Rebuttal To Creationists - "Since We Can't Directly Observe Evolution..."

No he won't. You are Taq's toy and he has you running around in circles. I would not dream of interfering. It's too much fun watching him fillet you.

What the hell did you do? Fix your latex equations, man. Go to Online LaTeX Equation Editor - create, integrate, download and play to your hearts content until you get your latex equations right.--Percy

The calculation of the number of generations it takes a single mutation to reach fixation wouldn't need the mutation rate. Why do you think it would?What does require the mutation rate is a calculation of the number of mutations that will move towards fixation. Ne is usually drastically smaller than N.

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By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000.
Just a moment...

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I already explained this a previous post. Let's use an effective population size of 20,000 as described above. That would be 80,000 generations to fix a neutral allele, and at 25 years per generation that would be 2 million years. This means the earliest populations in the human lineage that had just split away from the chimp population would be fixing neutral mutation that occurred 2 million years before that. Every generation after that would be fixing neutral mutations that occurred 2 million years before them. Where is the problem? You still haven't figured out that lineages combine in a sexually reproducing population. Your genome is the merger of your father's and mother's lineage. Every single birth is a mixture of lineages.

Fish stories? Who is the one claiming that 98% of the human genome outside of coding regions is one monolithic sequence that is all moving towards fixation as a single unit in a way that magically excludes any new mutations that occur?Do you even think about this? Let's see what consequences this would have. According to you, only coding sequences can differ. This would mean that 98% of the human genome should be 100% conserved across the entire human population. Do you think this is true? If not, how do you explain the differences between non-coding sequences in human genomes? How do you even explain the differences between the two copies of the same chromosome in non-coding DNA?The other hilarious fish story you tell is that lineages are isolated in human populations. This insane claim shows a near complete ignorance of how human genetics works. It's as if you have never even seen a Punnett square. Mendel knew more about genetics than you do. You can't even understand how two independent mutations can end up in the same genome.For the peanut gallery, ghost ancestors are an interesting outcome of sexual reproduction and meiosis. There are some human ancestors that are the ancestors of everyone alive today, and yet none of us carry any of their DNA.

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In a randomly-mating biparental population of size N there are, with high probability, individuals who are genealogical ancestors of every extant individual within approximately log2(N) generations into the past. We use this result of J. Chang to prove a curious corollary under standard models of recombination: there exist, with high probability, individuals within a constant multiple of generations into the past who are simultaneously (i) genealogical ancestors of each of the individuals at the present, and (ii) genetic ancestors to none of the individuals at the present. Such ancestral individuals–ancestors of everyone today that left no genetic trace–represent ‘ghost’ ancestors in a strong sense. In this short note, we use simple analytical argument and simulations to estimate how many such individuals exist in finite Wright–Fisher populations.
https://www.sciencedirect.com/...ticle/pii/S0040580915000167

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Percy:

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You're claiming it, you explain it. First provide the specific equation from Haldane's paper that you're referring to, then convert it into units of Joules.

Kleinman:

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I already have but I'll do it again.

Percy:

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There was no equation in what followed. Please present the Haldane equation you're talking about, then convert it to Joules. Using math equations.

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OK, here's Haldane's frequency equation again:pnA + qna = 1Do this in the context of the Lenski experiment.Call the total amount of energy available in the glucose for survival and replication is "T". We can use units of Joules though I prefer the units of (stones*furlongs^2)/(fortnight^2). That energy is sufficient to support 495 million replications of his E. coli. Let n_p = the total number of replications of the p variant in one day's growth. Let n_q = the total number of replications of the q variant in one day's growth. Thenn_p + n_q = 495,000,000 and n_p/495,000,000 + n_q/495,000,000 = 1Now, let the amount of energy for a single replication of a p variant be er_p and the energy of replication of the q variant be er_q. Note that er_p < er_q and that energy difference is the selection parameter. Then, applying the first law,n_p*er_p + n_q*er_q = T and if you want the equation in the form of Haldane's frequency equation, divide by T which gives:(n_p*er_p)/T + (n_q*er_q)/T = 1

That's merely an identity. Since any locus can possess only one of A or a, then by definition p(A) + p(a) = 1 by definition. Where does the 495 million figure come from? Selection is a function of expression and adaptation, not how much energy is used in microbiological processes. And could you either learn latex or at least how to do subscripts? Are you trying to say er_p and er_q?And you're not deriving anything mathematically. You're simply declaring that the energy is er_p and er_q, so this is meaningless and I have no idea why you think it's useful as a conservation of energy equation. There's certainly no useful conclusions to be drawn from it: --Percy

Kleinman:

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Now the effective population size can be slightly smaller than the actual population size under certain circumstances that I'm sure you know what they are. Remind me again what the population size you use is. Wasn't it 100,000? That gives the generations to fixation of that mutant gene of 4*100,000=400,000 generations.

Taq:

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Ne is usually drastically smaller than N.

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By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000.
Just a moment...

Kleinman:

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That gives the generations to fixation of that mutant gene of 4*100,000=400,000 generations. That really helps. Your lower division equation gave an estimate of 900,000 generations for the fixation of a neutral mutation. How many generations since the divergence of humans and chimps from the common ancestor?

Taq:

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I already explained this a previous post. Let's use an effective population size of 20,000 as described above. That would be 80,000 generations to fix a neutral allele, and at 25 years per generation that would be 2 million years. This means the earliest populations in the human lineage that had just split away from the chimp population would be fixing neutral mutation that occurred 2 million years before that. Every generation after that would be fixing neutral mutations that occurred 2 million years before them. Where is the problem?

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Let's do a little math. 2,000,000 years/25 years/generation = 80,000 generations. Congratulations, you've fixed 1 neutral mutation.

Kleinman:

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You still haven't figured out that different combinations of adaptive mutations give different lineages on different evolutionary trajectories.

Taq:

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You still haven't figured out that lineages combine in a sexually reproducing population. Your genome is the merger of your father's and mother's lineage. Every single birth is a mixture of lineages.

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Since you won't attempt to do the mathematics of recombination, let's talk about a simpler case, cells that do replication by mitosis, such as cancer cells. How would you compute the probability of a mutant drug-resistant cancer cell line evolving from an original progenitor cancer cell? You do know that cancer cells are diploid and they reproduce by mitosis. And how does this affect the possible success or failure of targeted cancer therapies?

Kleinman:

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Taq likes to tell fish stories.

Taq:

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Fish stories? Who is the one claiming that 98% of the human genome outside of coding regions is one monolithic sequence that is all moving towards fixation as a single unit in a way that magically excludes any new mutations that occur?

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Don't be silly. I don't think the non-coding region is one monolithic sequence. This is the region that contains the control system that turns on and off the genes in the coding region that allows differentiation of the original stem cell into a fully formed adult and controls all the biological processes in that individual to sustain life.You are squirming like a worm, you must be fishing.

You could use any frequency distribution you want. If we divided the world into those who prefer vanilla ice cream and those that prefer chocolate ice cream we could get the same comparisons. That doesn't mean preference for ice cream flavor is a conservation of energy process.

First, there are about 50 mutations that fix in every generation, not 1. Second, every generation has new neutral mutations, and some of those neutral mutations will begin to move towards fixation. The first generation in our lineage would have already had neutral mutations they inherited from their ancestors 2 million years ago. Why do any mathematics for someone who claims recombination doesn't even exist? Yes, you do. You claimed that all non-coding sequence is a single allele that moves towards fixation together.It is like an assembly line. If it takes 24 hours for Ford to make a specific car on a single assembly line, start to finish, does this mean that they only produce one car every day on that assembly line? Obviously not. As the car is finished at one station it is passed to the next, and a new car is placed at the previous station. They are all lined up behind each other moving along the assembly line. Fixation of neutral mutations work the exactly same way. Yes, you do. You claimed all non-coding sequence was a single allele that moved towards fixation together.

Kleinman:

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OK, here's Haldane's frequency equation again:
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pnA + qna = 1

Percy:

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That's merely an identity. Since any locus can possess only one of A or a, then by definition p(A) + p(a) = 1 by definition.

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Yes, the math and equation is quite straightforward.

Kleinman:

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Call the total amount of energy available in the glucose for survival and replication is "T". We can use units of Joules though I prefer the units of (stones*furlongs^2)/(fortnight^2). That energy is sufficient to support 495 million replications of his E. coli.

Percy:

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Where does the 495 million figure come from?

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My bad, I thought you had some familiarity with the Lenski experiment. It comes from the Lenski Michigan State website:
DM25 Liquid Medium

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The basic medium used for propagating the long-term lines is Davis minimal broth (Carlton and Brown 1981*) supplemented with glucose at a concentration of 25 mg per L, which we refer to as DM25. This medium supports a stationary-phase density of about 5 x 107 cells per ml for the founding strain of E. coli B.

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Culture volume is 10 ml, and cultures are maintained in 50-ml Erlenmeyer flasks loosely capped with small inverted beakers. Flasks are incubated at 37C and 120 rpm. Cultures are propagated daily by transferring 0.1 ml of each culture into 9.9 ml of fresh medium.

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Kleinman:

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Now, let the amount of energy for a single replication of a p variant be er_p and the energy of replication of the q variant be er_q. Note that er_p < er_q and that energy difference is the selection parameter.

Percy:

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Selection is a function of expression and adaptation, not how much energy is used in microbiological processes. And could you either learn latex or at least how to do subscripts? Are you trying to say er_p and er_q?
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And you're not deriving anything mathematically. You're simply declaring that the energy is er_p and er_q, so this is meaningless and I have no idea why you think it's useful as a conservation of energy equation. There's certainly no useful conclusions to be drawn from it:

(n_p*er_p)/T + (n_q*er_q)/T = 1

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Hey, you are the one that wanted me to put the Haldane equation in terms of energy! Do you think the p variants require more energy to replicate than the q variants? And I know, this equation is not needed, that's why I didn't do the solution for the Lenski experiment using that formulation. Haldane's version of the energy equation works just fine. Haldane's equation is normalized. This is a trivially simple conservation of energy process.And you obviously were able to understand my notation. Why should I spend my time learning another formatting protocol when you are still confused about the physics and mathematics of Darwinian evolution? Will making my notation prettier make it easier to understand? I doubt it.

Kleinman:

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OK, here's Haldane's frequency equation again:

Taq:

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You could use any frequency distribution you want. If we divided the world into those who prefer vanilla ice cream and those that prefer chocolate ice cream we could get the same comparisons. That doesn't mean preference for ice cream flavor is a conservation of energy process.

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You are confused again on this issue. Not all frequency equations are conservation of energy equations. Some frequency equations are conservation of ice cream equations (that's conservation of mass). Haldane's frequency equation pertains to the conservation of energy. What did they actually teach you about the laws of thermodynamics in your survey of physics course?

Kleinman:

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Let's do a little math. 2,000,000 years/25 years/generation = 80,000 generations. Congratulations, you've fixed 1 neutral mutation.

Taq:

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First, there are about 50 mutations that fix in every generation, not 1. Second, every generation has new neutral mutations, and some of those neutral mutations will begin to move towards fixation. The first generation in our lineage would have already had neutral mutations they inherited from their ancestors 2 million years ago.

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LOL!

Kleinman:

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Since you won't attempt to do the mathematics of recombination,

Taq:

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Why do any mathematics for someone who claims recombination doesn't even exist?

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I'm starting to wonder if Taq actually exists.

Kleinman:

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I don't think the non-coding region is one monolithic sequence.

Taq:

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Yes, you do. You claimed that all non-coding sequence is a single allele that moves towards fixation together.
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It is like an assembly line. If it takes 24 hours for Ford to make a specific car on a single assembly line, start to finish, does this mean that they only produce one car every day on that assembly line? Obviously not. As the car is finished at one station it is passed to the next, and a new car is placed at the previous station. They are all lined up behind each other moving along the assembly line. Fixation of neutral mutations work the exactly same way.

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Is Taq now an advocate for intelligent design? Living things are now made on a Ford assembly line.

Kleinman:

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I don't think the non-coding region is one monolithic sequence.

Taq:

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Yes, you do. You claimed all non-coding sequence was a single allele that moved towards fixation together.

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Now Taq is claiming that all 54.5 of the mutations in a genome don't get fixed. Taq, would you make up your mind?

That's all you got? Given your lack of response, are you tacitly agreeing that we should see fixation of neutral mutations in each generation?Or are you still so confused that you think only 1 mutation can move towards fixation at a time, and that all other neutral mutations can not begin to move towards fixation until that 1 neutral mutation is fixed? That's what I have claimed all along.

Kleinman:

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LOL!

Taq:

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That's all you got?

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Actually, no. It makes me really sad that a microbiologist can't explain the evolution of antimicrobial drug resistance.

Kleinman:

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Is Taq now an advocate for intelligent design? Living things are now made on a Ford assembly line.

Taq:

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Given your lack of response, are you tacitly agreeing that we should see fixation of neutral mutations in each generation?
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Or are you still so confused that you think only 1 mutation can move towards fixation at a time, and that all other neutral mutations can not begin to move towards fixation until that 1 neutral mutation is fixed?

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Watch out, there's a stampede of neutral mutation coming down a Ford assembly line. Obviously, they need better quality control.

Kleinman:

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Now Taq is claiming that all 54.5 of the mutations in a genome don't get fixed.

Taq:

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That's what I have claimed all along.

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How many neutral mutations are lost?

In the case of beta-lactam resistance, one pathway is mutations produce an enzyme capable of breaking down the antibiotic.What does this have to do with human evolution? Then I will assume you accept the claim that around 50 neutral mutations reach fixation in each generation. (N*u)-uwhere N is the population size and u is the number of mutations per individual per generation.

Kleinman:

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It makes me really sad that a microbiologist can't explain the evolution of antimicrobial drug resistance.

Taq:

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In the case of beta-lactam resistance, one pathway is mutations produce an enzyme capable of breaking down the antibiotic.

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Pathway? What pathway? How do mutations take a pathway?

Taq:

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What does this have to do with human evolution?

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Don't both humans and bacteria have DNA? Do human mutations have a pathway?

Kleinman:

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Watch out, there's a stampede of neutral mutation coming down a Ford assembly line.

Taq:

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Then I will assume you accept the claim that around 50 neutral mutations reach fixation in each generation.

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On what do you base that assumption?

Kleinman:

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How many neutral mutations are lost?

Taq:

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(N*u)-u

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where N is the population size and u is the number of mutations per individual per generation.

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You better use Latex or you will get Percy angry. So for human evolution using your equation you get:
(100,000*54.5)-54.5
Is that new math?