[__ Science __ ] Evolution and Harmless Mutations

[Michael74]

BTW, there's a reason Ross is tossing out claims without showing his math.

Thanks Barbarian. I wondered where he got the 1 in 10,000. Seems to be just a guess.

He is an astrophysicist by training. Biology may not be his area. His books on astrophysics seemed interesting, so I wondered.

 

[Barbarian]

Thanks Barbarian. I wondered where he got the 1 in 10,000. Seems to be just a guess.

I think he just pulled it of his, um, hat.

He is an astrophysicist by training.

Which is why he feels so qualified to talk about gentics, I suppose.

Biology may not be his area.

Or probabilty, it seems. The world is full of bright guys who think a degree in X makes them experts on everything.

 

[Barbarian]

The correct answer is (and I quote the source):

​

This:​

"The distribution has been studied experimentally and has been found to conform with the conclusions drawn from the hypothesis that the resistant bacteria arise by mutations of sensitive cells independently of the action of virus."​

​

As you now see, the hypothesis that favorable mutations appear randomly, is shown by the data (the distribution).​

I asked you:
what is the “distribution” of that’s been “studied experimentally”?

As you now see, it's the data that refuted the idea that favorable mutations are not random.

The correct answer is:

MUTATIONS OF BACTERIA FROM VIRUS SENSITIVITY TO VIRUS RESISTANCE’-’
S.E. LURIAS AND M. DELBROCK
Genetics. 28 (6): 491–511
SUMMARY
The distribution of the numbers of virus resistant bacteria in series of similar cultures of a virus-sensitive strain has been analyzed theoretically on the basis of two current hypotheses concerning the origin of the resistant bacteria.

The distribution has been studied experimentally and has been found to conform with the conclusions drawn from the hypothesis that the resistant bacteria arise by mutations of sensitive cells independently of the action of virus.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1209226/pdf/491.pdf

That's it. Your error was to confuse the data with the conclusion.

 

[Barbarian]

The ratio of favorable to unfavorable mutations will depend on how well the population is fitted to the particular environment. As Darwin remarked, a well-fitted population, in a constant environment should have few favorable mutations relative to unfavorable ones, compared to a poorly-fitted population. Hence such well-fitted populations should show little evolution so long as the environment stays the same. This is what the Grants observed on Daphne Major, with Galapagos finches, confirming Darwin's prediction.

This can be demonstrated mathematically. It's been known for a long time by population geneticists. Anyone with a reasonable grasp of integral calculus can confirm it for himself:
https://tinyurl.com/y893c5gm

This points out another error made by Ross; his assumption that there is some kind of invariable ratio of "good" mutations as opposed to "bad" mutations. Mutations are neutral, favorable, or unfavorable, only in context of the environment.

Everything looks simple when one doesn't know anything about it.

 

[Michael74]

The ratio of favorable to unfavorable mutations will depend on how well the population is fitted to the particular environment. As Darwin remarked, a well-fitted population, in a constant environment should have few favorable mutations relative to unfavorable ones, compared to a poorly-fitted population. Hence such well-fitted populations should show little evolution so long as the environment stays the same. This is what the Grants observed on Daphne Major, with Galapagos finches, confirming Darwin's prediction.

Yes, that makes sense. Doesn't give an empirical number, but it makes sense that the ratio should be such.

 

[Barbarian]

If you do a lot of data collection on a population, you can use the equations of population genetics to get a pretty good idea.

The simplest method is called the Hardy-Weinberg Equilibrium.

It has a number of required conditions in order for it to perfectly predict the distribution of alleles in the next generation.
The seven assumptions underlying Hardy–Weinberg equilibrium are as follows:

• organisms are diploid
• only sexual reproduction occurs
• generations are nonoverlapping
• mating is random
• population size is infinitely large
• allele frequencies are equal in the sexes
• there is no migration, gene flow, admixture, mutation or selection
  These conditions can be relaxed to a degee without much loss in accuracy. For example, a population in the millions pretty much fits the assumption of an infinitely large population.

The simplest case is where there are only 2 alleles for a gene, with frequencies of p and q. In that case, if the assumptions are met to a reasonable degree, the the assortment of alleles in the next generation will closely approximate: p2 + 2pq + q2 ,remembering that p and q added together in the n generation are equal to 1.

It is an effective method of determining if selective pressure is present for that particular gene. If all conditions approximately hold and the equation does not match the assortment of alleles in the n+1 generation, then there is selective pressure.

It gets more complicated from there.

 

[Michael74]

"From a biblical creation perspective, God endows the different kinds of life he creates with a capacity for natural selection so that through natural selection the kinds of life can effectively adapt to random changes in their habitats." Hugh Ross

Hugh mentioned the studies by Daphne Major that you did. He seems to acknowledge natural selection, but relegates it to a limited role.

The presence of natural selection does not preclude active intervention from time to time.

 

[Barbarian]

"From a biblical creation perspective, God endows the different kinds of life he creates with a capacity for natural selection so that through natural selection the kinds of life can effectively adapt to random changes in their habitats." Hugh Ross

Hugh mentioned the studies by Daphne Major that you did. He seems to acknowledge natural selection, but relegates it to a limited role.

The presence of natural selection does not preclude active intervention from time to time.

That's not creationism exactly, it's more like "intelligent design." In a relatively defensible form, it's found in Michael Behe's acknowledgement that evolution is largely responsible for the way life is today, but modified by his belief God has to step in from time to time to make it work.

An even more defensible position is IDer Michael Denton's idea that an intelligent agent "preloaded" the universe so that life would appear as it does:

it is important to emphasize at the outset that the argument presented here is entirely consistent with the basic naturalistic assumption of modern science--that the cosmos is a seamless unity which can be comprehended in its entirety by human reason and in which all phenomena, including life and evolution and the origin of man, are ultimately explicable in terms of natural processes. This is an assumption which is entirely opposed to that of the so-called "special creationist school." According to special creationism, living organisms are not natural forms, whose origin and design were built into the laws of nature from the beginning, but rather contingent forms analogous in essence to human artifacts, the result of a series of supernatural acts, involving God's direct intervention in the course of nature, each of which involved the suspension of natural law. Contrary to the creationist position, the whole argument presented here is critically dependent on the presumption of the unbroken continuity of the organic world--that is, on the reality of organic evolution and on the presumption that all living organisms on earth are natural forms in the profoundest sense of the word, no less natural than salt crystals, atoms, waterfalls, or galaxies.

In large measure, therefore, the teleological argument presented here and the special creationist worldview are mutually exclusive accounts of the world. In the last analysis, evidence for one is evidence against the other. Put simply, the more convincing is the evidence for believing that the world is prefabricated to the end of life, that the design is built into the laws of nature, the less credible becomes the special creationist worldview.
Michael Denton, Nature's Destiny

This is essentially a theological argument, but it comes very close to being science, and it is largely in accord with the universe we see.

 

[Michael74]

...mating is random...

Hmm.

...population size is infinitely large...

Insects and bacteria would have an advantage in approximating this.

...there is no migration, gene flow, admixture, mutation or selection...

No mutation? I thought mutation was how natural selection worked.

Where p2 represents the frequency of the homozygous dominant genotype, q2 represents the frequency of the recessive genotype and 2pq is the frequency of the heterozygous genotype.

This doesn't really seem to estimate the ratio of helpful to counterproductive mutations. Maybe I misunderstood.

 

[Michael74]

That's not creationism exactly, it's more like "intelligent design." In a relatively defensible form, it's found in Michael Behe's acknowledgement that evolution is largely responsible for the way life is today, but modified by his belief God has to step in from time to time to make it work.

Maybe not have to step in, more like may choose to. He heals people today, and guides people today. That is active intervention. What in science would preclude Him from shepherding the animals He wants to keep going? Like telling some of them to move toward Noah's ark.

Look at the birds of the air; they do not sow or reap or store away in barns, and yet your heavenly Father feeds them. Matthew 6:26a NIV

Birds were told to feed Elijah. Another example of active intervention. Animals listen to Him.

For only a penny you can buy two sparrows, yet not one sparrow falls to the ground without your Father's consent. Matthew 10:29 GNT

 

[Barbarian]

Hmm.
Insects and bacteria would have an advantage in approximating this.

Yes. But a million individuals will suffice to give you an answer so close to that of an infinite number that it doesn't matter.

The binomial distribution is used when (a) there are two possible outcomes of a trial, (b) the probability of each outcome remains the same across all trials, and (c) all trials are independent of each other. Here, the two possible outcomes (i.e., the allele sampled in a gamete) are A and a, the probability of sampling a gamete with the A allele is p, there are n = 2N trials (i.e., gametes sampled), and k of these trials result in the A allele. The term [n! / (k! (n -k)!)] gives the number of ways that one can observe exactly k "successes" (defined here as A alleles) and n -k "failures" (defined here as a alleles). The term pk (1-p)n - k is the exact probability of observing any given order of k "successes" and n - k "failures." Therefore, the product of these terms gives the exact probability of observing k "successes" and n - k "failures," given that one is unconcerned about their order.

Using the formula for the binomial distribution, we can calculate the exact probability that k = 2pN for a range of N. Doing so yields the following results:




At first glance, these results might seem backward. According to the table, the probability that the allele frequencies will remain unchanged is higher for the smaller populations! However, that's only part of the story. In all of these cases, it's more likely that the allele frequencies will change, and it is actually the magnitude of the change that matters. To see what this means, let's focus on those populations where N = 5, N = 50, and N = 500. Figures 1 through 3 show the probabilities of allele frequencies in the next generation of each of these populations.
Population size (N)..........Pr(k | p, n = 2N)
2............................................ .375
5............................................ .246
10.......................................... .176
50......................................... .080
100........................................ .056
500........................................ .025
1,000.................................... .018
10,000................................. .006

As you see, the likely error drops off asymptotically as the population size increases.

Other assumptions:

...there is no migration, gene flow, admixture, mutation or selection...

No mutation? I thought mutation was how natural selection worked.

If the Hardy Wienberg Equillibrium holds, it's an indication that natural selection is not acting on that particular gene. Hence, if it doesn't hold, it indicates natural selection at work.

Where p2 represents the frequency of the homozygous dominant genotype, q2 represents the frequency of the recessive genotype and 2pq is the frequency of the heterozygous genotype.

This doesn't really seem to estimate the ratio of helpful to counterproductive mutations. Maybe I misunderstood.

If the equation doesn't hold, the allele with a greater than expected frequency has a higher selection value than the other. In real life, most alleles aren't "good" or "bad"; one just might have a better fitness than the other, with neither actually harmful.

 

[Barbarian]

Maybe not have to step in, more like may choose to. He heals people today, and guides people today. That is active intervention. What in science would preclude Him from shepherding the animals He wants to keep going? Like telling some of them to move toward Noah's ark.

Look at the birds of the air; they do not sow or reap or store away in barns, and yet your heavenly Father feeds them. Matthew 6:26a NIV

Birds were told to feed Elijah. Another example of active intervention. Animals listen to Him.

For only a penny you can buy two sparrows, yet not one sparrow falls to the ground without your Father's consent. Matthew 10:29 GNT

Miracles are a fact, but God doesn't do miracles because He can't create things to work as He wishes. He does miracles to teach us things.

Look at the birds of the air; they do not sow or reap or store away in barns, and yet your heavenly Father feeds them. Matthew 6:26a NIV

He doesn't actually come out and give them food. He provides by creating living things with the ability to change and adapt over time.

 

[Michael74]

As you see, the likely error drops off asymptotically as the population size increases.

Okay, that's pretty close.

If the equation doesn't hold, the allele with a greater than expected frequency has a higher selection value than the other.

Yes, I get that. However, it pretty much assumes that all alleles are already in the gene pool. They only need to be selected for a particular environment. That is, a protozoa has all of the alleles necessary to turn into a whale. Given the right set of circumstances.

If mutations are necessary, they will only be present in a single animal at first. Why are mutations excluded from the formula? Are mutations rejected by science as part of species change over time?

 

[Michael74]

He does miracles to teach us things.

Interesting that you think teaching people is the only reason. I shall ponder.

 

[Barbarian]

Okay, that's pretty close.

Yes, I get that. However, it pretty much assumes that all alleles are already in the gene pool.

Right. Hardy-Weinberg isn't about mutation, it's about alleles already in the population. However, once a mutation becomes established, it can be analyzed for selective advantage by Hardy-Weinberg.

They only need to be selected for a particular environment. That is, a protozoa has all of the alleles necessary to turn into a whale.

No. Eukaryotes generally have only two versions of each gene, so no organism could have even a tiny fraction of all genes found in living things. But of course, we do have evidence for the way animals evolved from protists, and how chordates evolved from deuterostomes, and how vertebrates evolved from chordates and how tetrapods evolved from early vertebrates, and how mammals evolved from other tetrapods and how ungulates evolved from early mammals, and how cetaceans evolved from early ungulates.

So there is that.

Given the right set of circumstances.

Yep.

If mutations are necessary, they will only be present in a single animal at first.

Or in a single litter. Right. This was a huge problem for evolutionary theory, until it was discovered that heredity is like sorting beads rather than like mixing paint.

Why are mutations excluded from the formula?

They aren't. For example, the mutation that gives about 10% of people with European ancestry complete immunity to HIV, can be and has been analyzed by Hardy-Weinberg. It's just that the allele has to exist before it has a frequency in a population.

Are mutations rejected by science as part of species change over time?

Nope.

 

[Barbarian]

Interesting that you think teaching people is the only reason. I shall ponder.

Think about the miracles you know about. All have a teaching function, far as I know.

 

[Barbarian]

By, the way, I very much appreciate the calm and civil tone of your posts. We could all do a better job of following your example.

 

[Razeontherock]

Did you intend the pun?

And God said, “Let the earth produce green plants that will bear seed—fruit trees bearing fruit in which there is seed —according to its kind, on the earth.” And it was so.​

Genesis 1:11 - https://www.biblegateway.com/passage?search=Genesis 1:11&version=LEB

Took me a minute, but that’s good.

Yes, absolutely I did.

Thank you; thank you very much.

I'll be here all week

 

[Razeontherock]

Barbarian observes:
It has everything to do with creationism. If species were created separately

Again, Scripture says nothing, I repeat

NOTHING

about species.

Please do not pretend this is too difficult for you to comprehend.

That's quite true. "Kind", in the context of Genesis, isn't about biological entities at all. It puts flying birds and bats in the same "kind", and cattle and ostriches in the same "kind", and whales, sharks, and squid in the same kind.

You are again making a hot mess out of Scripture . <-- don't make me sick Reba on you

Genesis "kinds" absolutely ARE about "biological entities," as there is nothing else they could possibly be about; however it does NOT state ANY of the things you falsely assert here!! It doesn't say bats are the same kind as birds as bats are not specified or accounted for, it doesn't say cattle and ostriches are the same kind, it doesn't say whales sharks and squid are the same kind, and it most certainly says nothing about species.

How is it you don't fear to absolutely butcher Scripture like this?!?

And of course, scripture says nothing about protons, either. There are many, many things that are true, that are not in scripture.

You're demonstrating woeful unfamiliarity with Scripture

So your argument is that all land animals are one kind,all flying birds and bats are another kind, all sea creatures are a kind, and all plants are of one kind?

Did I say that?

You assume entirely too much - and it is not in the least bit civil

 

[Barbarian]

Barbarian observes:
It has everything to do with creationism. If species were created separately, instead of evolving from other species it would be easy to define them. But because they evolve from other species, and generally take a long time to do so, we have all the intermediate steps that can't be neatly classified. This is one of the problems creationists cannot solve. But it's a prediction of evolutionary theory.

Again, Scripture says nothing, I repeat

NOTHING

about species.

Barbarian observes:
That's quite true. "Kind", in the context of Genesis, isn't about biological entities at all. It puts flying birds and bats in the same "kind", and cattle and ostriches in the same "kind", and whales, sharks, and squid in the same kind. And of course, scripture says nothing about protons, either. There are many, many things that are true, that are not in scripture.

You are again making a hot mess out of Scripture

I'm just taking it as it's written.

Genesis "kinds" absolutely ARE about "biological entities,"

It says "kind", not "kinds." And it lumps birds and bats together and ostriches and cattle together and whales and sharks and octopi together. This is not biological, it's a functional description of things in the same environment. This is why early Christians like Augustine realized that it wasn't a literal description but a discussion of the categories of creation. The Bible often does not reflect our modern idea of classifying things by biological criteria.

as there is nothing else they could possibly be about; however it does NOT state ANY of the things you falsely assert here!! It doesn't say bats are the same kind as birds

Leviticus 11:13 “‘These are the birds you are to regard as unclean and not eat because they are unclean: the eagle,[a] the vulture, the black vulture, 14 the red kite, any kind of black kite, 15 any kind of raven, 16 the horned owl, the screech owl, the gull, any kind of hawk, 17 the little owl, the cormorant, the great owl, 18 the white owl, the desert owl, the osprey, 19 the stork, any kind of heron, the hoopoe and the bat.

The Hebrews weren't using biological divisions, but functional descriptions. Hence whales were tossed in with fish and bats were included as birds. Whales were called "dag godol" or "giant fish."

We conclude, therefore, that the word used in the book of Jonah to refer to the sea creature that swallowed Jonah, refers indiscriminately to any type of fish—without regard for the technical taxonomic, classification schemes developed by the scientific community in the last few centuries. It has the same generic latitude that inheres in the English word “fish” has, which can refer to any number of cold-blooded aquatic vertebrates—from a trout, bass, or crappie to sharks, rays, jellyfish, and crayfish (American Heritage Dictionary, 2000, p. 665).

However, a point of clarification needs to be sounded even here. According to the present zoological nomenclature, a “whale” is not a “fish”—it is classified as a mammal. Hebrew linguistic experts note no such distinction in the terms used in the Old Testament. The ordinary term for “fish” (dahg) would not necessarily exclude the whale in its application.
http://apologeticspress.org/apcontent.aspx?category=6&article=69

How is it you don't fear to absolutely butcher Scripture like this?!?

See above. Once you get away from the message God actually wants you to hear, the incidentals require a lot of prayerful reading and study. Otherwise, you can get pulled off into all sorts of things. While it is an interesting matter for scholars to note that the Hebrews classified bats as birds and whales as fish,(and in the context of their culture, it was no more "wrong" than our habit of classifying organisms by biology instead of function) these details are entirely unimportant as far as the message God is giving to us in scripture.

I don't want to rile you further, so we might best leave off this discussion.