How is there reality without God?

[EarthScienceguy]

Neils Bohr
"No Phenomenon is a phenomenon until it is an observed phenomenon." Or another way to say this is that a tree does not fall in a forest unless it is observed.

The only way for there to be an objective reality is if God is the constant observer everywhere.

Physicist John Archibald Wheeler: "It is wrong to think of the past as 'already existing' in all detail. The 'past' is theory. The past has no existence except as it is recorded in the present."

God is everywhere so He can observe everywhere and produce objective reality.

[EarthScienceguy]

[Replying to The Barbarian in post #0]

Yes. Precisely what your interpretation of Haldane's Dilemma holds to be impossible. That should be a clue for you.

No, Haldane's Dilemma does not say that mutations becoming fixed in the genome is impossible. Haldane's dilemma says that there has not been enough time for the number of mutations that are needed for evolution to take place.

This is like asking "what is the ideal size for an animal?" It's much, much more involved than most creationists imagine. This is why they keep thinking that there must be a single "beneficial mutation rate" for all organisms. Notice too, that this is another reason that Haldane's Dilemma is not a dilemma at all. I think you can see why if you think about it.

It is actually not. This is what Haldane was calculating.

He put evolution in terms of cost.

The cost of continuity – a reproduction rate of 1, which is required merely for continuing into the next generation. Usually written B-1= the number of births -1. So that all the cost (or genetic deaths) obeys the following equation. B-1= total cost. Below are the costs.

The cost of mutation – the extra reproduction rate required for preventing genetic deterioration due to harmful mutations.
The cost of segregation – the extra reproduction rate required for maintaining polymorphisms in a population.
The cost of random loss – the extra reproduction rate required for coping with random losses to the population, (such as fire, flood, famine, selection for non-heritable traits, and many other factors).
The cost of substitution – the extra reproduction rate required specifically for making substitutions – that is, required for increasing the number of copies of the substituting mutations. [Haldane’s version of the cost concept was far more indirect and confusing, but (when correctly reinterpreted) it was effectively identical in how it operated, and in the results it produced.

Cost of evolution = Cost of continuity + Cost of mutation + Cost of segregation + Cost of random loss + Cost of substitution

Through experimentation, Haldane calculated the average cost as 30. Through experiments on higher vertebrates, Haldane measured that they have a reproductive rate that leaves only 0.1 left over to pay for the substitutions. 30/.1 Haldane calculated that substitutions can occur no more frequently than one per 300 generations from selective breeding.

That is Haldane's Dilemma

Perhaps you don't know what synonymous mutations are. They are only a subset of all mutations. There are some amino acids that can be coded by more than one sequence of nucleotides. But your source considers 1.3% of those to be significantly beneficial. Now, since we all have about 100 mutations, if even half of them significantly reduced our likelihood of surviving long enough to reproduce, we'd be extinct. So natural selection takes care of this rather effectively. Part of this is because so many of them are recessive. But there are vertebrates that inbreed as a rule and (no surprise) they have few if any harmful recessives. If you thought it over, it is easy to see why.

Ok, so what about non-synonymous mutations? They are also largely deleterious. You have to have a change in the proteins for evolution to take place. So eventually one of your 100 mutations has to change the coding for proteins. And when that happens it will be deleterious and selected out.

So how many of these 100 mutations are beneficial and what cost is the selective cost of these beneficial mutations?

Now, Kimura used a different mechanism than selection. He preferred genetic drift. Kimura understood that most mutations are deleterious but he reasoned that over 99% of the genome was inert because of evolution. Because over 99% of the genome was inert, then a large number of deleterious mutations did not matter.

One, of the problems with genetic drift as a mechanism for evolution, is the fact that genetic drift works best in small populations.
Second, Beneficial traits are just as likely to be selected out as any other trait.

• Coyne further observes: “The influence of this process on important evolutionary change, though, is probably minor, because it does not have the molding power of natural selection. Natural selection remains the only process that can produce adaptation.” But in a sense agreeing with Lynch, even he recognizes that “genetic drift is not only powerless to create adaptations but can actually overpower natural selection.”Jerry A. Coyne, Why Evolution is True, p. 123 (Viking, 2009).

How could genetic drift produce any of the multiple coordinated mutations that are required for some traits?

No, that's wrong, too. When I was an undergraduate in the 1960s, there were numerous articles in the literature about the functions of non-coding DNA (what creationists call "junk DNA") Creationists aren't entirely wrong; some of it is junk. But much of it has important functions. Moreover, it has been noted that non-coding DNA is a major source of new genes by mutation. Would you like to learn about that?

Kimura actually believed that over 99% of the was inert. It had to be for his theory. Read his work.

No, that's wrong, too. When I was an undergraduate in the 1960s, there were numerous articles in the literature about the functions of non-coding DNA (what creationists call "junk DNA") Creationists aren't entirely wrong; some of it is junk. But much of it has important functions. Moreover, it has been noted that non-coding DNA is a major source of new genes by mutation. Would you like to learn about that?

Scientists did not believe that because of the C-value paradox. Which says:

• If the entire human genome were functional (in the sense of being under selective pressure), we would have too many deleterious mutations per generation.

[EarthScienceguy]

[Replying to The Barbarian in post #200]

Genetics 1982 Jul-Aug;101(3-4):335-44
Evolution of a regulated operon in the laboratory
The evolution of new metabolic functions is being studied in the laboratory using the EBG system of E. coli as a model system. It is demonstrated that the evolution of lactose utilization by lacZ deletion strains requires a series of structural and regulatory gene mutations. Two structural gene mutations act to increase the activity of ebg enzyme toward lactose, and to permit ebg enzyme to convert lactose into allolactose, and inducer of the lac operon. A regulatory mutation increases the sensitivity of the ebg repressor of lactose, and permits sufficient ebg enzyme activity for growth. The resulting fully evolved ebg operon regulates its own expression, and also regulates the synthesis of the lactose permease.

Here, an irreducibly complex enzyme system evolved over a relatively short time. It is irreducibly complex because the system will not work with unless both the enzyme and the regulator are present. Yet it evolved. A strain of bacteria that could not utilize lactose was given a lactose-rich environment. A series of mutations and natural selection led to the evolution of a strain that could utilize lactose. But it also evolved a regulator, such that the system would not work unless lactose was actually present (this reduces metabolic costs when there is not much lactose present).

So is there a new system or is there a new phenotype?

1st. Adaptive mutagenesis has allowed the bacteria to make a minimal number of changes in pre-existing systems to regain a previously lost function. Which is usually the case.
2nd. The cells may possess the beneficial mutation which allows them to utilize lactose, They also possess the deleterious mutation that resulted in the loss of the ability to utilize xylose or maltose.

Evolution I don't think so.

[Difflugia]

So is there a new system or is there a new phenotype?

Yes.

1st. Adaptive mutagenesis has allowed the bacteria to make a minimal number of changes in pre-existing systems to regain a previously lost function. Which is usually the case.

Using this sentence to describe what happened is akin to the old joke about turning a block of stone into a statue of an elephant: "Just remove everything that isn't an elephant!" It's like saying that a stand of trees already had the ability to be a quaint little A-frame; the construction crew just helped the trees find the house that was already there.

I'm starting to think you're an old-school Platonist. The bacteria don't evolve, we just get different projections of the ideal bacterium from the Realm of Ideal Forms depending on what media they're growing in.

2nd. The cells may possess the beneficial mutation which allows them to utilize lactose, They also possess the deleterious mutation that resulted in the loss of the ability to utilize xylose or maltose.

Even if that's true, does that negate the beneficial series of mutations? "Look over there" isn't a valid argument.

Evolution I don't think so.

We know. We know.

[The Barbarian]

Here, an irreducibly complex enzyme system evolved over a relatively short time. It is irreducibly complex because the system will not work with unless both the enzyme and the regulator are present. Yet it evolved. A strain of bacteria that could not utilize lactose was given a lactose-rich environment. A series of mutations and natural selection led to the evolution of a strain that could utilize lactose. But it also evolved a regulator, such that the system would not work unless lactose was actually present (this reduces metabolic costs when there is not much lactose present).

So is there a new system or is there a new phenotype?

Yes and yes. The system consists of a new enzyme, plus a regulator. An irreducibly complex system, since the substrate, the enzyme, and the regulator must all be present for it to work. And of course a bacterium with an observably different function is a new phenotype.

Phenotype refers to an individual’s observable traits, such as height, eye color and blood type. A person’s phenotype is determined by both their genomic makeup (genotype) and environmental factors.
https://www.genome.gov/genetics-glossary/Phenotype

1st. Adaptive mutagenesis has allowed the bacteria to make a minimal number of changes in pre-existing systems to regain a previously lost function.

No. The enzyme is new and the regulator did not exist before the system evolved.

But it worth noting that evolution never does anything from nothing. It always modifies something already there. Hence "descent with modification" as Darwin put it.

2nd. The cells may possess the beneficial mutation which allows them to utilize lactose,

Remember, "beneficial" only counts in terms of environment. This environment happened to be one in which lactose was in abundance, with very little availability of other saccharides.

They also possess the deleterious mutation that resulted in the loss of the ability to utilize xylose or maltose.

"Deleterious" also only counts in terms of environment. So that mutation was neutral. In a similar way the broken vitamin C gene in humans and other apes is not deleterious, because we get sufficient vitamin C in our diets. But it was deleterious for ancient and medieval sailors, who did not have ready access to fresh fruit or vegetables.

Tusks are a means by which elephants defend themselves and settle dominance and mating competition. A mutation that results in a tuskless bull elephant was quite deleterious, for such a bull was unlikely to reproduce. But with the advent of ivory poachers, tuskless males tended to not be shot before they could reproduce, and then the mutation was beneficial.

Evolution I don't think so.

Demonstrably so. Remember what biological evolution is. "Descent with modification." Or after the rediscover of Mendel's work in genetics, "a change in allele frequencies in a population over time."

And that's what these are. Evolution does not have to improve fitness of a population. It only tends to do so. There are plenty of evolutionary dead ends, resulting in population extinction. You may be thinking of common descent, which is a consequence of evolution.

There is abundant evidence for that as well, but not all evolution is about common descent.

[The Barbarian]

Re: Haldane's Dilemma:

I am quite aware that my conclusions will probably need drastic revision
https://www.blackwellpublishing.com/rid ... ldane2.pdf

Not even Haldane thought it was a serious problem for evolution. And one of the reasons that it's not, is because it only applies to alleles under selection, and not neutral mutations that have little or no selective pressure.

According to Ian Musgrave (2007), it generally is accepted that most gene substitutions are the result of neutral mutations, which become fixed by means other than natural selection. Haldane’s estimate concerns only the rate of fixation for gene substitutions by natural selection, so it does not place a limit on the rate of gene substitution as a whole. To know whether Haldane’s dilemma poses a potential problem for the evolution of humans requries first that one first determine how many positively-selected gene substitutions actually have occurred since the human-chimpanzee split. Musgrave (2007) sets a generous upper bound of around 960 such substitutions, with the actual number likely somewhere between 340 and 580.
https://ninewells.vuletic.com/science/d ... evolution/

Perhaps you don't know what synonymous mutations are. They are only a subset of all mutations. There are some amino acids that can be coded by more than one sequence of nucleotides. But your source considers 1.3% of those to be significantly beneficial. Now, since we all have about 100 mutations, if even half of them significantly reduced our likelihood of surviving long enough to reproduce, we'd be extinct. So natural selection takes care of this rather effectively. Part of this is because so many of them are recessive. But there are vertebrates that inbreed as a rule and (no surprise) they have few if any harmful recessives. If you thought it over, it is easy to see why.

Ok, so what about non-synonymous mutations? They are also largely deleterious.

Each of us has dozens of them. If they were largely deleterious, genetic diseases would be rampant in human populations. But they aren't. But non-synonymous mutations are likewise mostly recessive. If humans started exclusively mating with siblings, human population would drop precipitously. But we don't. And so selection doesn't operate on those mutations very much.

And Kimura's estimate of functional DNA did not include non-coding DNA that has other functions. So that's not an issue, either.

The issue is unresolved, but observed evolution of new traits clearly shows that it happens. And reality beats anyone's theory.

[Purple Knight]

Not even Haldane thought it was a serious problem for evolution. And one of the reasons that it's not, is because it only applies to alleles under selection, and not neutral mutations that have little or no selective pressure.

Humans still shouldn't be able to evolve further and may even be bound to degrade because they would need like 10 babies per pair to make even reasonably sure that a bad mutation didn't creep in and you get the same quality in the next generation that you had when you had those two parents, and they don't have that many. The other large animal I can think of that would be vulnerable to this is the elephant, and one female can have about a dozen calves, which should be just barely enough.

[The Barbarian]

Humans still shouldn't be able to evolve further

But we are evolving. For example, we are seeing the number of tetrachromats (people who see four colors, not just three) is increasing. We are seeing the Milano mutation, which protects people from arteriosclerosis, increasing in a population. Body temperature is dropping in most human populations. The allele for lactase in adults is spreading.

A population of endogamous Koreans has evolved an exceptional ability to dive deeply in the sea and to hold their breath for a very long time.

An interesting issue is that some genetic disorders in Ashkenazi (European) Jews are associated with intelligence.

“People would like every group to be exactly the same,” Cochran says, “but they’re not.” The study claims that intelligence evolved in this genetically isolated population because, historically, Ashkenazim had cognitively demanding occupations such as financiers and merchants. Prowess in these fields provided prosperity and, so the theory goes, more success in reproduction. Thus, the “IQ gene” passed down through generations.

At the same time, the researchers noted that genetic diseases common to the group, including Tay-Sachs and Gaucher's, result from increased levels of a chemical that also promotes neuronal growth. After assessing the genetic clustering of mutant genes and correlating these with IQ scores, the researchers contend that the genetic diseases are linked to a propensity for greater intelligence. The survival edge conferred by higher IQs in the group makes up for individual penalties from the diseases.
https://www.scientificamerican.com/arti ... elligence/

If the individual is heterozygous for Tay-Sachs, the gene seems to be associated with high IQ. If the individual is homozygous for this allele, it's generally lethal. Pretty much what you see with sickle cell alleles and malaria.

[Purple Knight]

Humans still shouldn't be able to evolve further

But we are evolving. For example, we are seeing the number of tetrachromats (people who see four colors, not just three) is increasing.

I happen to be one! I am told this happened primarily because my mother was colourblind. However, being male and having it is ultra, ultra rare. I'm even told it shouldn't be possible. I should just be colourblind, but I'm not. I only discovered this a few years ago and before that, I was always the butt end of a running joke with everybody I know who constantly refer to me as simply being wrong about certain colours, usually purples and blues. I know there is a mouse living in my yard because wherever it has peed, it appears to be tinted very very slightly what I would call ice-purple when fresh. Nobody else can see it, but other animals can smell it.

(It does also seem that there aren't necessarily more people like this, but that more are simply being discovered.)

We are seeing the Milano mutation, which protects people from arteriosclerosis, increasing in a population. Body temperature is dropping in most human populations. The allele for lactase in adults is spreading.

A population of endogamous Koreans has evolved an exceptional ability to dive deeply in the sea and to hold their breath for a very long time.

The question is whether we can fix any of this in the population without adding a lot of worse stuff along with it. I'm not surprised that oddities spark up and flourish for a time in select populations. I'm not surprised that one good allele is becoming more common because a part of this general pattern of degradation is that all alleles are becoming more common (except perhaps one basic one).

Some populations don't even replace, and one lesson from Haldane is that to really replace (by that I mean get the same quality you had with your initial pair and reasonably insure against bad random mutation) you don't need 2.3 babies in case of unforeseen death, you need like 10. Only outbreeding will hold us for a time but that will someday be expended and we may be looking at a population that is so full of garbage that every pair will be looking at multiple separate chances to produce that bad 1/4 recessive trait. And at that point 2 babies definitely won't cut it. If you were looking at just 2 chances to get that bad result, you would need 4 children, just on that generation, and assuming more recessives from the mother that the father didn't possess (and vice-versa) are being allowed to pile up. Eugenics can't even solve this. It won't find everything. We don't know how many animals went down the path of, "I think I'll be large and invest heavily in just a few offspring," and experienced huge initial success but then went extinct due to genetic degradation.

[JoeyKnothead]

No, Haldane's Dilemma does not say that mutations becoming fixed in the genome is impossible. Haldane's dilemma says that there has not been enough time for the number of mutations that are needed for evolution to take place.

Well about that, it only takes the one mutation for evolution to occur. Speciation though, may take a few more, or many more.

[EarthScienceguy]

[Replying to Difflugia in post #203]

2nd. The cells may possess the beneficial mutation which allows them to utilize lactose, They also possess the deleterious mutation that resulted in the loss of the ability to utilize xylose or maltose.
Even if that's true, does that negate the beneficial series of mutations? "Look over there" isn't a valid argument.

As an example of evolution, this one statement most assuredly does negate the beneficial series mutations as an example. This adaptive change does not add function, it subtracts function.

It is not adding a new phenotype type it is reverting to an old phenotype type that was already contained within the genome.

But regardless this discussion really has no bearing on the discussion we were having. How long did it take to make this adaptive change? How many nucleotides had to change to make this change? The problem with evolution is the number of synonymous substitutions that evolution has to produce. Kimura estimated that 90 to 95 percent of all synonymous mutations are deleterious. I already quoted research that expressed how 75% of non-synonymous mutations were deleterious so the 90 to 95% still seems very plausible.