charitable interpretation of your statement is that you're making a declaration that similar genes weren't produced by duplication events. That turns your entire argument into a circular one in which beneficial genes that evolutionary theory assigns to duplication events actually came about by some other means. However, if obvious homologs weren't actually the result of gene duplication, then your claim that gene duplications are primarily deleterious is meaningless and we need to focus on your unspecified mechanism instead. Does the finger of God produce primarily deleterious mutations (or whatever you call them)?

How is this BlastP system looking back in the past? What framework is the program using?

So you are trying to use evolutionary principles to prove evolutionary principles, I would call that very circular.

Any beneficial duplications yet?

With one exception, those are duplications of entire chromosomes, which is not what gene duplication refers to. And yes, if a gene that serves a regulatory function based on concentration is duplicated, the result would likely be deleterious. In that one instance, nobody is surprised.

The evolutionary hypothesis needs entire genomes to be duplicated. How is that possible? Entire chromosomes would have to be duplicated.


EarthScienceguy wrote: ↑Tue Nov 02, 2021 3:05 pm

Can you name any duplications that are beneficial that are not part of some phylogenetic story but based on actual observation?
In your mind, what does "actual observation" entail here if not a "phylogenetic story"? If the "actual observation" of a genome shows historical gene duplication events that were beneficial, but you deny that they were duplication events, then on what basis are you claiming that duplication events are deleterious? If you deny the validity of scientific observation, how would you identify a duplication event to claim that it's deleterious?

I will take that as a no you cannot give me an example of a beneficial duplication.

Cancer can be caused by duplication do you call that beneficial?

Again how can a theory be validated if the computer program that is being used is based on the theory that is being validated?

Again, evolutionary theory has to have a mechanism to duplicate entire chromosomes and genomes. All observed evidence indicates that this is not possible. Therefore the evolution of molecules to man is nothing but a fabricated story.

[EarthScienceguy]

[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. Please either site your statement or be more specific.

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.

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?

Or do you not believe in Dollo's law? https://www.nytimes.com/2009/09/29/science/29evol.html

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?

[Difflugia]

How is this BlastP system looking back in the past? What framework is the program using?

What framework? What do you even mean? They define their methodology:

Briefly, for each query sequence its closest human paralog was identified as the non-self hit which can be aligned over more than 80% of the length of both sequences.

BLAST is alignment software. Despite your incorrect assertion earlier, the "P" means that it's for protein amino acid sequences rather than nucleic acid nucleotides.

So you are trying to use evolutionary principles to prove evolutionary principles, I would call that very circular.

I have no doubt that you would, but you shouldn't. It's no different than using some mathematical principles to prove others. Your contention wasn't that duplication events don't happen or that closely homologous genes aren't the result of duplication, but that duplication events are primarily deleterious. Since this paper is presented within a scientific framework in which gene duplication as a mechanism has been abundantly demonstrated, the paper doesn't need to reinvent that wheel. It doesn't matter how many wheel-denialists its authors passed on the way to work.

Any beneficial duplications yet?

Considering that the methods section of the linked paper includes the means to recreate the list of the 1600 or so genes used in the study and the study concluded that they were beneficial overall, your question is, if not disingenuous, at least myopic.

The evolutionary hypothesis needs entire genomes to be duplicated. How is that possible? Entire chromosomes would have to be duplicated.

You're going to have to support that somehow.

I will take that as a no you cannot give me an example of a beneficial duplication.

Myopic.

Cancer can be caused by duplication do you call that beneficial?

No, of course not.

Again how can a theory be validated if the computer program that is being used is based on the theory that is being validated?

It's not. The question is whether gene duplication is beneficial, not whether homologous genes are the result of duplication events. If you want to start your argument with the premise that established science is wrong in general, you'll need to state that or be guilty of the fallacy of the unstated major premise, which is itself a form of question-begging. Your argument is the circular one.

Again, evolutionary theory has to have a mechanism to duplicate entire chromosomes and genomes.

So you've said, but not established in any way.

All observed evidence indicates that this is not possible.

I don't think you're right about this, but it doesn't really matter until you support the previous statement.

Therefore the evolution of molecules to man is nothing but a fabricated story.

QED!

[EarthScienceguy]

[Replying to Difflugia in post #0]

[Replying to Difflugia in post #409]

What framework? What do you even mean? They define their methodology:

We obtained H. sapiens to D. rerio, H. sapiens to G. gallus, and H. sapiens to M. musculus orthology information as well as paralogous relationships within D. rerio, G. gallus, and M. musculus from the Ensembl database [27]. Ka and Ka/Ks values of all 1∶1 human-mouse orthologous pairs were calculated using the PAML package and obtained directly from the Ensembl database [27].

The only thing this paper is good for, is a laugh.

Humans to zebra fish
Humans to Red jungle fowl
Humans to house mouse

I give you actual diseases that are caused by duplication and you give me a fantasy story. To support your claim of beneficial mutations.

BLAST is alignment software. Despite your incorrect assertion earlier, the "P" means that it's for protein amino acid sequences rather than nucleic acid nucleotides.

P probably stands for positively preposterous.

I have no doubt that you would, but you shouldn't. It's no different than using some mathematical principles to prove others.

It 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.

Your contention wasn't that duplication events don't happen or that closely homologous genes aren't the result of duplication, but that duplication events are primarily deleterious. Since this paper is presented within a scientific framework in which gene duplication as a mechanism has been abundantly demonstrated, the paper doesn't need to reinvent that wheel.

So you are admitting that this paper is using evolutionary theory to prove the evolutionary theory.

Considering that the methods section of the linked paper includes the means to recreate the list of the 1600 or so genes used in the study and the study concluded that they were beneficial overall, your question is, if not disingenuous, at least myopic.

Ok, I did not realize that I had to narrow my question down to just homo-sapiens. No mouse genome, no chicken genome, and no fish genome. If duplications are so common and needed for evolution or have humans stopped evolving.

The evolutionary hypothesis needs entire genomes to be duplicated. How is that possible? Entire chromosomes would have to be duplicated.
You're going to have to support that somehow.

Gene and genome duplications provide a source of genetic material for mutation, drift, and selection to act upon, making new evolutionary opportunities possible. As a result, many have argued that genome duplication is a dominant factor in the evolution of complexity and diversity.
https://academic.oup.com/mbe/article/23/5/887/1058364